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1. Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

   https://doi.org/10.1073/pnas.2109235119  

   Holmes, Jacob B. ; Liu, Viktoriia ; Caulkins, Bethany G. ; Hilario, Eduardo ; Ghosh, Rittik K. ; Drago, Victoria N. ; Young, Robert P. ; Romero, Jennifer A. ; Gill, Adam D. ; Bogie, Paul M. ; et al ( January 2022 , Proceedings of the National Academy of Sciences)

   NMR-assisted crystallography—the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry—holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5′-phosphate–dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid–base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bondmore »formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate C β and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.« less
2. Conformationally Rigid Cyclic Tungsten Bis-Alkyne Complexes Derived from 1,1’-Dialkynylferrocenes

   https://doi.org/10.1016/j.jorganchem.2017.05.048  

   Curran, T. P. ; Lawrence, A. P. ; Murtaugh, T. S. ; Ji, W. ; Pokharel, N. ; Gober, C. B. ; Suitor, J. ( October 2017 , Journal of organometallic chemistry)

   In exploring the conformational behavior of cyclic tungsten bis-alkyne complexes, two dialkynylamides (14a and 14c) and two dialkynylesters (14b and 14d) derived from 1,1’-ferrocenedicarboxylic acid were prepared. They were subsequently reacted with W(CO)3(dmtc)2 to yield the desired cyclic tungsten bis-alkyne complexes 8-11. In the cyclization of 14a to yield 8 a dimeric macrocyclic complex, 15, featuring two tungsten bis-alkyne complexes in the ring, also was isolated. The conformational behavior of these complexes was assessed by analysis of the 1H NMR resonances for the alkyne hydrogens, which appear around 11 ppm. The spectra for complexes 10, 11 and 15 show multiple singlets of varying integrations for these protons, while the spectra for complexes 8 and 9 show only two resonances of equal integration for the alkyne hydrogens. The spectra for 8 and 9 changed very little when examined at higher temperatures, indicating that the solution conformation is robust. A ROESY spectrum was obtained for 8. It did not show any crosspeaks between the two alkyne hydrogens. The NMR data shows that the alkyne ligands in 10, 11 and 15 are able to rotate about the tungsten-alkyne bond; these complexes adopted several different solution conformations relating to syn and anti arrangements ofmore »the alkyne ligands. In contrast, complexes 8 and 9 adopt only one solution conformation, and the alkyne ligands in these species do not rotate about the tungsten-alkyne bond. The NMR spectra for 8 and 9 also show that these complexes are asymmetric. The 1H NMR spectra for 8 and 9 show that each hydrogen atom has its own unique resonance in the 1H NMR spectrum. There are 8 resonances for the 8 Cp protons, 4 resonances for the methylene protons, 2 resonances for the alkyne protons, and in the case of 8, 2 resonances for the NH protons. The two NH protons on complex 8 were found to have widely different chemical shifts. A DMSO titration was performed and it showed that one of the two NH protons in 8 is involved in an intramolecular hydrogen bond. Given that the diester 9 adopts a similar conformation as the diamide 8, this intramolecular hydrogen bond appears to result from the conformation imposed by cyclization of the ring system. Overall, the data show that the ring system for 8 and 9 provides a unique, rigid, robust, and air stable cyclic molecule where the alkyne ligands are limited to one orientation, presumably the syn orientation. The lack of mobility for the alkyne ligands limits the cyclic molecule to only one solution conformation. Complexes 8 and 9 are the first reported examples of cyclic tungsten bis-alkyne complexes that only adopt a single, robust conformation in solution.« less
3. Lewis acid–base pair doping of p-type organic semiconductors

   https://doi.org/10.1039/D2TC00605G  

   Peterson, Kelly A. ; Chabinyc, Michael L. ( April 2022 , Journal of Materials Chemistry C)

   Doping is required to increase the electrical conductivity of organic semiconductors for uses in electronic and energy conversion devices. The limited number of commonly used p-type dopants suggests that new dopants or doping mechanisms could improve the efficiency of doping and provide new means for processing doped polymers. Drawing on Lewis acid–base pair chemistry, we combined Lewis acid dopant B(C 6 F 5 ) 3 (BCF) with the weak Lewis base benzoyl peroxide (BPO). The detailed behavior of p-type doping of the model polymer poly(3-hexylthiophene) (P3HT) with this Lewis acid–base pair in solution was examined. Solution 19 F-NMR spectra confirmed the formation of the expected counterion, as well as side products from reactions with solvent. BCF : BPO was also found to efficiently dope a range of semiconducting polymers with varying chemical structures demonstrating that the BCF : BPO combination has an effective electron affinity of at least 5.3 eV. In thin films of regioregular P3HT cast from the doped solutions, delocalized polarons formed due to the large counterions leading to a large polaron-counterion distance. At and above 0.2 eq. BCF : BPO doping, amorphous areas of the film became doped, disrupting the structural order of the films. Despite the change in structural order, thin filmsmore »of regioregular P3HT doped with 0.2 eq. BCF : BPO had a conductivity of 25 S cm −1 . This study demonstrates the effectiveness of a two-component Lewis acid–base doping mechanism and suggests additional two-component Lewis acid–base chemistries should be explored.« less
4. Shortwave infrared luminescent Pt-nanowires: a mechanistic study of emission in solution and in the solid state

   https://doi.org/10.1039/c7dt02317k  

   Cheadle, Carl ; Ratcliff, Jessica ; Berezin, Mikhail ; Pal'shin, Vadim ; Nemykin, Victor N. ; Gerasimchuk, Nikolay N. ( January 2017 , Dalton Trans.)

   Several complexes of “PtL 2 ” composition containing two cyanoxime anions – 2-oximino-2-cyano- N -piperidineacetamide (PiPCO − ) and 2-oximino-2-cyano- N -morpholylacetamide (MCO − ) – have been obtained and characterized both in solution and in the solid state. Complexes exist as two distinct polymorphs: monomeric yellow complexes and dark-green [PtL 2 ] n 1D polymers, while for the MCO − anion a red, solvent containing dimeric [Pt(MCO) 2 ·DMSO] 2 complex has also been isolated. The interconversion of polymorphs was investigated. The monomeric PtL 2 units are arranged into anisotropic extended solid [PtL 2 ] n polymers with the help of Pt⋯Pt metallophilic interactions. Crystal structures of monomeric PtL 2 (L = PiPCO − , MCO − ) and red dimeric [Pt(MCO) 2 ·DMSO] 2 complexes were determined and revealed the cis -arrangement of cyanoxime anions. The Pt–Pt distance in the “head-to-tail” red dimer was found to be 3.133 Å. The structure of the polymeric [Pt(PiPCO) 2 ] n compound was elucidated using the EXAFS method and evidenced the formation of Pt-wires with ∼3.15 Å intermetallic separation. The EPR spectra of both 1D polymers at variable temperatures indicate the absence of Pt( iii ) species. Both pure dark-green [PtLmore »2 ] n polymers showed a considerable room temperature electrical conductivity of 20–30 S cm −1 , which evidences the formation of a mixed valence Pt( ii )/Pt( iv ) system. We discovered that these 1D polymeric [PtL 2 ] n complexes show an intense NIR fluorescence beyond 1000 nm, while yellow monomeric PtL 2 complexes are not emissive at all. The room temperature excitation spectra of 1D polymeric [PtL 2 ] n complexes demonstrated their strong emission beyond 1000 nm regardless of the used excitation wavelength between 350 and 800 nm, which is typical of systems with delocalized charge carriers. For the first time the formation of mixed valence “metal wires” held together by metallophilic interactions is directly linked both with an intense fluorescence in the NIR region of the spectrum and with the electrical conductivity. The effect of the concentration of [PtL 2 ] n complexes dispersed in the dielectric salt matrix on the photoluminescence wavelength and intensity was investigated. Both polymers show a quantum yield that is remarkably high for this region of the spectrum, reaching ∼2%. Variable temperature emission of polymeric [PtL 2 ] n in the −190–+60 °C range was studied as well.« less
5. Introducing DDEC6 atomic population analysis: part 3. Comprehensive method to compute bond orders

   https://doi.org/10.1039/c7ra07400j  

   Manz, Thomas A. ( January 2017 , RSC Adv.)

   Developing a comprehensive method to compute bond orders is a problem that has eluded chemists since Lewis's pioneering work on chemical bonding a century ago. Here, a computationally efficient method solving this problem is introduced and demonstrated for diverse materials including elements from each chemical group and period. The method is applied to non-magnetic, collinear magnetic, and non-collinear magnetic materials with localized or delocalized bonding electrons. Examples studied include the stretched O 2 molecule, 26 diatomic molecules, 3d and 5d transition metal solids, periodic materials with 1 to 8748 atoms per unit cell, a biomolecule, a hypercoordinate molecule, an electron deficient molecule, hydrogen bound systems, transition states, Lewis acid–base complexes, aromatic compounds, magnetic systems, ionic materials, dispersion bound systems, nanostructures, and other materials. From near-zero to high-order bonds were studied. Both the bond orders and the sum of bond orders for each atom are accurate across various bonding types: metallic, covalent, polar-covalent, ionic, aromatic, dative, hypercoordinate, electron deficient multi-centered, agostic, and hydrogen bonding. The method yields similar results for correlated wavefunction and density functional theory inputs and for different S Z values of a spin multiplet. The method requires only the electron and spin magnetization density distributions as input andmore »has a computational cost scaling linearly with increasing number of atoms in the unit cell. No prior approach is as general. The method does not apply to electrides, highly time-dependent states, some extremely high-energy excited states, and nuclear reactions.« less