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86 results on '"P, Sanders"'

1. Computational Investigation of the Mechanism of Diels–Alderase PyrI4

Author

Zou, Yike, Yang, Song, Sanders, Jacob N, Li, Wei, Yu, Peiyuan, Wang, Hongbo, Tang, Zhijun, Liu, Wen, and Houk, KN

Subjects
Bacterial Proteins, Binding Sites, Biocatalysis, Biological Products, Crystallography, X-Ray, Cycloaddition Reaction, Density Functional Theory, Ligases, Macrolides, Molecular Docking Simulation, Stereoisomerism, Streptomyces, Chemical Sciences, General Chemistry
Abstract

We studied the mechanisms of activation and stereoselectivity of a monofunctional Diels-Alderase (PyrI4)-catalyzed intramolecular Diels-Alder reaction that leads to formation of the key spiro-tetramate moiety in the biosynthesis of the pyrroindomycin family of natural products. Key activation effects of PyrI4 include acid catalysis and an induced-fit mechanism that cooperate with the unique "lid" feature of PyrI4 to stabilize the Diels-Alder transition state. PyrI4 enhances the intrinsic Diels-Alder stereoselectivity of the substrate and leads to stereospecific formation of the product.

Published
2020

2. Structure and Function of NzeB, a Versatile C–C and C–N Bond-Forming Diketopiperazine Dimerase

Author

Shende, Vikram V, Khatri, Yogan, Newmister, Sean A, Sanders, Jacob N, Lindovska, Petra, Yu, Fengan, Doyon, Tyler J, Kim, Justin, Houk, KN, Movassaghi, Mohammad, and Sherman, David H

Subjects
Organic Chemistry, Chemical Sciences, Bioengineering, Generic health relevance, Alkaloids, Amination, Biocatalysis, Biological Products, Carbon, Cytochrome P-450 Enzyme System, Diketopiperazines, Dimerization, Models, Molecular, Molecular Conformation, Mutagenesis, Site-Directed, Nitrogen, Streptomyces, Substrate Specificity, General Chemistry, Chemical sciences, Engineering
Abstract

The dimeric diketopiperazine (DKPs) alkaloids are a diverse family of natural products (NPs) whose unique structural architectures and biological activities have inspired the development of new synthetic methodologies to access these molecules. However, catalyst-controlled methods that enable the selective formation of constitutional and stereoisomeric dimers from a single monomer are lacking. To resolve this long-standing synthetic challenge, we sought to characterize the biosynthetic enzymes that assemble these NPs for application in biocatalytic syntheses. Genome mining enabled identification of the cytochrome P450, NzeB (Streptomyces sp. NRRL F-5053), which catalyzes both intermolecular carbon-carbon (C-C) and carbon-nitrogen (C-N) bond formation. To identify the molecular basis for the flexible site-selectivity, stereoselectivity, and chemoselectivity of NzeB, we obtained high-resolution crystal structures (1.5 Å) of the protein in complex with native and non-native substrates. This, to our knowledge, represents the first crystal structure of an oxidase catalyzing direct, intermolecular C-H amination. Site-directed mutagenesis was utilized to assess the role individual active-site residues play in guiding selective DKP dimerization. Finally, computational approaches were employed to evaluate plausible mechanisms regarding NzeB function and its ability to catalyze both C-C and C-N bond formation. These results provide a structural and computational rationale for the catalytic versatility of NzeB, as well as new insights into variables that control selectivity of CYP450 diketopiperazine dimerases.

Published
2020

3. Controlling, Understanding, and Redirecting the Thermal Rearrangement of 3,3-Dicyano-1,5-enynes

Author

Scott, Sarah K, Sanders, Jacob N, White, Katherine E, Yu, Roland A, Houk, KN, and Grenning, Alexander J

Subjects
Chemical Sciences, General Chemistry
Abstract

The thermal [3,3] rearrangement of 3,3-dicyano-1,5-enynes to γ-allenyl alkylidenemalononitriles (the "enyne Cope rearrangement") has largely eluded synthetic value as the desired products, too, are thermally reactive and ultimately yield 6π electrocyclization products. Herein, we describe experimental and computational studies related to the thermal rearrangement of 1,5-enynes, structural features to halt the thermal rearrangement at the allene stage, and a reductive variant for preparing bifunctional allenyl malononitriles. We also describe various ways that the bifunctional building blocks can be manipulated and converted to cyclic and acyclic architectures.

Published
2018

4. Backbone Hydrogen Bond Strengths Can Vary Widely in Transmembrane Helices

Author

Cao, Zheng, Hutchison, James M, Sanders, Charles R, and Bowie, James U

Subjects
Aging, Hydrogen Bonding, Membrane Proteins, Nuclear Magnetic Resonance, Biomolecular, Spectrophotometry, Ultraviolet, Thermodynamics, Chemical Sciences, General Chemistry
Abstract

Although backbone hydrogen bonds in transmembrane (TM) helices have the potential to be very strong due to the low dielectric and low water environment of the membrane, their strength has never been assessed experimentally. Moreover, variations in hydrogen bond strength might be necessary to facilitate the TM helix breaking and bending that is often needed to satisfy functional imperatives. Here we employed equilibrium hydrogen/deuterium fractionation factors to measure backbone hydrogen bond strengths in the TM helix of the amyloid precursor protein (APP). We find an enormous range of hydrogen bond free energies, with some weaker than water-water hydrogen bonds and some over 6 kcal/mol stronger than water-water hydrogen bonds. We find that weak hydrogen bonds are at or near preferred γ-secretase cleavage sites, suggesting that the sequence of APP and possibly other cleaved TM helices may be designed, in part, to make their backbones accessible for cleavage. The finding that hydrogen bond strengths in a TM helix can vary widely has implications for membrane protein function, dynamics, evolution, and design.

Published
2017

6. The Nature of Secondary Interactions at Electrophilic Metal Sites of Molecular and Silica-Supported Organolutetium Complexes from Solid-State NMR Spectroscopy

Author

Conley, Matthew P, Lapadula, Giuseppe, Sanders, Kevin, Gajan, David, Lesage, Anne, del Rosal, Iker, Maron, Laurent, Lukens, Wayne W, Copéret, Christophe, and Andersen, Richard A

Subjects
Inorganic Chemistry, Chemical Sciences, General Chemistry, Chemical sciences, Engineering
Abstract

Lu[CH(SiMe3)2]3 reacts with [SiO2-700] to give [(≡SiO)Lu[CH(SiMe3)2]2] and CH2(SiMe3)2. [(≡SiO)Lu[CH(SiMe3)2]2] is characterized by solid-state NMR and EXAFS spectroscopy, which show that secondary Lu···C and Lu···O interactions, involving a γ-CH3 and a siloxane bridge, are present. From X-ray crystallographic analysis, the molecular analogues Lu[CH(SiMe3)2]3-x[O-2,6-tBu-C6H3]x (x = 0-2) also have secondary Lu···C interactions. The (1)H NMR spectrum of Lu[CH(SiMe3)2]3 shows that the -SiMe3 groups are equivalent to -125 °C and inequivalent below that temperature, ΔG(⧧)(Tc = 148 K) = 7.1 kcal mol(-1). Both -SiMe3 groups in Lu[CH(SiMe3)2]3 have (1)JCH = 117 ± 1 Hz at -140 °C. The solid-state (13)C CPMAS NMR spectrum at 20 °C shows three chemically inequivalent resonances in the area ratio of 4:1:1 (12:3:3); the J-resolved spectra for each resonance give (1)JCH = 117 ± 2 Hz. The (29)Si CPMAS NMR spectrum shows two chemically inequivalent resonances with different values of chemical shift anisotropy. Similar observations are obtained for Lu[CH(SiMe3)2]3-x[O-2,6-tBu-C6H3]x (x = 1 and 2). The spectroscopic data point to short Lu···Cγ contacts corresponding to 3c-2e Lu···Cγ-Siβ interactions, which are supported by DFT calculations. Calculated natural bond orbital (NBO) charges show that Cγ carries a negative charge, while Lu, Hγ, and Siβ carry positive charges; as the number of O-based ligands increases so does the positive charge at Lu, which in turns shortens the Lu···Cγ distance. The change in NBO charges and the resulting changes in the spectroscopic and crystallographic properties show how ligands and surface-support sites rearrange to accommodate these changes, consistent with Pauling's electroneutrality concept.

Published
2016

17. Bicelles Rich in both Sphingolipids and Cholesterol and Their Use in Studies of Membrane Proteins.

Author

Hutchison, James M., Kuo-Chih Shih, Scheidt, Holger A., Fantin, Sarah M., Parson, Kristine F., Pantelopulos, George A., Harrington, Haley R., Mittendorf, Kathleen F., Qian, Shuo, Stein, Richard A., Collier, Scott E., Chambers, Melissa G., Katsaras, John, Voehler, Markus W., Ruotolo, Brandon T., Huster, Daniel, McFeeters, Robert L., Straub, John E., Nieh, Mu-Ping, and Sanders, Charles R.

Published
2020
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19. Isotopically Directed Symmetry Breaking and Enantioenrichment in Attrition-Enhanced Deracemization

Author

Murray, James I., Sanders, Jacob N., Richardson, Paul F., Houk, K. N., and Blackmond, Donna G.

Abstract

The evolution of homochirality via attrition-enhanced deracemization (AED) of enantiomorphic solids is carried out using molecules that differ only in the isotopic composition of a phenyl group positioned remote from the chiral center. Enantioenrichment consistently favors the enantiomorph containing a deuterated phenyl group over the protio or 13C version, and the protio version is consistently favored over the 13C version. While these isotopic compounds exhibit identical crystal structures and solubilities, the trend in deracemization correlates with melting points. Understanding the origin of this isotope bias provides fundamental clues about overcoming stochastic behavior to direct the stereochemical outcome in attrition-enhanced deracemization processes. The energy required for breaking symmetry with chiral bias is compared for this near-equilibrium AED process and the far-from-equilibrium Soai autocatalytic reaction. Implications for the origin of biological homochirality are discussed.

Published
2020
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22. A Simple and Efficient Synthesis of Functionalized Cyclic Carbonate Monomers Using a Versatile Pentafluorophenyl Ester Intermediate

Author

Alshakim Nelson, Kazuki Fukushima, Manabu Yasumoto, James L. Hedrick, Daniel J. Coady, Daniel P. Sanders, and Masaki Fujiwara

Subjects
chemistry.chemical_classification, Substitution reaction, Biocompatible polymers, Chemistry, Carbonates, Halide, Esters, General Chemistry, Biochemistry, Catalysis, Fluorobenzenes, chemistry.chemical_compound, Colloid and Surface Chemistry, Monomer, Phenols, Nucleophile, Cyclization, Click chemistry, Carbonate, Organic chemistry, Alkyl
Abstract

An improved two-step synthetic route to functionalized cyclic carbonate monomers that features a novel cyclic carbonate intermediate with an active pentafluorophenyl ester group (MTC-OPhF(5)) has been developed. The versatile pentafluorophenyl ester intermediate can be synthesized on the gram to kilogram scale in one high-yielding step and is easy to store and handle on the benchtop. The active pentafluorophenyl ester of MTC-OPhF(5) is amenable to further substitution with suitable nucleophiles such as alcohols and amines to generate functionalized cyclic carbonates in high yields. The substitution reaction is tolerant of a wide variety of functionalities, including various hydrophobic and hydrophilic groups, reactive functionalities (via thiol-ene click chemistry or alkyl halides), and protected acids, alcohols, thiols, and amines. In view of the ever-increasing need for biodegradable and biocompatible polymers, this new methodology provides a simple and versatile platform for the synthesis of new and innovative materials.

Published
2010
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26. Tetrafluorophosphite, PF4-, Anion

Author

Helene P. A. Mercier, Karl O. Christe, William W. Wilson, David A. Dixon, Jeremy C. P. Sanders, and Gary J. Schrobilgen

Subjects
Colloid and Surface Chemistry, Chemistry, General Chemistry, Biochemistry, Medicinal chemistry, Catalysis, Ion
Published
1994
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27. Osmium tetrafluoride dioxide, cis-OsO2F4

Author

Karl O. Christe, Gary J. Schrobilgen, Heinz Oberhammer, Hans Georg Mack, Alain Pagelot, Jeremy C. P. Sanders, and David A. Dixon

Subjects
Chemistry, chemistry.chemical_element, Infrared spectroscopy, General Chemistry, Biochemistry, Catalysis, chemistry.chemical_compound, Colloid and Surface Chemistry, Electron diffraction, Tetrafluoride, Anhydrous, Molecule, Physical chemistry, Osmium, Density functional theory, Fluoride
Abstract

The new osmium(VIII) oxo fluoride obtained from the reaction of KrF 2 and OsO 4 in anhydrous HF solution and originally identifed as OsOF 6 is shown by quantitative material balance, electron diffraction, NMR and vibrational spectroscopy, and density functional theory calculations to be cis-OsO 2 F 4 . The combined electron diffraction study and DFT calculations result in the following geometry: r Os=0 =1.674(4) A, r Os-Fe =1.883(3) A, r Os-Fe =1.843(3) A, O=Os-O=103.5(25) o , F e -Os-F e =77.3(26) o , F a -Os-F a =172.0(3) o , O-Os-F a = 92.4(17) o

Published
1993
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28. Heptacoordination: pentagonal bipyramidal heptafluoroxenon(1+) XeF7+ and heptafluorotellurate(1-) TeF7- ions

Author

Gary J. Schrobilgen, David A. Dixon, Jeremy C. P. Sanders, Karl O. Christe, and William W. Wilson

Subjects
Chemistry, General Chemistry, Electronic structure, Biochemistry, Catalysis, Crystallography, Colloid and Surface Chemistry, Pentagonal bipyramidal molecular geometry, Octahedron, Computational chemistry, Ab initio quantum chemistry methods, Saddle point, Intramolecular force, Molecule, Density functional theory, Physics::Chemical Physics
Abstract

The TeF 7 - anion was studied experimentally by vibrational and 19 F and 125 Te NMR spectroscopy. Ab initio calculations employing effective core potentials and density functional theory calculations at the self-consistent nonlocal level with the nonlocal exchange potential of Becke and the nonlocal correlation functional of Perdew were fixed for the analysis of the isoelectronic series TeF 7 - , IF 7 , XeF 7 + . It is shown that XeF 7 + is a stable structure, that all three members of this series possess a pentagonal bipyramidal equilibum geometry, and that from the two closest lying saddle point geometries only the monocapped trigonal prism, but not the monocapped octahedron, is a transition state for the intramolecular axial-equatorial ligand exchange

Published
1993
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29. The IOF6- anion: the first example of a pentagonal bipyramidal AX5YZ species

Author

Jeremy C. P. Sanders, Helene P. A. Mercier, Gary J. Schrobilgen, Konrad Seppelt, A. R. Mahjoub, William W. Wilson, Karl O. Christe, and David A. Dixon

Subjects
Steric effects, Chemistry, Stereochemistry, VSEPR theory, Coordination number, General Chemistry, Biochemistry, Catalysis, Colloid and Surface Chemistry, Molecular geometry, Pentagonal bipyramidal molecular geometry, Octahedron, Main group element, Valence electron
Abstract

In main group element chemistry, coordination numbers in excess of six are relatively rare, but they are of considerable interest due to special features caused by steric crowding of the ligands, free valence electron pairs being sterically either active or inactive, and the propensity of the molecules to exhibit fluxionality. Of particular interest are heptacoordinated species which could exist either as a monocapped octahedron, a monocapped trigonal prism, or a pentagonal bipyramid. According to the VSEPR model of 'repelling points on a sphere', the preferred structures should be the monocapped octahedron or trigonal prism

Published
1993
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30. The pentafluoroxenate(IV) anion, XeF5-: the first example of a pentagonal planar AX5 species

Author

Jeremy C. P. Sanders, Helene P. A. Mercier, David A. Dixon, Gary J. Schrobilgen, Karl O. Christe, and E. C. Curtis

Subjects
Electron pair, Chemistry, chemistry.chemical_element, General Chemistry, Crystal structure, Biochemistry, Molecular physics, Catalysis, Ion, Colloid and Surface Chemistry, Xenon, Molecule, Valence bond theory, Valence electron, Basis set
Abstract

The results from the crystal structure determination and a normal coordinate analysis show that the XeF 5 plane of XeF 5 − is considerably more rigid than that in the fluxional IF 7 molecule due to the increased repulsion from the xenon free valence electron pairs. Local density functional calculations were carried out for XeF 5 − and XeF 4 with a double-numerical basis set augmented by polarization functions and confirm the experimentally observed geometries and vibrational spectra. It is shown that the bonding in XeF 5 − closely resembles that in XeF 4 . In a valence bond description, it can be visualized as the two axial positions being occupied by two sp-hybridized free valence electron pairs and the equatorial fluorines being bound by two Xe 5p electron pairs through semiionic multicenter four-electron bonds

Published
1991
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31. Tuning Singlet Fission in p-Bridge-p Chromophores.

Author

Kumarasamy, Elango, Sanders, Samuel N., Tayebjee, Murad J. Y., Asadpoordarvish, Amir, Hele, Timothy J. H., Fuemmeler, Eric G., Pun, Andrew B., Yablon, Lauren M., Low, Jonathan Z., Paley, Daniel W., Dean, Jacob C., Choi, Bonnie, Scholes, Gregory D., Steigerwald, Michael L., Ananth, Nandini, McCamey, Dane R., Sfeir, Matthew Y., and Campos, Luis M.

Published
2017
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46. Quantitative Operando7Li NMR Investigations of Silicon Anode Evolution during Fast Charging and Extended Cycling

Author

Sanders, Kevin J., Ciezki, Amanda A., Berno, Alexander, Halalay, Ion C., and Goward, Gillian R.

Abstract

The development and optimization of fast battery charging protocols require detailed information regarding lithium speciation inside a battery. Nuclear magnetic resonance (NMR) spectroscopy has the unique capability of identifying the Li phases formed in an anode during Li-ion cell operation and quantifying their relative amounts. In addition, both Li metal films and dendrites are readily detected and quantified. Here, our recently reported parallel-plate resonator radio frequency (RF) probe and the cartridge-type single-layer full cell were used to track the behavior of Si electrodes during cycling and during fast charging. The LixSi compounds formed during electrochemical cycling exhibit an unexpected intrinsic nonequilibrium behavior at both slow and fast rates, evolving toward increasingly disordered local environments. The evolution with time of lithiated phases is nonlinear during both charging and discharging at constant current, unlike the case for pure graphite, and asymmetric between charge and discharge. During charging at rates of 1C, 2C, and 3C, metallic Li in both films and (to a lesser extent) dendritic forms are deposited on the Si anode. Part of the Li metal film formation is reversible, but a fraction remains on the electrode surface as dead Li, while all of the dendritic Li, even though formed in a considerably smaller amount, is entirely irreversible. Such performance-governing properties are critical to the development of fast-charging protocols for lithium-ion batteries (LIBs) and are exceptionally well evaluated and quantified by 7Li magnetic resonance strategies such as those presented here.

Published
2023
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