Isoorotamide-based peptide nucleic acid nucleobases with extended linkers aimed at distal base recognition of adenosine in double helical RNA

• Grant D. Walby,
• Brandon R. Tessier,
• Tristan L. Mabee,
• Jennah M. Hoke,
• Hallie M. Bleam,
• Angelina Giglio-Tos,
• Emily E. Harding,
• Vladislavs Baskevics,
• Martins Katkevics,
• Eriks Rozners and
• James A. MacKay

Beilstein J. Org. Chem. 2025, 21, 2513–2523, doi:10.3762/bjoc.21.193

• UV melting and ITC, Db2 showed especially poor affinity for the U–A base pair in HRP1. To help explain experimental binding results, we turned to computational molecular dynamics modeling using HRP1 and PNA1–3 as a model based on the PNA–dhRNA triplex provided by previous NMR studies [41] (for

• details see Supporting Information File 1). The Db nucleobases were individually incorporated into the PNA model oligonucleotide and subjected to 50 ns unrestricted Desmond molecular dynamics. Pictures from the molecular dynamics simulations shown in Figure 7 represent the conformation of the PNA bases

• from glutaric anhydride [30]. In fact, molecular dynamics simulations did confirm that the amide carbonyl of the linker forms a stable H-bond to the amino group of C (Figure 7C). Since the distal guanosine in the C–G base pair is a mismatch with the isoorotic acid binding moiety, the isoorotamide

Effect of a photoswitchable rotaxane on membrane permeabilization across lipid compositions

• Udyogi N. K. Conthagamage,
• Lilia Lopez,
• Zuliah A. Abdulsalam and
• Víctor García-López

Beilstein J. Org. Chem. 2025, 21, 2498–2512, doi:10.3762/bjoc.21.192

• ; membrane fluidity; membrane permeability; photoswitchable rotaxane; Introduction Lipid membranes play a vital role in biology by acting as protective barriers for cells and organelles while regulating the passage of substances. Additionally, their structure and dynamics influence the activity of membrane

• more membrane perturbation compared to the axle alone, in agreement with our previous molecular dynamics simulations, which highlight the importance of the macrocycle to modulate lipid packing [15]. As cholesterol content increased, sulforhodamine B release progressively decreased, consistent with the

• previous molecular dynamics simulations of rotaxane 1 in POPC bilayers, a major component of EYPC [16], showed that rotaxane 1 disrupts lipid packing and promotes water accumulation within the bilayer [15]. These effects enhance membrane permeability to hydrophilic molecules such as sulforhodamine B. The

Conformational effects on iodide binding: a comparative study of flexible and rigid carbazole macrocyclic analogs

• Guang-Wei Zhang,
• Yong Zhang,
• Le Shi,
• Chuang Gao,
• Hong-Yu Li and
• Lei Xue

Beilstein J. Org. Chem. 2025, 21, 2369–2375, doi:10.3762/bjoc.21.181

• interplay between conformational dynamics and localized structural adaptations governing anion recognition. The findings advance the rational design of tunable, high-affinity anion receptors and deepen the understanding of conformational regulation in supramolecular systems. Keywords: anion recognition

• ]. Notably, the anion-binding performance of these macrocycles is inherently governed by their conformational dynamics [9][10]. Flexible hosts adaptively adjust their cavities via induced-fit mechanisms to accommodate diverse guests, while rigid hosts rely on preorganized spatial complementarity for

• conformational dynamics, prompting a paradigm shift from static binding models to mechanistic insights into induced fit [17] and conformational selection [18]. This cognitive shift marks the transition of molecular recognition research from a simple description of binding phenomena to a deep understanding at the

Rotaxanes with integrated photoswitches: design principles, functional behavior, and emerging applications

• Jullyane Emi Matsushima,
• Khushbu,
• Zuliah Abdulsalam,
• Udyogi Navodya Kulathilaka Conthagamage and
• Víctor García-López

Beilstein J. Org. Chem. 2025, 21, 2345–2366, doi:10.3762/bjoc.21.179

• shuttling dynamics. In this review, we discuss key examples of photoswitchable rotaxanes, organized according to the position of the photoswitch, either embedded in the axle or incorporated into the macrocycle. We examine the major classes of photoswitches used, including their switching mechanisms and the

• intermolecular interactions is a powerful strategy for designing sophisticated molecular systems that operate across multiple length scales, from nanoscale dynamics to macroscopic functions [1][2][3]. Light is particularly attractive compared to other stimuli due to its non-invasive nature, high spatial and

• lipid membrane, leading to reversible changes in giant lipid vesicles. In the trans isomer, the membrane tension decreased, resulting in deformation and pronounced membrane undulations. Isomerization to the cis form increased membrane tension, causing vesicle contraction. Molecular dynamics simulations

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

• synthetic organic chemists. We report a computational study on the mechanism of diazabicyclo[2.2.1]heptenes to address long standing mechanistic questions. Indeed, the mechanism of these reactions has been disputed for over six decades. We employed non-adiabatic molecular dynamics (NAMD) simulations

• two possible S1/S0-MECIs. Our dynamics simulations illustrate that inversion begins in the excited state immediately after the first σCN bond breaks. This inversion is driven by the atomic momenta acquired after the bond breaks. These dynamical effects promote the formation of the inverted housane

• , thereby explaining the observed selectivities. A minority of trajectories undergo thermal conversion in the ground state, producing the minor retained housane product from inverted housane/diradical. Keywords: non-adiabatic molecular dynamics; photochemistry; quantum mechanical calculations

Synthesis of N-doped chiral macrocycles by regioselective palladium-catalyzed arylation

• Shuhai Qiu and
• Junzhi Liu

Beilstein J. Org. Chem. 2025, 21, 1917–1923, doi:10.3762/bjoc.21.149

• -bridged structural analogs of [1n]metacyclophanes. In comparison to all-carbon [1n]metacyclophanes, the incorporation of N atoms endows them with unique features, such as enhanced molecular dynamics and tunable redox property, positioning them as key precursors to construct organic high-spin materials [20

Continuous-flow-enabled intensification in nitration processes: a review of technological developments and practical applications over the past decade

• Feng Zhou,
• Chuansong Duanmu,
• Yanxing Li,
• Jin Li,
• Haiqing Xu,
• Pan Wang and
• Kai Zhu

Beilstein J. Org. Chem. 2025, 21, 1678–1699, doi:10.3762/bjoc.21.132

• in storage vessels. In mixed acid nitration systems, the typical liquid–liquid biphasic nature critically governs reaction efficiency through interfacial mass transfer dynamics. Continuous-flow configurations provide diverse mixing solutions ranging from passive geometries (T-junction, Y-junction

Thermodynamic equilibrium between locally excited and charge transfer states in perylene–phenothiazine dyads

• Issei Fukunaga,
• Shunsuke Kobashi,
• Yuki Nagai,
• Hiroki Horita,
• Hiromitsu Maeda and
• Yoichi Kobayashi

Beilstein J. Org. Chem. 2025, 21, 1577–1586, doi:10.3762/bjoc.21.121

• Issei Fukunaga Shunsuke Kobashi Yuki Nagai Hiroki Horita Hiromitsu Maeda Yoichi Kobayashi Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, Japan 10.3762/bjoc.21.121 Abstract We report the excited-state dynamics of π-orthogonal

• featuring high photostability and strong visible absorption. Perylene–phenothiazine (Pe–PTZ) derivatives have been previously investigated for their excited-state dynamics [15]. Incorporating additional electron-donating groups such as triphenylamine (TPA) onto the PTZ core is expected not only to enhance

• dynamics of these molecules, transient absorption spectroscopy measurements spanning the femtosecond to microsecond timescales were conducted. When electron transfer occurs between the donor and acceptor, the spin–spin interaction becomes weaker, facilitating the formation of triplet excited states upon

Synthesis of an aza[5]helicene-incorporated macrocyclic heteroarene via oxidation of an o-phenylene-pyrrole-thiophene icosamer

• Yusuke Matsuo,
• Aoi Nakagawa,
• Shu Seki and
• Takayuki Tanaka

Beilstein J. Org. Chem. 2025, 21, 1561–1567, doi:10.3762/bjoc.21.119

• study illuminated that a partially fused macrocyclic molecule is an intriguing structural motif which comprises a rigid backbone, yet showing somewhat flexible structural dynamics under ambient temperature conditions. (a) Increased ring-strain from macrocyclic oligoarene to partially fused oligoarene

Wittig reaction of cyclobisbiphenylenecarbonyl

• Taito Moribe,
• Junichiro Hirano,
• Hideaki Takano,
• Hiroshi Shinokubo and
• Norihito Fukui

Beilstein J. Org. Chem. 2025, 21, 1454–1461, doi:10.3762/bjoc.21.107

• low racemization barrier as with structurally similar methylenedioxy-substituted DBC derivative [22]. Racemization dynamics The racemization barriers of CBBC 1, mono-olefin 3, and bis-olefin 5 were evaluated by monitoring the decrease of circular dichroism (CD) signals in 1,2-dichlorobenzene at 170 °C

• . The racemization dynamics of 5 was investigated by DFT calculations at the B3LYP/6-31G(d) level of theory, employing the Gaussian 16 software package and the global reaction route mapping (GRRM17) [23] program (Figure 4). The interconversion between figure-eight conformation (M,M)-B and bathtub

• circle and red triangle mean selected signals due to figure-eight and bathtub conformations, respectively. Simulated dynamics of bis-olefin 5 at the B3LYP/6-31G(d) level of theory. The description for the configuration of A and B are based on the helical chirality of the 1,1-diphenylethylene units and

Advances in nitrogen-containing helicenes: synthesis, chiroptical properties, and optoelectronic applications

• Meng Qiu,
• Jing Du,
• Nai-Te Yao,
• Xin-Yue Wang and
• Han-Yuan Gong

Beilstein J. Org. Chem. 2025, 21, 1422–1453, doi:10.3762/bjoc.21.106

• and high BCPL of 66.5 M−1 cm−1 underscore its potential for advanced chiral photonic applications. Heteroatom engineering in double helicenes has emerged as a powerful strategy for tuning chiroptical properties and excited-state dynamics. In 2021, Sakamaki’s group synthesized a novel double N,O-hetero

On the photoluminescence in triarylmethyl-centered mono-, di-, and multiradicals

• Daniel Straub,
• Markus Gross,
• Mona E. Arnold,
• Julia Zolg and
• Alexander J. C. Kuehne

Beilstein J. Org. Chem. 2025, 21, 964–998, doi:10.3762/bjoc.21.80

• of reviews covering the different molecular structures of mono-, di-, and multiradicals, synthetic approaches [22][23][24][25], state dynamics in luminescent radicals [26], and their application in light-emitting devices [27][28][29]. Instead, we aim to provide insight and understanding into the

• the excited state dynamics, there is evidence for this fast relaxation in donor-functionalized TTM radicals [26]. Moreover, transient absorption has been employed to elucidate the formation of a non-luminescent side-product in trityl radicals. During photodegradation, two halogens are lost and two

Substituent effects in N-acetylated phenylazopyrazole photoswitches

• Radek Tovtik,
• Dennis Marzin,
• Pia Weigel,
• Stefano Crespi and
• Nadja A. Simeth

Beilstein J. Org. Chem. 2025, 21, 830–838, doi:10.3762/bjoc.21.66

• NAc-PAP-H and -Me), even surpassing the effects of methylation. Hammett analysis showed that the thermal population of the triplet state seem to be preferred as the thermal relaxation mechanisms of the back isomerization. EWGs and EDGs accelerated the relaxation dynamics compared to NAc-PAP-H

Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

• Leon M. Friedrich and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

• every case, a terminal α-ᴅ-mannopyranoside unit is complexed within the FimH CRD. However, controlling the exact relative orientation of glycoligands in three-dimensional space is difficult in case of 1 and 2 as the degrees of freedom connected to the conformational dynamics are too large. Nevertheless

Synthesis of HBC fluorophores with an electrophilic handle for covalent attachment to Pepper RNA

• Raphael Bereiter and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 727–735, doi:10.3762/bjoc.21.56

• aptamer (FLAP) in the family of “RNA mimics of GFP”, called Spinach [3]. This aptamer was used to study intracellular RNA dynamics in living cells and was the starting point for a series of in vitro selected FLAPs, e.g., Corn [4], Chili [5], Mango [6], Pepper [7], Clivia [8], and Okra [9]. All known FLAPs

Origami with small molecules: exploiting the C–F bond as a conformational tool

• Patrick Ryan,
• Ramsha Iftikhar and
• Luke Hunter

Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54

• -membered ring of pyranoses. However, it must be remembered that pyranoses are reactive molecules that can undergo, e.g., glycosylation, and it emerges that fluorine can play a much more significant conformational role during the dynamics of such chemical reactions [125][126][127][128][129][130

Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

• Keith G. Andrews

Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30

• enzyme dynamics. The wider history of supramolecular and cavity catalysis [3][13][15][16][17][18][19][21][48][49], and catalysis using confined transition-metal catalysts [50][51][52], dendrimers [53] or synzymes [54], micelles [55] or vesicles [56], catalytic antibodies [57][58][59] or molecularly

• , sometimes under the moniker “enzyme mimic” [22][138]. MOCs are typically soluble in polar organic solvents or water [156][157], and so their dynamics can be studied using solution-phase techniques [22]. Isolation from solution is not always possible, since their dynamic nature can make them sensitive to

• (increased flexibility) (Figure 9B) [41]. The ability to tune catalytic activity by tuning the cage rigidity, conformation, or dynamics is certainly an advantage rather than a liability [395][398][399][400][401][402]. It is perhaps unsurprising that the balance of rigidity and flexibility [403][404

Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia

• Rita Toshe,
• Syeda J. Khalid,
• Blondelle Matio Kemkuignou,
• Esteban Charria-Girón,
• Paul Eckhardt,
• Birthe Sandargo,
• Kunlapat Nuchthien,
• J. Jennifer Luangsa-ard,
• Till Opatz,
• Hedda Schrey,
• Sherif S. Ebada and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23

• . aureus biofilms with farinosones D (1) and A (2). This distinction is pivotal in the evaluation of compounds for their antibiofilm efficacy, considering the potential scenario wherein a compound may affect the growth dynamics of cells without substantially disrupting the biofilm architecture or

Oxidation of [3]naphthylenes to cations and dications converts local paratropicity into global diatropicity

• Abel Cárdenas,
• Zexin Jin,
• Yong Ni,
• Jishan Wu,
• Yan Xia,
• Francisco Javier Ramírez and
• Juan Casado

Beilstein J. Org. Chem. 2025, 21, 277–285, doi:10.3762/bjoc.21.20

• vibrational dynamics in connection with the fundamental role in the stabilization of the dications. A second feature, measured at 1596 cm−1 in 2, split into three peaks upon oxidation which are typically arising from ν(CC)NAP modes. However, while the single peak of 1•+ at 1567 cm−1 can be taken as an

Hydrogen-bonded macrocycle-mediated dimerization for orthogonal supramolecular polymerization

• Wentao Yu,
• Zhiyao Yang,
• Chengkan Yu,
• Xiaowei Li and
• Lihua Yuan

Beilstein J. Org. Chem. 2025, 21, 179–188, doi:10.3762/bjoc.21.10

• = −0.416 ppm) could be explained by ring translocation along the guest axle due to dynamics in the binding process, which is often observed in pseudorotaxanes [50]. When the H1/G2 molar ratio reached 1:1, the original proton signals of the macrocycle disappeared completely (Figure 4). Further addition of

Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

Tailored charge-neutral self-assembled L₂Zn₂ container for taming oxalate

• David Ocklenburg and
• David Van Craen

Beilstein J. Org. Chem. 2024, 20, 3007–3015, doi:10.3762/bjoc.20.250

• calculated distance from the NOE cross peaks is roughly 2 Å for both contacts. We know that the triazole units can rotate by some degree at ambient temperature based on previous investigations [87]. Thus, dynamic tilting up and downwards of the triazole groups is expected. Molecular dynamics simulations (xTB

Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels

• Connor R. M. MacDonald and
• Emily R. Draper

Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• , both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics

• , such as in the case of 1-6 linked sugars, an additional torsion, namely ω (O6–C6–C5–O5), must be defined and three staggered conformers, denoted as gg/tg/gt (ω angles of −60°/180°/60°, respectively), should be considered (Figure 1). Longer and branched glycans exhibit heightened structural dynamics

• web servers and downloadable software, which can help researchers in designing the workflow to study a glycan–protein system, are also reported. Computational tools to study glycans in the free state Since the first molecular dynamics simulations performed in the late 1980s on oligomannose type

2-Heteroarylethylamines in medicinal chemistry: a review of 2-phenethylamine satellite chemical space

• Carlos Nieto,
• Alejandro Manchado,
• Ángel García-González,
• David Díez and
• Narciso M. Garrido

Beilstein J. Org. Chem. 2024, 20, 1880–1893, doi:10.3762/bjoc.20.163

• envisaged by Heffernan et al. [40], including human TAAR1 agonist activity and structural evaluation via homology model development followed by molecular docking and molecular dynamics studies (Scheme 6). Structural features like sulfur location and ring opening of the aminoethyl section were investigated