Helical twists and ß-turns in structures at serine-proline sequences: Stabilization of cis-proline and type VI ß-turns via C-H/O interactions.

Structures at serine-proline sites in proteins were analyzed using a combination of peptide synthesis with structural methods and bioinformatics analysis of the PDB. Dipeptides were synthesized with the proline derivative (2S,4S)-(4-iodophenyl)hydroxyproline [hyp(4-I-Ph)]. The crystal structure of Boc-Ser-hyp(4-I-Ph)-OMe had two molecules in the unit cell. One molecule exhibited cis-proline and a type VIa2 ß-turn (BcisD). The cis-proline conformation was stabilized by a C-H/O interaction between Pro C-Hα and the Ser side-chain oxygen. NMR data were consistent with stabilization of cis-proline by a C-H/O interaction in solution. The other crystallographically observed molecule had trans-Pro and both residues in the PPII conformation. Two conformations were observed in the crystal structure of Ac-Ser-hyp(4-I-Ph)-OMe, with Ser adopting PPII in one and the ß conformation in the other, each with Pro in the δ conformation and trans-Pro. Structures at Ser-Pro sequences were further examined via bioinformatics analysis of the PDB and via DFT calculations. Ser-Pro versus Ala-Pro sequences were compared to identify bases for Ser stabilization of local structures. C-H/O interactions between the Ser side-chain Oγ and Pro C-Hα were observed in 45% of structures with Ser-cis-Pro in the PDB, with nearly all Ser-cis-Pro structures adopting a type VI ß-turn. 53% of Ser-trans-Pro sequences exhibited main-chain COi•••HNi+3 or COi•••HNi+4 hydrogen bonds, with Ser as the i residue and Pro as the i + 1 residue. These structures were overwhelmingly either type I ß-turns or N-terminal capping motifs on α-helices or 310-helices. These results indicate that Ser-Pro sequences are particularly potent in favoring these structures. In each, Ser is in either the PPII or ß conformation, with the Ser Oγ capable of engaging in a hydrogen bond with the amide N-H of the i + 2 (type I ß-turn or 310-helix; Ser χ1 t) or i + 3 (α-helix; Ser χ1 g+) residue. Non-proline cis amide bonds can also be stabilized by C-H/O interactions.

Nickel-Catalyzed Atroposelective Cross-Electrophile Coupling of Aryl Halides: A General and Practical Route to Diverse MOP-Type Ligands.

We report a highly cross- and atroposelective coupling between ortho-(chloro)arylphosphine oxides and ortho-(bromo)aryl ethers. This previously unknown asymmetric nickel-catalyzed reaction offers a direct route to highly enantioenriched axially chiral biaryl monophosphine oxides that are difficult to access by other means. These products can be readily reduced to generate chiral MOP-type ligands bearing complex skeletal backbones. The utility of these chiral ligands in asymmetric catalysis is also demonstrated.

4,4-Difluoroproline as a Unique 19F NMR Probe of Proline Conformation.

Despite the importance of proline conformational equilibria (trans versus cis amide and exo versus endo ring pucker) on protein structure and function, there is a lack of convenient ways to probe proline conformation. 4,4-Difluoroproline (Dfp) was identified to be a sensitive 19F NMR-based probe of proline conformational biases and cis-trans isomerism. Within model compounds and disordered peptides, the diastereotopic fluorines of Dfp exhibit similar chemical shifts (ΔδFF = 0-3 ppm) when a trans X-Dfp amide bond is present. In contrast, the diastereotopic fluorines exhibit a large (ΔδFF = 5-12 ppm) difference in chemical shift in a cis X-Dfp prolyl amide bond. DFT calculations, X-ray crystallography, and solid-state NMR spectroscopy indicated that ΔδFF directly reports on the relative preference of one proline ring pucker over the other: a fluorine which is pseudo-axial (i.e., the pro-4R-F in an exo ring pucker, or the pro-4S-F in an endo ring pucker) is downfield, while a fluorine which is pseudo-equatorial (i.e., pro-4S-F when exo, or pro-4R-F when endo) is upfield. Thus, when a proline is disordered (a mixture of exo and endo ring puckers, as at trans-Pro in peptides in water), it exhibits a small Δδ. In contrast, when the Pro is ordered (i.e., when one ring pucker is strongly preferred, as in cis-Pro amide bonds, where the endo ring pucker is strongly favored), a large Δδ is observed. Dfp can be used to identify inherent induced order in peptides and to quantify proline cis-trans isomerism. Using Dfp, we discovered that the stable polyproline II helix (PPII) formed in the denatured state (8 M urea) exhibits essentially equal populations of the exo and endo proline ring puckers. In addition, the data with Dfp suggested the specific stabilization of PPII by water over other polar solvents. These data strongly support the importance of carbonyl solvation and n → π* interactions for the stabilization of PPII. Dfp was also employed to quantify proline cis-trans isomerism as a function of phosphorylation and the R406W mutation in peptides derived from the intrinsically disordered protein tau. Dfp is minimally sterically disruptive and can be incorporated in expressed proteins, suggesting its broad application in understanding proline cis-trans isomerization, protein folding, and local order in intrinsically disordered proteins.

Influence of Controlled Chirality on the Crystallization of Maleimide-Functionalized 3,4-Ethylenedioxythiophene (EDOT-MA) Monomers.

Conjugated poly(alkoxythiophenes) such as poly(3,4-ethylenedioxythiophene) (PEDOT) have attracted considerable interest for use in a variety of applications such as biomedical devices, energy storage, and chemical sensing. Functionalized versions of the 3,4-ethylenedioxythiophene (EDOT) monomer make it possible to create polymers with properties tailored for specific applications. The maleimide functional group shows particular promise due to the wide variety of chemical modifications that it can undergo. Here, we examine the role that control of the chirality of the maleimide (MA) substituent has on the crystal structure and crystallization of the EDOT-MA monomer. We describe a method for the synthesis of a homochiral (S) variant of EDOT-MA and compare its crystallography, morphology, and thermal properties to that of the (R,S) EDOT-MA racemic compound. The conformation of the EDOT-MA molecule was substantially different, with the molecules adopting an "L" shape in the homochiral crystal, while in the racemic crystals, they were more colinear. The thermal stability of the homochiral crystals (Tm = 128.6 °C) was slightly higher than the racemic ones (Tm = 102.8 °C). We expect these results to be important in better understanding the solid-state assembly of the corresponding polymers prepared from these monomers.

Crystal structure of (S)-5-(3-acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazolidinone.

The structure of (S)-5-(3-acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazolidinone, C13H13ClFNO4, at 100 K has monoclinic (P21) symmetry. The compound has a polymeric structure propagated by a screw axis parallel to the b axis with N-H⋯O hydrogen bonding. It is of inter-est with respect to efforts in the synthesis of a candidate anti-cancer drug, parsaclisib.

Increasing the stability of calixarene-capped porous cages through coordination sphere tuning.

Chemically and thermally stable permanently porous coordination cages are appealing candidates for separations, catalysis, and as the porous component of new porous liquids. However, many of these applications have not turned to microporous cages as a result of their poor solubility and thermal or hydrolytic stability. Here we describe the design and modular synthesis of iron and cobalt cages where the carboxylate groups of the bridging ligands of well-known calixarene capped coordination cages have been replaced with more basic triazole units. The resultingly higher M-L bond strengths afford highly stable cages that are amenable to modular synthetic approaches and potential functionalization or modification. Owing to the robust nature of these cages, they are highly processable and are isolable in various physical states with tunable porosity depending on the solvation methods used. As the structural integrity of the cages is maintained upon high activation temperatures, apparent losses in porosity can be mediated by resolvation and crystallization or precipitation.

Synthesis, Characterization, and Reactivity of Tris(imido)chromium(VI) Complexes.

Multiple tris(imido)chromium(VI) complexes, including neutral and ionic compounds, have been synthesized and characterized. (tBuN)2Cr(NHtBu)Cl can be deprotonated by KN(SiMe3)2, yielding K[(tBuN)3CrCl]. This tris(imido) anion undergoes nucleophilic substitution by PPh3 and tBuNH2 to form (tBuN)3Cr(PPh3) and (tBuN)2Cr(NHtBu)2, respectively. (tBuN)2Cr(NHtBu)2 loses one amido proton to form K[(tBuN)3Cr(NHtBu)] upon reaction with KN(SiMe3)2. The imido ligands of K[(tBuN)3CrCl] and (tBuN)3Cr(PPh3) are attacked by the electrophile MeI to produce (tBuN)2Cr(NMetBu)Cl and (tBuN)2Cr(NMetBu)I, respectively. An alternate way to make tris(imido) anions is deprotonation of (tBuN)2Cr(NHtBu)Cl by an alkyl lithium reagent, e.g., Me3SiCH2Li. The resulting Li[(tBuN)3CrCl] was alkylated by a second equivalent of Me3SiCH2Li to form Li[(tBuN)3Cr(CH2SiMe3)]. Reactivity studies of tris(imido) complexes show cycloaddition with PhNCO or CO2 to form metallacycles.

Diversification of the Carbodicarbene Class by Embedding an Anionic Component in its Scaffold.

Carbodicarbene (CDC) has become an emerging ligand in many fields due to its strong σ-donating ability.

An Inherent Difference between Serine and Threonine Phosphorylation: Phosphothreonine Strongly Prefers a Highly Ordered, Compact, Cyclic Conformation.

Phosphorylation and dephosphorylation of proteins by kinases and phosphatases are central to cellular responses and function. The structural effects of serine and threonine phosphorylation were examined in peptides and in proteins, by circular dichroism, NMR spectroscopy, bioinformatics analysis of the PDB, small-molecule X-ray crystallography, and computational investigations. Phosphorylation of both serine and threonine residues induces substantial conformational restriction in their physiologically more important dianionic forms. Threonine exhibits a particularly strong disorder-to-order transition upon phosphorylation, with dianionic phosphothreonine preferentially adopting a cyclic conformation with restricted ϕ (ϕ ∼ -60°) stabilized by three noncovalent interactions: a strong intraresidue phosphate-amide hydrogen bond, an n → π* interaction between consecutive carbonyls, and an n → σ* interaction between the phosphate Oγ lone pair and the antibonding orbital of C-Hß that restricts the χ2 side-chain conformation. Proline is unique among the canonical amino acids for its covalent cyclization on the backbone. Phosphothreonine can mimic proline's backbone cyclization via noncovalent interactions. The preferred torsions of dianionic phosphothreonine are ϕ,ψ = polyproline II helix > α-helix (ϕ ∼ -60°); χ1 = g-; χ2 ∼ +115° (eclipsed C-H/O-P bonds). This structural signature is observed in diverse proteins, including in the activation loops of protein kinases and in protein-protein interactions. In total, these results suggest a structural basis for the differential use and evolution of threonine versus serine phosphorylation sites in proteins, with serine phosphorylation typically inducing smaller, rheostat-like changes, versus threonine phosphorylation promoting larger, step function-like switches, in proteins.

Molybdenum(III) Amidinate: Synthesis, Characterization, and Vapor Phase Growth of Mo-Based Materials.

The synthesis, characterization, and thermogravimetric analysis of tris(N,N'-di-isopropylacetamidinate)molybdenum(III), Mo(iPr-AMD)3, are reported. Mo(iPr-AMD)3 is a rare example of a homoleptic mononuclear complex of molybdenum(III) and fills a longstanding gap in the literature of transition metal(III) trisamidinate complexes. Thermogravimetric analysis (TGA) reveals excellent volatilization at elevated temperatures, pointing to potential applications as a vapor phase precursor for higher temperature atomic layer deposition (ALD), or chemical vapor deposition (CVD) growth of Mo-based materials. The measured TGA temperature window was 200-314 °C for samples in the 3-20 mg range. To validate the utility of Mo(iPr-AMD)3, we demonstrate aerosol-assisted CVD growth of MoO3 from benzonitrile solutions of Mo(iPr-AMD)3 at 500 °C using compressed air as the carrier gas. The resulting films are characterized by X-ray photoelectron spectroscopy, X-ray diffraction, and Raman spectroscopy. We further demonstrate the potential for ALD growth at 200 °C with a Mo(iPr-AMD)3/Ar purge/300 W O2 plasma/Ar purge sequence, yielding ultrathin films which retain a nitride/oxynitride component. Our results highlight the broad scope utility and potential of Mo(iPr-AMD)3 as a stable, high-temperature precursor for both CVD and ALD processes.

Binuclear Macrocyclic Silver(I) Complex of a Bis(carbone) Pincer Ligand: Synthesis and Application as a Carbone-Transfer Agent.

A facile synthesis of a binuclear AgI complex 2 of a bis(carbone) ligand L and its application as a carbone-transfer agent for the generation of other transition-metal complexes of AuI (3), NiII (4), and PdII (5) is presented. Complex 2 was synthesized through multiple synthetic routes under mild reaction conditions using the tetracationic [LH4][OTf·Cl]2 precursor salt, the dicationic [LH2][OTf]2 ylide salt, and the free ligand L. The first two synthesis routes require no prior isolation of the air-, moisture-, and temperature-sensitive free ligand L, thus affording complex 2 with high yield and purity. Multinuclear NMR techniques, high-resolution mass spectrometry, and single-crystal X-ray diffraction analysis confirmed the identity of complex 2 as a binuclear AgI complex of L with a molecular formula of [L2Ag2][OTf]2 and a 16-membered-ring metallomacrocyclic structure. During the transmetalation reaction with AuI, the binuclear nature of complex 2 remains intact to give analogous complex 3 ([L2Au2][OTf]2). However, the dimeric structure was disrupted upon the carbone-transfer reaction with NiII and PdII, yielding mononuclear C-N-C pincer-type complexes 4 ([LNiCl][OTf]) and 5 ([LPdCl][OTf]), respectively. These results demonstrated the versatile use of complex 2 as a carbone-transfer agent to other transition metals regardless of the type or size of the metals or the geometry they prefer.

Anion-accelerated asymmetric Nazarov cyclization: access to vicinal all-carbon quaternary stereocenters.

We have developed a catalytic asymmetric Nazarov cyclization that results in the formation of two contiguous all-carbon quaternary stereocenters in high yield with excellent levels of asymmetric induction. This method requires no catalyst recognition elements in the starting materials that are simple diketoesters. Geometrically pure E or Z isomers of the starting material lead to diastereomerically pure products with high enantioselectivity because the species that undergoes cyclization is a rhodium enolate that is configurationally stable.

Rapid post-synthetic modification of porous coordination cages with copper-catalyzed click chemistry.

Novel cobalt calixarene-capped and zirconium-based porous coordination cages were prepared with alkyne and azide functionality to leverage post-synthetic modification by click chemistry. While the calixarene-capped cages showed impressive stability when exposed to the most straightforward copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction conditions with copper(II) sulfate and sodium ascorbate as the reducing agent, milder reaction conditions were necessary to perform analogous CuAAC reactions on zirconium-based cages. Reaction kinetics were monitored by IR spectroscopy, confirming rapid reaction times (<3 hours).

Mapping the influence of ligand electronics on the spectroscopic and 1O2 sensitization characteristics of Pd(II) biladiene complexes bearing phenyl-alkynyl groups at the 2- and 18-positions.

Photodynamic therapy (PDT) is a promising treatment for certain cancers that proceeds via sensitization of ground state 3O2 to generate reactive 1O2. Classic macrocyclic tetrapyrrole ligand scaffolds, such as porphyrins and phthalocyanines, have been studied in detail for their 1O2 photosensitization capabilities. Despite their compelling photophysics, these systems have been limited in PDT applications because of adverse biological side effects. Conversely, the development of non-traditional oligotetrapyrrole ligands metalated with palladium (Pd[DMBil1]) have established new candidates for PDT that display excellent biocompatibility. Herein, the synthesis, electrochemical, and photophysical characterization of a new family of 2,18-bis(phenylalkynyl)-substituted PdII 10,10-dimethyl-5,15-bis(pentafluorophenyl)-biladiene (Pd[DMBil2-R]) complexes is presented. These second generation biladienes feature extended conjugation relative to previously characterized PdII biladiene scaffolds (Pd[DMBil1]). We show that these new derivatives can be prepared in good yield and, that the electronic nature of the phenylalkynyl appendages dramatically influence the PdII biladiene photophysics. Extending the conjugation of the Pd[DMBil1] core through installation of phenylacetylene resulted in a ∼75 nm red-shift of the biladiene absorption spectrum into the phototherapeutic window (600-900 nm), while maintaining the PdII biladiene's steady-state spectroscopic 1O2 sensitization characteristics. Varying the electronics of the phenylalkyne groups via installation of electron donating or withdrawing groups dramatically influences the steady-state spectroscopic and photophysical properties of the resulting Pd[DMBil2-R] family of complexes. The most electron rich variants (Pd[DMBil2-N(CH3)2]) can absorb light as far red as ∼700 nm but suffer from significantly reduced ability to sensitize formation of 1O2. By contrast, Pd[DMBil2-R] derivatives bearing electron withdrawing functionalities (Pd[DMBil2-CN] and Pd[DMBil2-CF3]) display 1O2 quantum yields above 90%. The collection of results we report suggest that excited state charge transfer from more electron-rich phenyl-alkyne appendages to the electron deficient biladiene core circumvents triplet sensitization. The spectral and redox properties, as well as the triplet sensitization efficiency of each Pd[DMBil2-R] derivative is considered in relation to the Hammett value (σp) for each biladiene's R-group. More broadly, the results reported in this study clearly demonstrate that biladiene redox properties, spectral properties, and photophysics can be perturbed greatly by relatively minor alterations to biladiene structure.

Porous Salts as Platforms for Heterogeneous Catalysis.

The preparation of a new class of reactive porous solids, prepared via straightforward salt metathesis reactions, is described here. Reaction of the dimethylammonium salt of a magnesium-based porous coordination cage with the chloride salt of [CrII Cl(Me4 cyclam)]+ affords a porous solid with concomitant removal of dimethylammonium chloride. The salt consists of the ions combined in the expected ratio based on their charge as confirmed by UV-vis and X-ray photoelectron spectroscopies, ion chromatography (IC), and inductively coupled plasma mass spectrometry (ICP-MS). The porous salt boasts a Brunauer-Emmett-Teller (BET) surface area of 213 m2  g-1 . Single crystal X-ray diffraction reveals the chromium(II) cations in the structure reside in the interstitial space between porous cages. Importantly, the chromium(II) centers, previously shown to react with O2 to afford reactive chromium(III)-superoxide adducts, are still accessible in the solid state as confirmed by UV-vis spectroscopy. The site-isolated reactive centers have competence toward hydrogen atom abstraction chemistry and display significantly increased stability and reactivity as compared to dissolved ions.

Multi-technique structural analysis of zinc carboxylates (soaps).

A series of medium- and long-chain zinc carboxylates (zinc octanoate, zinc nonanoate, zinc decanoate, zinc undecanoate, zinc dodecanoate, zinc pivalate, zinc stearate, zinc palmitate, zinc oleate, and zinc azelate) was analyzed by ultra-high-field 67Zn NMR spectroscopy up to 35.2 T, as well as 13C NMR and FTIR spectroscopy. We also report the single-crystal X-ray diffraction structures of zinc nonanoate, zinc decanoate, and zinc oleate-the first long-chain carboxylate single-crystals to be reported for zinc. The NMR and X-ray diffraction data suggest that the carboxylates exist in three distinct geometric groups, based on structural and spectroscopic parameters. The ssNMR results presented here present a future for dynamic nuclear polarization (DNP)-NMR-based minimally invasive methods for testing artwork for the presence of zinc carboxylates.

Photoredox-Nickel Dual-Catalyzed C-Alkylation of Secondary Nitroalkanes: Access to Sterically Hindered α-Tertiary Amines.

The preparation of tertiary nitroalkanes via the nickel-catalyzed alkylation of secondary nitroalkanes using aliphatic iodides is reported. Previously, catalytic access to this important class of nitroalkanes via alkylation has not been possible due to the inability of catalysts to overcome the steric demands of the products. However, we have now found that the use of a nickel catalyst in combination with a photoredox catalyst and light leads to much more active alkylation catalysts. These can now access tertiary nitroalkanes. The conditions are scalable as well as air and moisture tolerant. Importantly, reduction of the tertiary nitroalkane products allows rapid access to α-tertiary amines.

Isocorrole-Loaded Polymer Nanoparticles for Photothermal Therapy under 980 nm Light Excitation.

Photothermal therapy (PTT) is a promising treatment option for diseases, including cancer, arthritis, and periodontitis. Typical photothermal agents (PTAs) absorb light in the near-infrared (NIR)-I region of 650-900 nm with a predominant focus around 800 nm, as these wavelengths are minimally absorbed by water and blood in the tissue. Recently, interest has grown in developing nanomaterials that offer more efficient photothermal conversion and that can be excited by light close to or within the NIR-II window of 1000-1700 nm, which offers less absorption by melanin. Herein, we report on the development of 5,5-diphenyl isocorrole (5-DPIC) complexes containing either Zn(II) or Pd(II) (Zn[5-DPIC] and Pd[5-DPIC], respectively) that absorb strongly across the 850-1000 nm window. We also show that poly(lactic-co-glycolic acid) (PLGA) nanoparticles loaded with these designer isocorroles exhibit low toxicity toward triple-negative breast cancer (TNBC) cells in the dark but enable efficient heat production and photothermal cell ablation upon excitation with 980 nm light. These materials represent an exciting new platform for 980 nm activated PTT and demonstrate the potential for designer isocorroles to serve as effective PTAs.

Proline C-H Bonds as Loci for Proline Assembly via C-H/O Interactions.

Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of the proline ring are all sterically accessible, with polarized C-H bonds at Hα and Hδ that exhibit greater partial positive character and can be utilized as alternative sites for molecular recognition. C-H/O interactions, between proline C-H bonds and oxygen lone pairs, have been previously identified as modes of recognition within protein structures and for higher-order assembly of protein structures. In order to better understand intermolecular recognition of proline residues, a series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular C-H/O interactions in the crystallographic state, with H⋅⋅⋅O distances as close as 2.3 Å. These observed distances are well below the 2.72 Šsum of the van der Waals radii of H and O, and suggest that these interactions are particularly favorable. In order to generalize these results, we further analyzed the role of C-H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular C-H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database of small-molecule crystal structures. We found that the majority of these structures exhibited intermolecular C-H/O interactions at proline C-H bonds, suggesting that C-H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized C-H bonds, proline residues are uniquely positioned as sites for binding and recognition via C-H/O interactions.

Reactive Dicarbon as a Flexible Ligand for Transition-Metal Coordination and Catalysis.

Dicarbon is a reactive carbon allotrope that naturally exists only in the high-temperature medium of stellar space. We report the successful preparation of a series of bottleable phosphine-stabilized dicarbon (PDC) molecules. We explore the use of these molecules as a new complementary class of carbene-like ligands featuring strong σ-donor (>NHCs and CAAcs) but weak π-acceptor properties. Steric map analysis of PDC based on Cavallo's SambVca program reveals comparable steric volume bulk of 32.5%, similar to the conventional IMes carbene. However, our PDCs exhibit dynamic steric flexibility modulated by the nature of the metal complexes and catalytic reaction environment. We demonstrate the catalytic utility of the PDC framework by its successful implementation for Suzuki-Miyaura cross-coupling and the reductive coupling reaction of an aldehyde and alkyne. Detailed investigations of the reductive coupling reaction reveal an important secondary interaction between PDC and metal complexes, which plays a critical role in the catalytic system.