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Automated parametrization of the coarse-grained Martini force field for small organic molecules.

Journal of chemical theory and computation

Bereau T, Kremer K.
PMID: 26575571
J Chem Theory Comput. 2015 Jun 09;11(6):2783-91. doi: 10.1021/acs.jctc.5b00056. Epub 2015 May 12.

The systematic exploration of chemical compound space holds many promises toward structure-function relationships and material design. In the context of computer simulations, progress is hampered by both the sheer number of compounds and the efforts associated with parametrizing a...

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Bereau T, Kremer K. Automated parametrization of the coarse-grained Martini force field for small organic molecules. J Chem Theory Comput. 2015;11(6):2783-91doi: 10.1021/acs.jctc.5b00056.
Bereau, T., & Kremer, K. (2015). Automated parametrization of the coarse-grained Martini force field for small organic molecules. Journal of chemical theory and computation, 11(6), 2783-91. https://doi.org/10.1021/acs.jctc.5b00056
Bereau, Tristan, and Kremer, Kurt. "Automated parametrization of the coarse-grained Martini force field for small organic molecules." Journal of chemical theory and computation vol. 11,6 (2015): 2783-91. doi: https://doi.org/10.1021/acs.jctc.5b00056
Bereau T, Kremer K. Automated parametrization of the coarse-grained Martini force field for small organic molecules. J Chem Theory Comput. 2015 Jun 09;11(6):2783-91. doi: 10.1021/acs.jctc.5b00056. Epub 2015 May 12. PMID: 26575571.
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A 11-Steps Total Synthesis of Magellanine through a Gold(I)-Catalyzed Dehydro Diels-Alder Reaction.

Angewandte Chemie (International ed. in English)

McGee P, Bétournay G, Barabé F, Barriault L.
PMID: 28079949
Angew Chem Int Ed Engl. 2017 May 22;56(22):6280-6283. doi: 10.1002/anie.201611606. Epub 2017 Jan 12.

We have developed an innovative strategy for the formation of angular carbocycles via a gold(I)-catalyzed dehydro Diels-Alder reaction. This transformation provides rapid access to a variety of complex angular cores in excellent diastereoselectivities and high yields. The usefulness of...

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McGee P, Bétournay G, Barabé F, et al. A 11-Steps Total Synthesis of Magellanine through a Gold(I)-Catalyzed Dehydro Diels-Alder Reaction. Angew Chem Int Ed Engl. 2017;56(22):6280-6283doi: 10.1002/anie.201611606.
McGee, P., Bétournay, G., Barabé, F., & Barriault, L. (2017). A 11-Steps Total Synthesis of Magellanine through a Gold(I)-Catalyzed Dehydro Diels-Alder Reaction. Angewandte Chemie (International ed. in English), 56(22), 6280-6283. https://doi.org/10.1002/anie.201611606
McGee, Philippe, et al. "A 11-Steps Total Synthesis of Magellanine through a Gold(I)-Catalyzed Dehydro Diels-Alder Reaction." Angewandte Chemie (International ed. in English) vol. 56,22 (2017): 6280-6283. doi: https://doi.org/10.1002/anie.201611606
McGee P, Bétournay G, Barabé F, Barriault L. A 11-Steps Total Synthesis of Magellanine through a Gold(I)-Catalyzed Dehydro Diels-Alder Reaction. Angew Chem Int Ed Engl. 2017 May 22;56(22):6280-6283. doi: 10.1002/anie.201611606. Epub 2017 Jan 12. PMID: 28079949.
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Multipolar force fields and their effects on solvent dynamics around simple solutes.

The journal of physical chemistry. B

Jakobsen S, Bereau T, Meuwly M.
PMID: 25584801
J Phys Chem B. 2015 Feb 19;119(7):3034-45. doi: 10.1021/jp508052q. Epub 2015 Jan 28.

The performance of multipole (MTP) and point charge (PC) force fields in classical molecular dynamics (MD) simulations of condensed-phase systems for both equilibrium and dynamical quantities is compared. MTP electrostatics provides an improved description of the anisotropic electrostatic potential,...

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Jakobsen S, Bereau T, Meuwly M. Multipolar force fields and their effects on solvent dynamics around simple solutes. J Phys Chem B. 2015;119(7):3034-45doi: 10.1021/jp508052q.
Jakobsen, S., Bereau, T., & Meuwly, M. (2015). Multipolar force fields and their effects on solvent dynamics around simple solutes. The journal of physical chemistry. B, 119(7), 3034-45. https://doi.org/10.1021/jp508052q
Jakobsen, Sofie, et al. "Multipolar force fields and their effects on solvent dynamics around simple solutes." The journal of physical chemistry. B vol. 119,7 (2015): 3034-45. doi: https://doi.org/10.1021/jp508052q
Jakobsen S, Bereau T, Meuwly M. Multipolar force fields and their effects on solvent dynamics around simple solutes. J Phys Chem B. 2015 Feb 19;119(7):3034-45. doi: 10.1021/jp508052q. Epub 2015 Jan 28. PMID: 25584801.
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Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information.

The Journal of chemical physics

Rudzinski JF, Kremer K, Bereau T.
PMID: 26851901
J Chem Phys. 2016 Feb 07;144(5):051102. doi: 10.1063/1.4941455.

Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between simulated and reference (e.g., from experiments or higher-level simulations)...

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Rudzinski JF, Kremer K, Bereau T. Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information. J Chem Phys. 2016;144(5):051102doi: 10.1063/1.4941455.
Rudzinski, J. F., Kremer, K., & Bereau, T. (2016). Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information. The Journal of chemical physics, 144(5), 051102. https://doi.org/10.1063/1.4941455
Rudzinski, Joseph F, et al. "Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information." The Journal of chemical physics vol. 144,5 (2016): 051102. doi: https://doi.org/10.1063/1.4941455
Rudzinski JF, Kremer K, Bereau T. Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information. J Chem Phys. 2016 Feb 07;144(5):051102. doi: 10.1063/1.4941455. PMID: 26851901.
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Highly stereoselective hydroxy-directed Diels-Alder reaction.

The Journal of organic chemistry

Barriault L, Thomas JD, Clément R.
PMID: 12636397
J Org Chem. 2003 Mar 21;68(6):2317-23. doi: 10.1021/jo020664m.

The successful stereocontrol of the Diels-Alder reaction of semicyclic dienes possessing a secondary and tertiary allylic magnesium alkoxide alcohol functionality and activated dienophiles such as methyl acrylate, methacrolein, acrolein, and N-phenylmaleimide is described.

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Barriault L, Thomas JD, Clément R. Highly stereoselective hydroxy-directed Diels-Alder reaction. J Org Chem. 2003;68(6):2317-23doi: 10.1021/jo020664m.
Barriault, L., Thomas, J. D., & Clément, R. (2003). Highly stereoselective hydroxy-directed Diels-Alder reaction. The Journal of organic chemistry, 68(6), 2317-23. https://doi.org/10.1021/jo020664m
Barriault, Louis, et al. "Highly stereoselective hydroxy-directed Diels-Alder reaction." The Journal of organic chemistry vol. 68,6 (2003): 2317-23. doi: https://doi.org/10.1021/jo020664m
Barriault L, Thomas JD, Clément R. Highly stereoselective hydroxy-directed Diels-Alder reaction. J Org Chem. 2003 Mar 21;68(6):2317-23. doi: 10.1021/jo020664m. PMID: 12636397.
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Tandem oxy-Cope/transannular ene reaction of 1,2-divinylcyclohexanols.

Organic letters

Warrington JM, Yap GP, Barriault L.
PMID: 10814404
Org Lett. 2000 Mar 09;2(5):663-5. doi: 10.1021/ol005502w.

[reaction: see text] The syntheses via tandem oxy-Cope/transannular ene reaction of 1,2-divinylcyclohexanols to bi- and tricyclic skeletons are described. This strategy generates a rapid method for the preparation of advanced polycyclic intermediates with high diastereoselectivity.

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Warrington JM, Yap GP, Barriault L. Tandem oxy-Cope/transannular ene reaction of 1,2-divinylcyclohexanols. Org Lett. 2000;2(5):663-5doi: 10.1021/ol005502w.
Warrington, J. M., Yap, G. P., & Barriault, L. (2000). Tandem oxy-Cope/transannular ene reaction of 1,2-divinylcyclohexanols. Organic letters, 2(5), 663-5. https://doi.org/10.1021/ol005502w
Warrington, et al. "Tandem oxy-Cope/transannular ene reaction of 1,2-divinylcyclohexanols." Organic letters vol. 2,5 (2000): 663-5. doi: https://doi.org/10.1021/ol005502w
Warrington JM, Yap GP, Barriault L. Tandem oxy-Cope/transannular ene reaction of 1,2-divinylcyclohexanols. Org Lett. 2000 Mar 09;2(5):663-5. doi: 10.1021/ol005502w. PMID: 10814404.
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Rates of Hypoglycemia Predicted in Patients with Type 2 Diabetes on Insulin Glargine 300 U/ml Versus First- and Second-Generation Basal Insulin Analogs: The Real-World LIGHTNING Study.

Diabetes therapy : research, treatment and education of diabetes and related disorders

Pettus J, Roussel R, Liz Zhou F, Bosnyak Z, Westerbacka J, Berria R, Jimenez J, Eliasson B, Hramiak I, Bailey T, Meneghini L.
PMID: 30767173
Diabetes Ther. 2019 Apr;10(2):617-633. doi: 10.1007/s13300-019-0568-8. Epub 2019 Feb 14.

INTRODUCTION: The LIGHTNING study applied conventional and advanced analytic approaches to model, predict, and compare hypoglycemia rates of people with type 2 diabetes (T2DM) on insulin glargine 300 U/ml (Gla-300) with those on first-generation (insulin glargine 100 U/ml [Gla-100];...

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Pettus J, Roussel R, Liz Zhou F, et al. Rates of Hypoglycemia Predicted in Patients with Type 2 Diabetes on Insulin Glargine 300 U/ml Versus First- and Second-Generation Basal Insulin Analogs: The Real-World LIGHTNING Study. Diabetes Ther. 2019;10(2):617-633doi: 10.1007/s13300-019-0568-8.
Pettus, J., Roussel, R., Liz Zhou, F., Bosnyak, Z., Westerbacka, J., Berria, R., Jimenez, J., Eliasson, B., Hramiak, I., Bailey, T., & Meneghini, L. (2019). Rates of Hypoglycemia Predicted in Patients with Type 2 Diabetes on Insulin Glargine 300 U/ml Versus First- and Second-Generation Basal Insulin Analogs: The Real-World LIGHTNING Study. Diabetes therapy : research, treatment and education of diabetes and related disorders, 10(2), 617-633. https://doi.org/10.1007/s13300-019-0568-8
Pettus, Jeremy, et al. "Rates of Hypoglycemia Predicted in Patients with Type 2 Diabetes on Insulin Glargine 300 U/ml Versus First- and Second-Generation Basal Insulin Analogs: The Real-World LIGHTNING Study." Diabetes therapy : research, treatment and education of diabetes and related disorders vol. 10,2 (2019): 617-633. doi: https://doi.org/10.1007/s13300-019-0568-8
Pettus J, Roussel R, Liz Zhou F, Bosnyak Z, Westerbacka J, Berria R, Jimenez J, Eliasson B, Hramiak I, Bailey T, Meneghini L. Rates of Hypoglycemia Predicted in Patients with Type 2 Diabetes on Insulin Glargine 300 U/ml Versus First- and Second-Generation Basal Insulin Analogs: The Real-World LIGHTNING Study. Diabetes Ther. 2019 Apr;10(2):617-633. doi: 10.1007/s13300-019-0568-8. Epub 2019 Feb 14. PMID: 30767173; PMCID: PMC6437256.
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A Nine-Step Formal Synthesis of (±)-Morphine.

Organic letters

Brousseau J, Xolin A, Barriault L.
PMID: 30785291
Org Lett. 2019 Mar 01;21(5):1347-1349. doi: 10.1021/acs.orglett.9b00044. Epub 2019 Feb 20.

A nine-step stereoselective formal synthesis of (±)-morphine from readily available o-vanillin is presented. The carbocyclic structure of morphine was quickly assembled through an orchestration of the intermolecular Diels-Alder/Claisen/Friedel-Crafts sequential reaction. This approach involves many one-pot procedures and no protecting...

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Brousseau J, Xolin A, Barriault L. A Nine-Step Formal Synthesis of (±)-Morphine. Org Lett. 2019;21(5):1347-1349doi: 10.1021/acs.orglett.9b00044.
Brousseau, J., Xolin, A., & Barriault, L. (2019). A Nine-Step Formal Synthesis of (±)-Morphine. Organic letters, 21(5), 1347-1349. https://doi.org/10.1021/acs.orglett.9b00044
Brousseau, Julie, et al. "A Nine-Step Formal Synthesis of (±)-Morphine." Organic letters vol. 21,5 (2019): 1347-1349. doi: https://doi.org/10.1021/acs.orglett.9b00044
Brousseau J, Xolin A, Barriault L. A Nine-Step Formal Synthesis of (±)-Morphine. Org Lett. 2019 Mar 01;21(5):1347-1349. doi: 10.1021/acs.orglett.9b00044. Epub 2019 Feb 20. PMID: 30785291.
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Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models.

The Journal of chemical physics

Rudzinski JF, Bereau T.
PMID: 29865838
J Chem Phys. 2018 May 28;148(20):204111. doi: 10.1063/1.5025125.

Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built...

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Rudzinski JF, Bereau T. Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models. J Chem Phys. 2018;148(20):204111doi: 10.1063/1.5025125.
Rudzinski, J. F., & Bereau, T. (2018). Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models. The Journal of chemical physics, 148(20), 204111. https://doi.org/10.1063/1.5025125
Rudzinski, Joseph F, and Bereau, Tristan. "Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models." The Journal of chemical physics vol. 148,20 (2018): 204111. doi: https://doi.org/10.1063/1.5025125
Rudzinski JF, Bereau T. Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models. J Chem Phys. 2018 May 28;148(20):204111. doi: 10.1063/1.5025125. PMID: 29865838.
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Resolution limit of data-driven coarse-grained models spanning chemical space.

The Journal of chemical physics

Kanekal KH, Bereau T.
PMID: 31675850
J Chem Phys. 2019 Oct 28;151(16):164106. doi: 10.1063/1.5119101.

Increasing the efficiency of materials design remains a significant challenge given the large size of chemical compound space (CCS). The use of a chemically transferable coarse-grained model enables different molecular fragments to map to the same bead type, significantly...

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Kanekal KH, Bereau T. Resolution limit of data-driven coarse-grained models spanning chemical space. J Chem Phys. 2019;151(16):164106doi: 10.1063/1.5119101.
Kanekal, K. H., & Bereau, T. (2019). Resolution limit of data-driven coarse-grained models spanning chemical space. The Journal of chemical physics, 151(16), 164106. https://doi.org/10.1063/1.5119101
Kanekal, Kiran H, and Bereau, Tristan. "Resolution limit of data-driven coarse-grained models spanning chemical space." The Journal of chemical physics vol. 151,16 (2019): 164106. doi: https://doi.org/10.1063/1.5119101
Kanekal KH, Bereau T. Resolution limit of data-driven coarse-grained models spanning chemical space. J Chem Phys. 2019 Oct 28;151(16):164106. doi: 10.1063/1.5119101. PMID: 31675850.
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Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics.

Physical review letters

Bereau T, Rudzinski JF.
PMID: 30608819
Phys Rev Lett. 2018 Dec 21;121(25):256002. doi: 10.1103/PhysRevLett.121.256002.

Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed. Here, we extend the concept of multisurface dynamics,...

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Bereau T, Rudzinski JF. Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics. Phys Rev Lett. 2018;121(25):256002doi: 10.1103/PhysRevLett.121.256002.
Bereau, T., & Rudzinski, J. F. (2018). Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics. Physical review letters, 121(25), 256002. https://doi.org/10.1103/PhysRevLett.121.256002
Bereau, Tristan, and Rudzinski, Joseph F. "Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics." Physical review letters vol. 121,25 (2018): 256002. doi: https://doi.org/10.1103/PhysRevLett.121.256002
Bereau T, Rudzinski JF. Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics. Phys Rev Lett. 2018 Dec 21;121(25):256002. doi: 10.1103/PhysRevLett.121.256002. PMID: 30608819.
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Divergent and Modular Synthesis of Terpenoid Scaffolds via a Au.

Angewandte Chemie (International ed. in English)

Tran H, Revol G, Poyser A, Barriault L.
PMID: 34714952
Angew Chem Int Ed Engl. 2022 Jan 03;61(1):e202110575. doi: 10.1002/anie.202110575. Epub 2021 Nov 23.

A one-pot cascade sequence to generate synthetically challenging polycyclic scaffolds is reported utilizing a novel Lewis acid gold catalyst for the key cyclization step, enabling the divergent synthesis of both 6,6,5-tricyclic and 6,6,6,5-tetracyclic cores through both ligand and reaction...

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Tran H, Revol G, Poyser A, et al. Divergent and Modular Synthesis of Terpenoid Scaffolds via a Au. Angew Chem Int Ed Engl. 2021;61(1):e202110575doi: 10.1002/anie.202110575.
Tran, H., Revol, G., Poyser, A., & Barriault, L. (2022). Divergent and Modular Synthesis of Terpenoid Scaffolds via a Au. Angewandte Chemie (International ed. in English), 61(1), e202110575. https://doi.org/10.1002/anie.202110575
Tran, Huy, et al. "Divergent and Modular Synthesis of Terpenoid Scaffolds via a Au." Angewandte Chemie (International ed. in English) vol. 61,1 (2022): e202110575. doi: https://doi.org/10.1002/anie.202110575
Tran H, Revol G, Poyser A, Barriault L. Divergent and Modular Synthesis of Terpenoid Scaffolds via a Au. Angew Chem Int Ed Engl. 2022 Jan 03;61(1):e202110575. doi: 10.1002/anie.202110575. Epub 2021 Nov 23. PMID: 34714952.
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Showing 1 to 12 of 94 entries