Understanding the origin of stereoselectivity in the photochemical denitrogenation of 2,3-diazabicyclo[2.2.1]heptene and its derivatives with non-adiabatic molecular dynamics

• Leticia A. Gomes and
• Steven A. Lopez

Beilstein J. Org. Chem. 2025, 21, 2007–2020, doi:10.3762/bjoc.21.156

• of 2,3-diazabicyclo[2.2.1]hept-2-enes (Scheme 2). This report shows the first multiconfigurational NAMD simulation studies to understand the photochemical denitrogenation mechanism of 2,3-diazabicyclo[2.2.1]hept-2-enes. Results and Discussion We started our studies on characterizing the photophysical

The effect of neighbouring group participation and possible long range remote group participation in O-glycosylation

• Rituparna Das and
• Balaram Mukhopadhyay

Beilstein J. Org. Chem. 2025, 21, 369–406, doi:10.3762/bjoc.21.27

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• , albeit with a slow but continuous deterioration of catalytic activity. Preliminary molecular docking and molecular dynamics simulation studies revealed that Thr40 and Ser105 residues played a crucial role in catalyzing the GBB reaction, forming hydrogen bonds with 2-aminopyridine substrate, increasing

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• topology as input to generate the topologies for glycolipids. The tools contained in doGlycans create 3D models and simulation files as a starting point for more complex molecular simulation studies. RosettaCarbohydrate. Rosetta is a software suite for macromolecular modelling as an extensive collection of

Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus

• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku,
• Nobuyasu Matsuura,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 297–304, doi:10.3762/bjoc.16.29

• ), were isolated from the culture broth of an actinomycete of the genus Micrococcus, which was associated with a stony coral, Catalaphyllia sp. Their chemical structures were elucidated by spectroscopic analysis including NMR and MS, with special assistance of spin system simulation studies for the

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

• Giuseppina Raffaini,
• Antonino Mazzaglia and
• Fabio Ganazzoli

Beilstein J. Org. Chem. 2015, 11, 2459–2473, doi:10.3762/bjoc.11.267

• building blocks may affect the structure and stability of the larger aggregates. Some papers already reported simulation studies of CD aggregates, or better dimers, in water in the presence of hydrophobic or at least amphiphilic moieties, such as ionic [31] and non-ionic [32][33][34] surfactants assuming a

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• . [23] reviewed the hydrophobic effect of supramolecular complexes from MD simulation studies and emphasized that the non-covalent driving force of high-energy water in the cavity of cyclodextrins, cyclophanes and cucurbiturils was an essential factor for complexation with the guest molecule. MD

Structure elucidation of β-cyclodextrin–xylazine complex by a combination of quantitative ¹H–¹H ROESY and molecular dynamics studies

• Syed Mashhood Ali,
• Kehkeshan Fatma and
• Snehal Dhokale

Beilstein J. Org. Chem. 2013, 9, 1917–1924, doi:10.3762/bjoc.9.226

• and molecular dynamics analysis. On the other hand, a ROESY spectrum with no spin diffusion can only compliment an averaged ensemble conformation obtained by molecular dynamics which is generally considered ambiguous. Keywords: β-cyclodextrin; inclusion complex; ROESY; simulation studies; xylazine

• clear. Thus, two geometries for the β-CD-xylazine complex can be assumed (Figure 5). We established the structure of the complex using this ROESY data and molecular dynamics simulation studies in vacuum. Earlier, we established the structure of a fexofenadine-α-CD complex [20] on the basis of molecular