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View article: Barry Carpenter—Pioneering physical organic chemist, teacher, mentor, and friend
Barry Carpenter—Pioneering physical organic chemist, teacher, mentor, and friend Open
This special issue of the Journal of Physical Organic Chemistry is dedicated to an outstanding physical organic chemist, mentor, and friend, Barry Carpenter, on the occasion of his official retirement. Knowing that great minds like his nev…
View article: Barry Carpenter. Pioneering Physical Organic Chemist, Teacher, Mentor and Friend
Barry Carpenter. Pioneering Physical Organic Chemist, Teacher, Mentor and Friend Open
This is the preface to a special issue of the Journal of Physical Organic Chemistry dedicated to an outstanding physical organic chemist, mentor and friend, Barry Carpenter on the occasion of his official retirement.
View article: Elucidating the role of catalytic amino acid residues in the peptide-mediated silica oligomerization reaction mechanism
Elucidating the role of catalytic amino acid residues in the peptide-mediated silica oligomerization reaction mechanism Open
This manuscript explores the reaction mechanisms of peptide-based biomineralization processes. Charged sidechains are known to play a role in silicate oligomerization, but the underlying mechanisms and energy landscapes have not been deter…
View article: Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking
Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking Open
Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of interac…
View article: Sampling protein-ligand binding pathways to recover crystallographic binding poses using interactive molecular dynamics in virtual reality
Sampling protein-ligand binding pathways to recover crystallographic binding poses using interactive molecular dynamics in virtual reality Open
Using molecular dynamics (MD) to simulate drug binding & unbinding is a challenge. Because it requires sampling rugged energy landscapes that separate bound and unbound states, it has a high cost and consumes significant computational reso…
View article: Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices
Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices Open
Low dimensional representations along reaction pathways were produced using newly created Python software that utilises Principal Component Analysis (PCA) to do dimensionality reduction. Plots of these pathways in reduced dimensional space…
View article: Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices
Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices Open
Low dimensional representations along reaction pathways were produced using newly created Python software that utilises Principal Component Analysis (PCA) to do dimensionality reduction. Plots of these pathways in reduced dimensional space…
View article: Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices
Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices Open
Low dimensional representations along reaction pathways were produced using newly created Python software that utilises Principal Component Analysis (PCA) to do dimensionality reduction. Plots of these pathways in reduced dimensional space…
View article: Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices
Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices Open
Principal Component Analysis on a series of molecular geometries ( e.g. , a reaction coordinate or trajectory) provides maximum structural variance in the fewest dimensions, and so can offer an objective, comprehensible depiction of the tr…
View article: CCDC 1859684: Experimental Crystal Structure Determination
CCDC 1859684: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: Post-transition state bifurcations induce dynamical detours in Pummerer-like reactions
Post-transition state bifurcations induce dynamical detours in Pummerer-like reactions Open
A post-transition state bifurcation (PTSB) involved in a Pummerer-type rearrangement is characterized using density functional theory (DFT) calculations on potential energy stationary points and direct dynamics simulations.
View article: CCDC 1859683: Experimental Crystal Structure Determination
CCDC 1859683: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: Correction: Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis
Correction: Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis Open
[This corrects the article DOI: 10.3762/bjoc.12.41.].
View article: Post-transition state bifurcations gain momentum – current state of the field
Post-transition state bifurcations gain momentum – current state of the field Open
The existence of post-transition state bifurcations on potential energy surfaces for organic and biological reaction mechanisms has been known for decades, but recently, new reports of bifurcations have been occurring at a much higher rate…
View article: CCDC 1586635: Experimental Crystal Structure Determination
CCDC 1586635: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586651: Experimental Crystal Structure Determination
CCDC 1586651: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586653: Experimental Crystal Structure Determination
CCDC 1586653: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586644: Experimental Crystal Structure Determination
CCDC 1586644: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586640: Experimental Crystal Structure Determination
CCDC 1586640: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586646: Experimental Crystal Structure Determination
CCDC 1586646: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586657: Experimental Crystal Structure Determination
CCDC 1586657: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586654: Experimental Crystal Structure Determination
CCDC 1586654: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586649: Experimental Crystal Structure Determination
CCDC 1586649: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586658: Experimental Crystal Structure Determination
CCDC 1586658: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586655: Experimental Crystal Structure Determination
CCDC 1586655: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586663: Experimental Crystal Structure Determination
CCDC 1586663: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1586650: Experimental Crystal Structure Determination
CCDC 1586650: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …