Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

• and organic molecules [6]. Our results here are consistent, but the dynamics of mixed solvent systems are complex – water in DCM enhances rates, while water in MeOH nearly shuts them down. We presume these are consistent with the solubility effects proposed by Michon. In DCM, protic co-solvents were

Spatial arrangements of cyclodextrin host–guest complexes in solution studied by ¹³C NMR and molecular modelling

• Konstantin Lebedinskiy,
• Ivan Barvík,
• Zdeněk Tošner,
• Ivana Císařová,
• Jindřich Jindřich and
• Radim Hrdina

Beilstein J. Org. Chem. 2024, 20, 331–335, doi:10.3762/bjoc.20.33

• ten classical molecular dynamics (MD) simulations [16] (each lasting 100 ns, Figure 3). Then, we superimposed α-CD structures from different snapshots of each MD run. Further, the 3D densities, showing the spatial distribution of prochiral atoms of ligands (that rotate and wobble towards α-CD), were

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• (λirr = 660 nm). The excited state dynamics of 18c was later studied in detail by Nagasawa and co-workers using femtosecond time-resolved transient absorption spectroscopy [44]. In 2022, Qiao and co-workers attempted to extend the thermal relaxation half-life of compound 18c by addition of cations such

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• the ICT band, respectively. This indicates that similar ultrafast charge-separation and charge-recombination dynamics will also be observed in toluene. For 60, the emergence of new maxima at 500, 660, and 742 nm and minima at 460 nm accompanied the decay of the excited singlet state of F12SubPc, which

• -empirical approach, which includes the nuclear factor, particularly the electron-vibration coupling. This indicates that the consideration of quantum chemical vibrational effects is important in explaining the electron-transfer processes in these conjugates. For these molecules, the dynamics of the charge

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

• metadynamics simulations provide hints on structures for the initial steps of the irreversible phase 2 where bond formation and breaking lead to important structural reorganizations within the coalescence process. Keywords: DFT; dimerization; fullerene; molecular dynamics; peapods; Introduction Transmission

• pressures and high temperatures [13][14][15]. We aim to shed light in these reaction mechanisms and energy profiles by using complementary methodologies as standard density functional theory (DFT) calculations and first-principles Car–Parrinello molecular dynamics (CPMD) simulations. Firstly, we have

• surface that describes the formation of irreversible C–C bonds. Molecular dynamics simulations were done in the radical C120 dimer alone; we did not consider the interaction with the CNT. After a 4 ps metadynamics, we observed the sequential formation of C–C bonds between the two C60 cages up to a number

Optimizing reaction conditions for the light-driven hydrogen evolution in a loop photoreactor

• Pengcheng Li,
• Daniel Kowalczyk,
• Johannes Liessem,
• Mohamed M. Elnagar,
• Dariusz Mitoraj,
• Radim Beranek and
• Dirk Ziegenbalg

Beilstein J. Org. Chem. 2024, 20, 74–91, doi:10.3762/bjoc.20.9

• hydrodynamic attributes occur during the process of scale-up [19][20]. Therefore, a suitable reactor, which ensures excellent fluid dynamics and transport properties during scale-up, is needed for photocatalytic hydrogen generation. Loop reactors utilize partial inner circulation of the chosen reaction medium

• hydrogen generation is designed and equipped with 365 nm LEDs. Fluid dynamics in the loop photoreactor are characterized using a color tracer mixing experiment and image analysis. Photonic characterization is performed with the ferrioxalate actinometer. Finally, the photocatalytic hydrogen evolution with

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• explanation and prediction of GAG specificity [35]. Computational methodologies like molecular docking and molecular dynamics (MD) have proven to be successful in modelling protein–GAG interactions, particularly examining the fundamental questions related to these interactions such as their specificity, the

• multipose character of GAG binding and the polarity of the binding poses of these periodic molecules. In the present work, all-atom MD simulations are conducted to study the dynamics of the protein–GAG complexes, and are complemented by free energy analysis. The free energy analysis of the protein–GAG

Aromatic systems with two and three pyridine-2,6-dicarbazolyl-3,5-dicarbonitrile fragments as electron-transporting organic semiconductors exhibiting long-lived emissions

• Karolis Leitonas,
• Brigita Vigante,
• Dmytro Volyniuk,
• Audrius Bucinskas,
• Pavels Dimitrijevs,
• Sindija Lapcinska,
• Pavel Arsenyan and
• Juozas Vidas Grazulevicius

Beilstein J. Org. Chem. 2023, 19, 1867–1880, doi:10.3762/bjoc.19.139

• nm, further allowing us to analyze the luminescence dynamics in detail. To determine photoluminescence quantum yields (PLQY), a dedicated integrated sphere with an inner diameter of 120 mm was used in conjunction with the Edinburgh Instruments FLS980 spectrometer. This specialized setup enabled

Quinoxaline derivatives as attractive electron-transporting materials

• Zeeshan Abid,
• Liaqat Ali,
• Sughra Gulzar,
• Faiza Wahad,
• Raja Shahid Ashraf and
• Christian B. Nielsen

Beilstein J. Org. Chem. 2023, 19, 1694–1712, doi:10.3762/bjoc.19.124

• properties and efficient charge transfer dynamics [48]. Arunkumar and colleagues demonstrated the utilization of indolocarbazole-Qx systems named ICZS4. The comprehensive investigation of ICZS4's optoelectronic properties highlighted its potential for high-performance DSSCs. The small energy gap, red-shifted

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• examples of such systems included Schiff porphyrinoids, a class of macrocyclic compounds incorporating an imine linkage connecting different parts of the macrocyclic skeleton (Figure 10) [30]. This class of compounds has received significant attention due to their intriguing dynamics [33][121] and

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• atoms, presenting a challenging and time-consuming task for geometry optimization calculations and screening via DFT methods. Recent advancements have introduced fast semi-empirical DFT methods such as xTB [15], which enable their use in preliminary screening for molecular dynamics or searching for

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

• functions of ether lipids offer an interesting overview of the current knowledge of the effect of plasmalogen and ELs on membrane properties at a molecular scale. Shortly, according to molecular dynamics simulation, PE-plasmalogens form thicker, compressed and rigid bilayers when compared to PE-diacyl

Light-responsive rotaxane-based materials: inducing motion in the solid state

• Adrian Saura-Sanmartin

Beilstein J. Org. Chem. 2023, 19, 873–880, doi:10.3762/bjoc.19.64

• mechanical bond, such as control over the dynamics of the components upon application of external stimuli. This perspective aims to highlight the relevance of these materials, by pointing out recent examples of photoresponsive materials prepared from a rotaxanated architecture in which motion of the

• scaffolds [11]. In particular, rotaxanes and pseudorotaxanes have led to a greater number of applications due to their inherent dynamics and the switching possibility through a rational design [12]. Thus, rotaxane-based materials have attracted the interest of the scientific community due to their enhanced

• dynamics of the components and/or macroscopic motion of the material are accomplished, dividing the article into three main sections: (i) photoresponsive rotaxane discrete crystals; (ii) photoresponsive rotaxane polymers; and (iii) photoresponsive metal-organic rotaxane frameworks (MORFs). Besides to

Bromination of endo-7-norbornene derivatives revisited: failure of a computational NMR method in elucidating the configuration of an organic structure

• Demet Demirci Gültekin,
• Arif Daştan,
• Yavuz Taşkesenligil,
• Cavit Kazaz,
• Yunus Zorlu and
• Metin Balci

Beilstein J. Org. Chem. 2023, 19, 764–770, doi:10.3762/bjoc.19.56

• configuration in a molecule, in short, it is the single most important spectroscopic tool aside from X-ray crystallography to provide an accurate ensemble-guided view of the structure, even conformational dynamics in a molecule. Quantum mechanical/nuclear magnetic resonance (NMR) approaches are used for the

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• in the cell membrane. Keywords: dipeptidyl peptidase enzyme; excimer; molecular dynamics simulations; phenanthridine; polynucleotide; pyrene; Introduction The design of small molecules that can selectively bind and discriminate different biomolecular structures (polynucleotides vs proteins, DNA or

• 48% for Phen-Py-1 and Phen-Py-2, respectively). The phenanthridine nitrogen was protonated under weakly acidic conditions, which made the phenanthridinium moiety relatively electron deficient compared to the electron-rich pyrene moiety that favored intramolecular stacking. Molecular dynamics

• dielectric constant and a lower polarity that influenced intramolecular stacking. To the best of our knowledge, this is the first reported phenanthridine–pyrene excimer in solution. Molecular dynamics calculations (see chapter Computational analysis) and hypochromism observed from UV–vis spectra pointed

Combretastatins D series and analogues: from isolation, synthetic challenges and biological activities

• Jorge de Lima Neto and
• Paulo Henrique Menezes

Beilstein J. Org. Chem. 2023, 19, 399–427, doi:10.3762/bjoc.19.31

• cancer cell growth when compared with compounds 2 and 28, due the same lack of phosphatase cited before. It is worth to note that the mechanism of action for these compounds is attributed to their ability to interfere in the dynamics of tubulin, a protein involved in the formation of the cytoskeleton

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

• Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

• recombination dynamics is primarily related to the electronic properties of the conjugates, such as electron affinity, orbital energies, and excited state energies. In another report, Nikolaou et al. [51] described the synthesis of two novel porphyrin dyads 107b and 108b containing terminal carboxylic acid

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• [21][24][36], and recent reports show that molecular dynamics methods can eliminate the need for empirical corrections [29][30][38]. However, these calculation-intensive methods are not likely to become routine soon, potentially leaving room for empirical scaling to be useful for some time. The

Inline purification in continuous flow synthesis – opportunities and challenges

• Jorge García-Lacuna and
• Marcus Baumann

Beilstein J. Org. Chem. 2022, 18, 1720–1740, doi:10.3762/bjoc.18.182

• successfully obtain a given polymorph. The work of Myerson and co-workers demonstrates this by examining polymorph dynamics to achieve a successful crystallization of ʟ-glutamic acid using a continuous mixed suspension mixed product removal crystallization (MSMPR) approach [113]. Recently, a kinetically

Naphthalimide-phenothiazine dyads: effect of conformational flexibility and matching of the energy of the charge-transfer state and the localized triplet excited state on the thermally activated delayed fluorescence

• Kaiyue Ye,
• Liyuan Cao,
• Davita M. E. van Raamsdonk,
• Zhijia Wang,
• Jianzhang Zhao,
• Daniel Escudero and
• Denis Jacquemin

Beilstein J. Org. Chem. 2022, 18, 1435–1453, doi:10.3762/bjoc.18.149

• calculations were used to obtain additional insights into both the excited states involved and the photo-deactivation dynamics. First, the ground state geometry of the compounds was optimized (Figure 9). For the compact NI-PTZ and NI-PTZ-O dyads, the two units adopt almost orthogonal geometry. A similar result

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• functional protein–protein binding. One theoretical option to identify putative binding sites of compound 1 on 14-3-3ζ would be by all-atom molecular dynamics (MD) simulations. However, as numerous studies have shown [21][22][23], the resources needed for a suitable sampling of such flexible systems by MD

• distribution; this approach captures ion-size effects and yields energy grids that are directly comparable to molecular dynamics simulation data. Accordingly, the 14-3-3ζ environment was scanned with the GCP and lysine ligands separately in Epitopsy using 150 rotations and a grid resolution of 0.4 Å to

• 1.5.2 [41]. To validate our method, we applied it to the QQJ-096/14-3-3/c-Raf complex for which the potential binding site was available from all-atom molecular dynamics simulations in a previous study [26]. Our results for this system are reported in the first part of the Supporting Information File 1

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

• Shani Zev,
• Marion Ringel,
• Ronja Driller,
• Bernhard Loll,
• Thomas Brück and
• Dan T. Major

Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97

• . Rather, an equilibrium may exist between GGDP and LGDP. Experimental Dynamics and Monte Carlo simulations We generated conformers using simulated annealing (SA) molecular dynamics followed by SA Monte Carlo simulation using CHARMM [28]. Force field parameters were generated using CGenFF [29] and an in

Structural basis for endoperoxide-forming oxygenases

• Takahiro Mori and
• Ikuro Abe

Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71

• molecular dynamics analyses, as well as DFT calculations of the FtmOx1 reaction, suggested a modified mechanism [72][73][74]. In this mechanism, the tyrosyl radical at Tyr224 is generated by the Fe(IV)=O species, which abstracts a hydrogen atom at C21 to form an endoperoxide ring through the reaction with

• dynamics of the active site during the enzyme reaction. Conclusion Endoperoxide compounds have recently attracted keen attention as a source of new drug leads, due to their unique structures and remarkable biological activities. To date, the total synthesis of endoperoxide-containing natural products and

Mechanochemical halogenation of unsymmetrically substituted azobenzenes

• Dajana Barišić,
• Mario Pajić,
• Ivan Halasz,
• Darko Babić and
• Manda Ćurić

Beilstein J. Org. Chem. 2022, 18, 680–687, doi:10.3762/bjoc.18.69

• reaction dynamics and characterization of the products was achieved by in situ Raman and ex situ NMR spectroscopy and PXRD analysis. A strong influence of the different 4,4’-substituents of azobenzene on the halogenation time and mechanism was found. Keywords: azo compounds; halogenation; mechanochemistry

• -bromosuccinimide (NBS) under neat grinding (NG) and liquid-assisted grinding (LAG) conditions in a ball mill [51]. Insight into the dynamics of the formation of reaction intermediates and products was obtained by in situ Raman monitoring that provided information on the nature of the catalytically active PdII

• dynamics of the formation of cyclopalladated intermediates In-I, LAG reactions of Pd(OAc)2 with L6–8 and TsOH were performed using 25 µL of MeCN as a liquid additive in a molar ratio of 1:1:1 (Ln/Pd(OAc)2/TsOH). In situ Raman monitoring of C–H bond activation was possible for L6 and L7, while in the case