Zachary D. Miller

Bio: Zachary D. Miller is an academic researcher from University of Michigan. The author has contributed to research in topics: Hydrosilylation & Allene. The author has an hindex of 6, co-authored 11 publications receiving 745 citations. Previous affiliations of Zachary D. Miller include University of Wisconsin-Madison.

RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

Abstract: State-of-the-art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500 proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints were obtained from the BioMagResBank FRED database. Although the original NMR struc- tures were determined by various methods, they all were recalculated by CNS and CYANA and refined subsequently by restrained molecular dynamics (CNS) in a hydrated environment. We present an extensive analysis of the results, in terms of various quality indicators generated by PROCHECK and WHAT- _CHECK. On average, the quality indicators for pack- ing and Ramachandran appearance moved one stan- dard deviation closer to the mean of the reference database. The structural quality of the recalculated structures is discussed in relation to various parame- ters, including number of restraints per residue, NOE completeness and positional root mean square devia- tion (RMSD). Correlations between pairs of these quality indicators were generally low; for example, there is a weak correlation between the number of restraints per residue and the Ramachandran appear- ance according to WHAT_CHECK (r 0.31). The set of recalculated coordinates constitutes a unified data- base of protein structures in which potential user- and software-dependent biases have been kept as small as possible. The database can be used by the structural biology community for further develop- ment of calculation protocols, validation tools, struc- ture-based statistical approaches and modeling. The RECOORD database of recalculated structures is pub- licly available from http://www.ebi.ac.uk/msd/reco-

Enantioselective photochemistry through Lewis acid–catalyzed triplet energy transfer

Abstract: Relatively few catalytic systems are able to control the stereochemistry of electronically excited organic intermediates. Here we report the discovery that a chiral Lewis acid complex can catalyze triplet energy transfer from an electronically excited photosensitizer. We applied this strategy to asymmetric [2 + 2] photocycloadditions of 2′-hydroxychalcones, using tris(bipyridyl) ruthenium(II) as a sensitizer. A variety of electrochemical, computational, and spectroscopic data rule out substrate activation by means of photoinduced electron transfer and instead support a mechanism in which Lewis acid coordination dramatically lowers the triplet energy of the chalcone substrate. We expect that this approach will enable chemists to more broadly apply their detailed understanding of chiral Lewis acid catalysis to stereocontrol in reactions involving electronically excited states.

Enantioselective Crossed Photocycloadditions of Styrenic Olefins by Lewis Acid Catalyzed Triplet Sensitization

Abstract: The synthesis of unsymmetrical cyclobutanes by controlled heterodimerization of olefins remains a substantial challenge, particularly in an enantiocontrolled fashion. Shown herein is that chiral Lewis acid catalyzed triplet sensitization enables the synthesis of highly enantioenriched diarylcyclobutanes by photocycloaddition of structurally varied 2'-hydroxychalcones with a range of styrene coupling partners. The utility of this reaction is demonstrated through the direct synthesis of a representative norlignan cyclobutane natural product.

Regioselective allene hydrosilylation catalyzed by N-heterocyclic carbene complexes of nickel and palladium.

Abstract: Regioselective methods for allene hydrosilylation have been developed, with regioselectivity being governed primarily by the choice of metal. Alkenylsilanes are produced via nickel catalysis with larger N-heterocyclic carbene (NHC) ligands, and allylsilanes are produced via palladium catalysis with smaller NHC ligands. These complementary methods allow either regioisomeric product to be obtained with exceptional regiocontrol.

Regiodivergent and Stereoselective Hydrosilylation of 1,3-Disubstituted Allenes†

Abstract: Methods for the highly stereoselective and regiodivergent hydrosilylation of 1,3-disubstituted allenes have been developed. The synthesis of E allylsilanes is accomplished with palladium NHC catalysts, and trisubstituted Z alkenylsilanes are accessed with nickel NHC catalysts. Unsymmetrically substituted allenes are well tolerated with nickel catalysis and afford Z alkenylsilanes. Evidence for a plausible mechanism was obtained through an isotopic double-labeling crossover study.

ACPYPE - AnteChamber PYthon Parser interfacE

Abstract: ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype . We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein–ligand complexes from the PDB. ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.

Evaluating protein structures determined by structural genomics consortia.

Abstract: Structural genomics projects are providing large quantities of new 3D structural data for proteins. To monitor the quality of these data, we have developed the protein structure validation software suite (PSVS), for assessment of protein structures generated by NMR or X-ray crystallographic methods. PSVS is broadly applicable for structure quality assessment in structural biology projects. The software integrates under a single interface analyses from several widely-used structure quality evaluation tools, including PROCHECK (Laskowski et al., J Appl Crystallog 1993;26:283-291), MolProbity (Lovell et al., Proteins 2003;50:437-450), Verify3D (Luthy et al., Nature 1992;356:83-85), ProsaII (Sippl, Proteins 1993;17: 355-362), the PDB validation software, and various structure-validation tools developed in our own laboratory. PSVS provides standard constraint analyses, statistics on goodness-of-fit between structures and experimental data, and knowledge-based structure quality scores in standardized format suitable for database integration. The analysis provides both global and site-specific measures of protein structure quality. Global quality measures are reported as Z scores, based on calibration with a set of high-resolution X-ray crystal structures. PSVS is particularly useful in assessing protein structures determined by NMR methods, but is also valuable for assessing X-ray crystal structures or homology models. Using these tools, we assessed protein structures generated by the Northeast Structural Genomics Consortium and other international structural genomics projects, over a 5-year period. Protein structures produced from structural genomics projects exhibit quality score distributions similar to those of structures produced in traditional structural biology projects during the same time period. However, while some NMR structures have structure quality scores similar to those seen in higher-resolution X-ray crystal structures, the majority of NMR structures have lower scores. Potential reasons for this "structure quality score gap" between NMR and X-ray crystal structures are discussed.

Energy transfer catalysis mediated by visible light: principles, applications, directions

Abstract: Harnessing visible light to access excited (triplet) states of organic compounds can enable impressive reactivity modes. This tutorial review covers the photophysical fundamentals and most significant advances in the field of visible-light-mediated energy transfer catalysis within the last decade. Methods to determine excited triplet state energies and to characterize the underlying Dexter energy transfer are discussed. Synthetic applications of this field, divided into four main categories (cyclization reactions, double bond isomerizations, bond dissociations and sensitization of metal complexes), are also examined.

Visible-Light-Induced Organic Photochemical Reactions through Energy-Transfer Pathways.

Abstract: Visible-light photocatalysis is a rapidly developing and powerful strategy to initiate organic transformations, as it closely adheres to the tenants of green and sustainable chemistry. Generally, most visible-light-induced photochemical reactions occur through single-electron transfer (SET) pathways. Recently, visible-light-induced energy-transfer (EnT) reactions have received considerable attentions from the synthetic community as this strategy provides a distinct reaction pathway, and remarkable achievements have been made in this field. In this Review, we highlight the most recent advances in visible-light-induced EnT reactions.

ARIA2: Automated NOE assignment and data integration in NMR structure calculation

Abstract: Summary: Modern structural genomics projects demand for integrated methods for the interpretation and storage of nuclear magnetic resonance (NMR) data Here we present version 21 of our program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and NMR structure calculation We report on recent developments, most notably a graphical user interface, and the incorporation of the object-oriented data model of the Collaborative Computing Project for NMR (CCPN) The CCPN data model defines a storage model for NMR data, which greatly facilitates the transfer of data between different NMR software packages Availability: A distribution with the source code of ARIA 21 is freely available at http://wwwpasteurfr/recherche/unites/Binfs/aria2 Contact: [email protected]