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3. Free energy of ligand-receptor systems forming multimeric complexes

Author

Di Michele, Lorenzo, Bachmann, Stephan J., Parolini, Lucia, and Mognetti, Bortolo M.

Subjects
Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter, Physics - Biological Physics
Abstract

Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although, complex functionalities often emerge from the simultaneous interaction of more than just two linker molecules, state of art theoretical frameworks enable the calculation of the free energy only in systems featuring one-to-one ligand/receptor binding. In this communication we derive a general formula to calculate the free energy of a system featuring simultaneous direct interaction between an arbitrary number of linkers. To exemplify the potential and generality of our approach we apply it to the systems recently introduced by Parolini et al. [ACS Nano 10, 2392 (2016)] and Halverson et al. [J. Chem. Phys. 144, 094903 (2016)], both featuring functioanlized Brownian particles interacting via three-linker complexes., Comment: 5 pages with 3 figures in the main text. 8 pages with 2 figures in the supporting information. Second version with updated bibliography and fixed typos. Accepted for publication J. Chem. Phys. (Communication)

Published
2016
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5. Synthesis of a Highly Functionalized Quinazoline Organozinc toward KRAS G12C Inhibitor Divarasib(GDC-6036), Enabled through Continuous Flow Chemistry

Author

Kelly, Sean M., Lebl, René, Malig, Thomas C., Bass, Thomas M., Kummli, Dominique, Kaldre, Dainis, Orcel, Ugo, Tröndlin, Lars, Linder, David, Sedelmeier, Joerg, Bachmann, Stephan, Han, Chong, Zhang, Haiming, and Gosselin, Francis

Abstract

The development of a scalable continuous flow process to synthesize a densely functionalized quinazoline organozinc intermediate toward KRAS G12C inhibitor divarasib(GDC-6036) is reported herein. A traditional cryogenic batch metalation process was initially employed, but instability of the quinazoline organomagnesium species above −60 °C presented a logistical roadblock, with limited flexibility for its implementation as the manufacturing scale increased. An investigation of the underlying component reaction kinetics in batch mode using PAT was followed by process modeling to develop a practical continuous flow process. Challenges relating to reactor fouling caused by precipitation of inorganic solids were addressed through the combination of plug flow and continuous stirred tank reactors in the final production system. Initial laboratory proof-of-concept experiments translated successfully to a multikilogram scale, with excellent yield and performance in the subsequent atroposelective Negishi cross-coupling.

Published
2024
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6. Second-Generation Atroposelective Synthesis of KRAS G12C Covalent Inhibitor GDC-6036

Author

Xu, Jie, primary, Lim, Ngiap-Kie, additional, Timmerman, Jacob C., additional, Shen, Jeff, additional, Clagg, Kyle, additional, Orcel, Ugo, additional, Bigler, Raphael, additional, Trachsel, Etienne, additional, Meier, Roland, additional, White, Nicholas A., additional, Burkhard, Johannes A., additional, Sirois, Lauren E., additional, Tian, Qingping, additional, Angelaud, Remy, additional, Bachmann, Stephan, additional, Zhang, Haiming, additional, and Gosselin, Francis, additional

Published
2023
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7. Thermomanagement für die PV-Anlage.

Author

Bachmann, Stephan

Subjects
SOLAR panels, RENEWABLE energy sources, POWER density, PHOTOVOLTAIC power generation, COOLING, PHOTOVOLTAIC power systems
Abstract

Copyright of Elektronik Industrie is the property of Hüthig GmbH and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2023

10. Stereoselective Synthesis of the IDO Inhibitor Navoximod

Author

St-Jean, Frédéric, primary, Angelaud, Rémy, additional, Bachmann, Stephan, additional, Carrera, Diane E., additional, Remarchuk, Travis, additional, Piechowicz, Katarzyna A., additional, Niedermann, Katrin, additional, Iding, Hans, additional, Meier, Roland, additional, Hou, Haiyun, additional, Sirois, Lauren E., additional, Xu, Jie, additional, Olbrich, Martin, additional, Rege, Pankaj, additional, Guillemot-Plass, Maud, additional, and Gosselin, Francis, additional

Published
2022
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14. Highly selective Suzuki reaction catalysed by a molecular Pd–P-MOF catalyst under mild conditions: role of ligands and palladium speciation

Author

Cartagenova, Daniele, primary, Bachmann, Stephan, additional, Püntener, Kurt, additional, Scalone, Michelangelo, additional, Newton, Mark A., additional, Peixoto Esteves, Fabio A., additional, Rohrbach, Thomas, additional, Zimmermann, Patrik P., additional, van Bokhoven, Jeroen A., additional, and Ranocchiari, Marco, additional

Published
2022
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17. Development of the Commercial Manufacturing Process for Ipatasertib

Author

Bachmann, Stephan, primary, Iding, Hans, additional, Lautz, Christian, additional, Thomé-Pfeiffer, Isabelle, additional, Maierhofer, Caroline, additional, Mondière, Régis, additional, Schmidt, Philipp, additional, Strasser, Christoph, additional, Bär, Thomas, additional, Aebi, André, additional, and Schuster, Andreas, additional

Published
2021
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22. Asymmetric Hydrogenation of Unfunctionalized Tetrasubstituted Acyclic Olefins

Author

Bigler, Raphael, primary, Mack, Kyle A., additional, Shen, Jeff, additional, Tosatti, Paolo, additional, Han, Chong, additional, Bachmann, Stephan, additional, Zhang, Haiming, additional, Scalone, Michelangelo, additional, Pfaltz, Andreas, additional, Denmark, Scott E., additional, Hildbrand, Stefan, additional, and Gosselin, Francis, additional

Published
2020
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27. Communication: Free energy of ligand-receptor systems forming multimeric complexes.

Author

Michele, Lorenzo Di, Bachmann, Stephan J., Parolini, Lucia, and Mognetti, Bortolo M.

Subjects
*RECEPTOR-ligand complexes, *MOLECULAR self-assembly, *FREE energy (Thermodynamics), *BINDING sites, *POTENTIAL energy
Abstract

Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although complex functionalities often emerge from the simultaneous interaction of more than just two linker molecules, state of the art theoretical frameworks enable the calculation of the free energy only in systems featuring one-to-one ligand/receptor binding. In this Communication, we derive a general formula to calculate the free energy of systems featuring simultaneous direct interaction between an arbitrary number of linkers. To exemplify the potential and generality of our approach, we apply it to the systems recently introduced by Parolini et al. [ACS Nano 10, 2392 (2016)] and Halverson and Tkachenko [J. Chem. Phys. 144, 094903 (2016)], both featuring functionalized Brownian particles interacting via three-linker complexes. [ABSTRACT FROM AUTHOR]

Published
2016
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28. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2.

Author

Zhixiong Lin, Bachmann, Stephan J., and van Gunsteren, Wilfred F.

Subjects
*THERMODYNAMICS, *UREA, *BIOMOLECULES, *COMPUTER simulation, *DENATURATION of proteins, *MIXTURES, *DIELECTRICS, *MATHEMATICAL models
Abstract

Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 models may be used in biomolecular simulations of protein denaturation. [ABSTRACT FROM AUTHOR]

Published
2015
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30. An improved simple polarisable water model for use in biomolecular simulation.

Author

Bachmann, Stephan J. and van Gunsteren, Wilfred F.

Subjects
*WATER, *MOLECULAR dynamics, *MOLECULAR models, *ELECTROSTATIC fields, *PERMITTIVITY, *SOLVATION
Abstract

The accuracy of biomolecular simulations depends to some degree on the accuracy of the water model used to solvate the biomolecules. Because many biomolecules such as proteins are electrostatically rather inhomogeneous, containing apolar, polar, and charged moieties or side chains, a water model should be able to represent the polarisation response to a local electrostatic field, while being compatible with the force field used to model the biomolecules or protein. The two polarisable water models, COS/G2 and COS/D, that are compatible with the GROMOS biomolecular force fields leave room for improvement. The COS/G2 model has a slightly too large dielectric permittivity and the COS/D model displays a much too slow dynamics. The proposed COS/D2 model has four interaction sites: only one Lennard-Jones interaction site, the oxygen atom, and three permanent charge sites, the two hydrogens, and one massless off-atom site that also serves as charge-on-spring (COS) polarisable site with a damped or sub-linear dependence of the induced dipole on the electric field strength for large values of the latter. These properties make it a cheap and yet realistic water model for biomolecular solvation. [ABSTRACT FROM AUTHOR]

Published
2014
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33. Möblierung für alle - Prototypen inklusiver Ausstattung

Author

Hagenbuch, Reto and Bachmann, Stephan

Subjects
Barrierefreiheit, 700: Künste und Unterhaltung, 712: Landschaftsgestaltung (Landschaftsdesign), 305: Soziale Gruppen, Inklusion, Möblierung
Abstract

Ein mit dem Rollstuhl unterfahrbarer Picknicktisch, ein Stuhl mit taktiler Markierung für den weissen Stock oder eine Liege mit kontrastreichen Latten. – Damit ein Park von allen Menschen genutzt und erlebt werden kann, muss dieser nicht nur barrierefrei erschlossen, sondern ebenso möbliert sein. Denn Menschen mit Behinderungen haben spezifische Ansprüche an eine Sitzbank oder eine Liege. Gemeinsam mit der Burri public elements AG entwickelt die ZHAW-Forschungsgruppe Freiraummanagement zurzeit eine neuartige, an die Bedürfnisse von Menschen mit Behinderungen angepasste Möblierung.

Published
2017
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34. Cover Feature: Highly Efficient Synthesis of a Staphylococcus aureus Targeting Payload to Enable the First Antibody-Antibiotic Conjugate (Chem. Eur. J. 12/2018)

Author

Linghu, Xin, primary, Segraves, Nathaniel L., additional, Abramovich, Ifat, additional, Wong, Nicholas, additional, Müller, Barbara, additional, Neubauer, Nadja, additional, Fantasia, Serena, additional, Rieth, Sebastian, additional, Bachmann, Stephan, additional, Jansen, Michael, additional, Sowell, C. Gregory, additional, Askin, David, additional, Koenig, Stefan G., additional, and Gosselin, Francis, additional

Published
2018
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37. Highly Efficient Synthesis of a Staphylococcus aureus Targeting Payload to Enable the First Antibody-Antibiotic Conjugate

Author

Linghu, Xin, primary, Segraves, Nathaniel L., additional, Abramovich, Ifat, additional, Wong, Nicholas, additional, Müller, Barbara, additional, Neubauer, Nadja, additional, Fantasia, Serena, additional, Rieth, Sebastian, additional, Bachmann, Stephan, additional, Jansen, Michael, additional, Sowell, C. Gregory, additional, Askin, David, additional, Koenig, Stefan G., additional, and Gosselin, Francis, additional

Published
2017
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38. Asymmetric Synthesis of Akt Kinase Inhibitor Ipatasertib

Author

Han, Chong, primary, Savage, Scott, additional, Al-Sayah, Mohammad, additional, Yajima, Herbert, additional, Remarchuk, Travis, additional, Reents, Reinhard, additional, Wirz, Beat, additional, Iding, Hans, additional, Bachmann, Stephan, additional, Fantasia, Serena M., additional, Scalone, Michelangelo, additional, Hell, André, additional, Hidber, Pirmin, additional, and Gosselin, Francis, additional

Published
2017
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42. Chemoselective semihydrogenation of alkynes catalyzed by manganese(i)-PNP pincer complexesElectronic supplementary information (ESI) available. See DOI: 10.1039/d0cy00992jDedicated to Prof. Uwe Rosenthal on the occasion of his 70th birthday.

Author

GarbeBoth authors contributed equally to this publication., Marcel, Budweg, Svenja, Papa, Veronica, Wei, Zhihong, Hornke, Helen, Bachmann, Stephan, Scalone, Michelangelo, Spannenberg, Anke, Jiao, Haijun, Junge, Kathrin, and Beller, Matthias

Abstract

A general manganese catalyzed chemoselective semihydrogenation of alkynes to olefins in the presence of molecular hydrogen is described. The best results are obtained by applying the aliphatic Mn PNP pincer complex Mn-3cwhich allows the transformation of various substituted internal alkynes to the respective Z-olefins under mild conditions and in high yields. Mechanistic investigations based on experiments and computations indicate the formation of the Z-isomer viaan outer-sphere mechanism.

Published
2020
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43. Asymmetric Synthesis of Akt Kinase Inhibitor Ipatasertib

Author

Han, Chong, Savage, Scott, Al-Sayah, Mohammad, Yajima, Herbert, Remarchuk, Travis, Reents, Reinhard, Wirz, Beat, Iding, Hans, Bachmann, Stephan, Fantasia, Serena M., Scalone, Michelangelo, Hell, André, Hidber, Pirmin, and Gosselin, Francis

Abstract

A highly efficient asymmetric synthesis of the Akt kinase inhibitor ipatasertib (1) is reported. The bicyclic pyrimidine 2starting material was prepared via a nitrilase biocatalytic resolution, halogen–metal exchange/anionic cyclization, and a highly diastereoselective biocatalytic ketone reduction as key steps. The route also features a halide activated, Ru-catalyzed asymmetric hydrogenation of a vinylogous carbamic acid to produce α-aryl-β-amino acid 3in high yield and enantioselectivity. The API was assembled in a convergent manner through a late-stage amidation/deprotection/monohydrochloride salt formation sequence.

Published
2024
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44. Synthesis and Characterization of Iron–Nitrogen-Doped Graphene/Core–Shell Catalysts: Efficient Oxidative Dehydrogenation of N-Heterocycles

Author

Cui, Xinjiang, Li, Yuehui, Bachmann, Stephan, Scalone, Michelangelo, Surkus, Annette-Enrica, Junge, Kathrin, Topf, Christoph, and Beller, Matthias

Abstract

An important goal for nanocatalysis is the development of flexible and efficient methods for preparing active and stable core–shell catalysts. In this respect, we present the synthesis and characterization of iron oxides surrounded by nitrogen-doped-graphene shells immobilized on carbon support (labeled FeOx@NGr–C). Active catalytic materials are obtained in a simple, scalable and two-step method via pyrolysis of iron acetate and phenanthroline and subsequent selective leaching. The optimized FeOx@NGr–C catalyst showed high activity in oxidative dehydrogenations of several N-heterocycles. The utility of this benign methodology is demonstrated by the synthesis of pharmaceutically relevant quinolines. In addition, mechanistic studies prove that the reaction progresses via superoxide radical anions (·O2–).

Published
2024
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45. Melting transition in lipid vesicles functionalised by mobile DNA linkers

Author

Bachmann, Stephan, Kotar, Jurij, Parolini, Lucia, Šarić, Andela, Cicuta, Pietro, Di Michele, Lorenzo, Mognetti, Bortolo Matteo, Bachmann, Stephan, Kotar, Jurij, Parolini, Lucia, Šarić, Andela, Cicuta, Pietro, Di Michele, Lorenzo, and Mognetti, Bortolo Matteo

Abstract

We study phase behaviour of lipid-bilayer vesicles functionalised by ligand-receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo simulations that combine a coarse grained description of the lipid bilayer with state of art analytical models for multivalent ligand-receptor interactions. Using density of state calculations, we derive the partition function in pairs of vesicles and compute the number of ligand-receptor bonds as a function of temperature. Numerical results are compared to microscopy and fluorimetry experiments on large unilamellar vesicles decorated by DNA linkers carrying complementary overhangs. We find that vesicle aggregation is suppressed when the total number of linkers falls below a threshold value. Within the model proposed here, this is due to the higher configurational costs required to form inter-vesicle bridges as compared to intra-vesicle loops, which are in turn related to membrane deformability. Our findings and our numerical/experimental methodologies are applicable to the rational design of liposomes used as functional materials and drug delivery applications, as well as to study inter-membrane interactions in living systems, such as cell adhesion., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2016

46. Bond formation kinetics affects self-assembly directed by ligand-receptor interactions

Author

Bachmann, Stephan, Petitzon, Marius, Mognetti, Bortolo Matteo, Bachmann, Stephan, Petitzon, Marius, and Mognetti, Bortolo Matteo

Abstract

In this paper we study aggregation kinetics in systems of particles functionalised by complementary linkers. Most of the coarse-grained models currently employed to study large-scale self-assembly of these systems rely on effective potentials between particles as calculated using equilibrium statistical mechanics. In these approaches the kinetic aspects underlying the formation of inter-particle linkages are neglected. We show how the rate at which supramolecular linkages form drastically changes the self-assembly pathway. In order to do this we develop a method that combines Brownian dynamics simulations with a Gillespie algorithm accounting for the evolution of inter-particle linkages. If compared with dynamics based on effective potentials, an explicit description of inter-particle linkages results in aggregates that in the early stages of self-assembly have a lower valency. Relaxation towards equilibrium is hampered by the time required to break existing linkages within one cluster and to reorient them toward free particles. This effect is more important at low temperature and high particle diffusion constant. Our results highlight the importance of including kinetic rates into coarse-grained descriptions of ligand-receptor systems., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2016

47. Communication: Free energy of ligand-receptor systems forming multimeric complexes

Author

Di Michele, Lorenzo, Bachmann, Stephan, Parolini, Lucia, Mognetti, Bortolo Matteo, Di Michele, Lorenzo, Bachmann, Stephan, Parolini, Lucia, and Mognetti, Bortolo Matteo

Abstract

Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although complex functionalities often emerge from the simultaneous interaction of more than just two linker molecules, state of the art theoretical frameworks enable the calculation of the free energy only in systems featuring one-to-one ligand/receptor binding. In this Communication, we derive a general formula to calculate the free energy of systems featuring simultaneous direct interaction between an arbitrary number of linkers. To exemplify the potential and generality of our approach, we apply it to the systems recently introduced by Parolini et al. [ACS Nano 10, 2392 (2016)] and Halverson and Tkachenko [J. Chem. Phys. 144, 094903 (2016)], both featuring functionalized Brownian particles interacting via three-linker complexes., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2016

48. Development of Models for Biomolecular Simulation: Polarisability and Solvation

Author

Bachmann, Stephan Jan, van Gunsteren, Wilfred F., and Hünenberger, Philippe H.

Subjects
POLARITÄT, HYDROPHILE UND LIPOPHOBE MOLEKÜLE UND INTERAKTIONEN (BIOPHYSIKALISCHE CHEMIE), MOLEKÜLDYNAMIK + MOLEKÜLMOBILITÄT + MOLEKÜLMOTILITÄT (BIOMOLEKÜLE), PROTEINE + POLYPEPTIDE (BIOCHEMIE), LÖSUNGSMITTELEINFLÜSSE + SOLVATATION + SOLVOLYSE (PHYSIKALISCHE CHEMIE), MOLEKULARE DYNAMIK (MOLEKÜLPHYSIK), POLARITY, HYDROPHILIC AND LIPOPHOBIC MOLECULES AND INTERACTIONS (BIOPHYSICAL CHEMISTRY), MOLECULAR DYNAMICS + MOLECULAR MOBILITY + MOLECULAR MOTILITY (BIOMOLECULES), PROTEINS + POLYPEPTIDES (BIOCHEMISTRY), SOLVENT EFFECTS + SOLVATATION + SOLVOLYSIS (PHYSICAL CHEMISTRY), MOLECULAR DYNAMICS (MOLECULAR PHYSICS), Life sciences, Chemistry, ddc:570, ddc:540
Published
2014

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