Excited state dynamics for visible-light sensitization of a photochromic benzil-subsituted phenoxyl-imidazolyl radical complex

• Yoichi Kobayashi,
• Yukie Mamiya,
• Katsuya Mutoh,
• Hikaru Sotome,
• Masafumi Koga,
• Hiroshi Miyasaka and
• Jiro Abe

Beilstein J. Org. Chem. 2019, 15, 2369–2379, doi:10.3762/bjoc.15.229

• sensitization of PIC expands the versatility of the rate-tunable photoswitches of PIC systems. In this study, we synthesized a novel PIC derivative conjugated with a visible-light photosensitizer (Benzil-PIC, Scheme 1) and investigated the excited state dynamics. We used a benzil framework as a photosensitizer

• difference in the photochromic properties between two isomers of Benzil-PIC, we measured the absorption spectra and nanosecond-to-microsecond transient absorption dynamics of isomer A in benzene upon repeated irradiation of 355 nm nanosecond laser pulses (355 nm, 7 mJ pulse−1, Figure S8a, Supporting

• (Figure S9, Supporting Information File 1). Figure S8b (Supporting Information File 1) shows the nanosecond-to-microsecond transient absorption dynamics of isomer A probed at 650 nm under repeated irradiation with the 355 nm nanosecond laser pulses at 298 K. While the transient absorption dynamics of

Perspective isomorphs – a new classification of molecular structures based on artistic and chemical concepts

• Jannis Neumann,
• Ansgar Schnurr and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2019, 15, 2319–2326, doi:10.3762/bjoc.15.224

• recognizable and comprehensible within the framework of the specifications. The focus of the graphic interpretation of Kern was on the movement and dynamics within the atom (Figure 4, right). Borchers emphasized more the filigree, almost substance-less form of atoms Figure 4, left). Flügge interpreted the

1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• concentration (10−5 mol/L) in a competitive aqueous–organic CHCl3/CH3OH/H2O mixture (45:45:10, v/v/v). Fluorescence spectroscopy measurements supported by molecular dynamics simulation data have revealed that the smaller macrocyclic rings move from the core-substituted PDI motif to the two 1,2,3-triazolium

• also determined the dissociation constant pKa of this acid−base switchable MIM system by an indicator method which could make a quantitative and precise estimation of its dynamics with environmental acidity change. By combining NMR spectroscopic data and quantum chemistry calculations, a motion

Naphthalene diimides with improved solubility for visible light photoredox catalysis

• Barbara Reiß and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2019, 15, 2043–2051, doi:10.3762/bjoc.15.201

• but also by their photophysical dynamics. To the best of our knowledge this is the first report on the usage of cNDIs as photoredox catalysts. The irradiation by visible light from LEDs as energy-saving light sources together with the use of an organic dye instead of a transition metal complex as

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• . Interestingly, we found that neither archangelolide nor its dansyl conjugate did exhibit cytotoxic effects in contrast to the structurally closely related counterparts trilobolide and thapsigargin. We explain this observation by a molecular dynamics simulation, in which, in contrast to trilobolide

• that this SL does not act as SERCA inhibitor. Therefore, we proceeded to confirm this hypothesis by a molecular dynamics simulation study. Molecular dynamics simulation of compounds 1 and 2 with SERCA The binding cavity for thapsigargin and compound 2 in the SERCA protein lies in the transmembrane

• of 10.309 × 10.111 × 15.063 nm3 with periodical boundary conditions and centered. For simulations of energy minimization and molecular dynamics, Gromacs-4.5.5 software was used. The first part of the simulations occurred in vacuum, the other then in water. In order to keep the solution neutral, 24

Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media – circular dichroism and diffusion studies of chirality transfer and solvent dependence

• Bartosz Setner and
• Agnieszka Szumna

Beilstein J. Org. Chem. 2019, 15, 1913–1924, doi:10.3762/bjoc.15.187

• dynamics and suggest formation of a well-defined structure. Additional proof of chirality transfer came from analyzing the 1H NMR spectra of 1 and LysOMe possessing different chirality (ʟ-, ᴅ/ʟ-, mixture of ʟ- and ᴅ/ʟ-, ᴅ-). No diastereotopic splitting was observed for [1(ᴅ/ʟ-LysOMe)2]MeOH and only minor

Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163

• disordered and mobile, and that the OH groups of the host β-CD may rotate [17]. Studies with molecular dynamics simulations have found only four water molecules inside the host β-CD cavity [18]. The energetics of the CD hydration/dehydration have been investigated as well. Experimental studies have been able

• details Different molecular modeling methods (quantum mechanics (QM), molecular dynamics (MD), docking and quantitative structure activity relationships (QSARs)) can be applied in studying the structure, dynamics, and energetics of the host CD systems. However, the results from different modeling (or

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• into the ice lattice [12], others investigated the adsorption process on different surfaces via atomic force microscopy [10][13][14]. The antifreeze activity has been correlated with long-range perturbation of hydration dynamics [15]. Latest molecular dynamics simulations suggest that AFGP reversibly

Transient and intermediate carbocations in ruthenium tetroxide oxidation of saturated rings

• Manuel Pedrón,
• Laura Legnani,
• Maria-Assunta Chiacchio,
• Pierluigi Caramella,
• Tomás Tejero and
• Pedro Merino

Beilstein J. Org. Chem. 2019, 15, 1552–1562, doi:10.3762/bjoc.15.158

• can lead to different products in a ratio that depends on reaction dynamics [31][32][33]. The study of molecular dynamics trajectories has allowed characterization of ambimodal transition states in reactions involving carbocations [34][35]. We have demonstrated computationally the presence of

Synthesis and biological evaluation of truncated derivatives of abyssomicin C as antibacterial agents

• Leticia Monjas,
• Peter Fodran,
• Johanna Kollback,
• Carlo Cassani,
• Thomas Olsson,
• Maja Genheden,
• D. G. Joakim Larsson and
• Carl-Johan Wallentin

Beilstein J. Org. Chem. 2019, 15, 1468–1474, doi:10.3762/bjoc.15.147

• docking of known and proposed ligands. The crystal structure contains a tryptophan molecule in the active site. Restrained molecular dynamics [20][21] was employed to position the active site cysteine (Cys-263) in a position that would allow covalent binding of the ligands in the active site. The

Synthesis of dipolar molecular rotors as linkers for metal-organic frameworks

• Sebastian Hamer,
• Fynn Röhricht,
• Marius Jakoby,
• Ian A. Howard,
• Xianghui Zhang,
• Christian Näther and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1331–1338, doi:10.3762/bjoc.15.132

• of rotor dynamics and dipole interactions in crystals by Price [28]. The predicted dipole moment of 1 with 2.6 D is small, but the molecule should be suitable for MOF preparation because the structurally similar parent compound 1,4-benzenedipropynoic acid has been successfully used for MOF synthesis

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• anchoring points for the positively charged guests. Cation–π interactions between the monoatomic cations and p-sulfonatocalix[4]arene in water are supposed (but not proven) to take part in the inclusion complex formation [31]. Mendes et al. have carried out molecular dynamics (MD) simulations of association

Understanding the unexpected effect of frequency on the kinetics of a covalent reaction under ball-milling conditions

• Ana M. Belenguer,
• Adam A. L. Michalchuk,
• Giulio I. Lampronti and
• Jeremy K. M. Sanders

Beilstein J. Org. Chem. 2019, 15, 1226–1235, doi:10.3762/bjoc.15.120

• various kinetic treatments, an understanding of mechanochemical reaction dynamics remains largely elusive. While mechanochemical kinetics must obey the general principles of reactivity (collision, energy gain and relaxation), there remains a poorly understood, complex interplay between physical and

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• been noted before as a factor that effects [2]rotaxane dynamics [56][63]. 3.3. Precious metals complexes The electrostatic interior surface of the amphiphilic tetralactam cavity is complementary to the electrostatic surface of the core of a squaraine dye which has a partial positive charge at the

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

Novel (2-amino-4-arylimidazolyl)propanoic acids and pyrrolo[1,2-c]imidazoles via the domino reactions of 2-amino-4-arylimidazoles with carbonyl and methylene active compounds

• Victoria V. Lipson,
• Tetiana L. Pavlovska,
• Nataliya V. Svetlichnaya,
• Anna A. Poryvai,
• Nikolay Yu. Gorobets,
• Erik V. Van der Eycken,
• Irina S. Konovalova,
• Svetlana V. Shiskina,
• Alexander V. Borisov,
• Vladimir I. Musatov and
• Alexander V. Mazepa

Beilstein J. Org. Chem. 2019, 15, 1032–1045, doi:10.3762/bjoc.15.101

• the disruptors of microtubule dynamics, therefore are of great interest in cancer drug discovery [6]. Thereby, the stereocontrolled total synthesis of marine alkaloids such as axinellamines [16] and the search of new 2-aminoimidazole and pyrrole containing compounds with a core structure that mimics

Halogen bonding and host–guest chemistry between N-alkylammonium resorcinarene halides, diiodoperfluorobutane and neutral guests

• Fangfang Pan,
• Mohadeseh Dashti,
• Michael R. Reynolds,
• Kari Rissanen,
• John F. Trant and
• Ngong Kodiah Beyeh

Beilstein J. Org. Chem. 2019, 15, 947–954, doi:10.3762/bjoc.15.91

• incredibly effective tool for observing privileged conformations and structures [15][16][17][18][19]. From the crystallographic information we can extract the polymorphism, high Z’-value, twining, and disorder that provide insight into the dynamics of prenucleation assembly, nucleation, and crystal growth

• the crystals form [26]. Twinning and disorder are generally seen as an undesirable complication in determining structures; however, the nature and extent of the disorder contains significant information regarding the dynamics and conformational sampling of the molecules [19][24][27]. Desiraju et al

Synthesis of polydicyclopentadiene using the Cp₂TiCl₂/Et₂AlCl catalytic system and thin-layer oxidation of the polymer in air

• Zhargolma B. Bazarova,
• Ludmila S. Soroka,
• Alex A. Lyapkov,
• Мekhman S. Yusubov and
• Francis Verpoort

Beilstein J. Org. Chem. 2019, 15, 733–745, doi:10.3762/bjoc.15.69

• for the DCPD polymerization. Additionally, optimization of the ratio between the two compounds of the catalyst system was performed using electron spectroscopy. Furthermore, the DCPD polymerization in toluene was investigated using the optimized catalyst system, and also the dynamics of the structural

Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

• Andrejs Šišuļins,
• Jonas Bucevičius,
• Yu-Ting Tseng,
• Irina Novosjolova,
• Kaspars Traskovskis,
• Ērika Bizdēna,
• Huan-Tsung Chang,
• Sigitas Tumkevičius and
• Māris Turks

Beilstein J. Org. Chem. 2019, 15, 474–489, doi:10.3762/bjoc.15.41

• heterocycles, which were additionally extended by triazole moieties, the compounds with electron-donating groups showed intramolecular charge transfer character (ICT/TICT) of the excited states which was proved by solvatochromic dynamics and supported by DFT calculations. In the 7-deazapurine series this led

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

N-Arylphenothiazines as strong donors for photoredox catalysis – pushing the frontiers of nucleophilic addition of alcohols to alkenes

• Fabienne Speck,
• David Rombach and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2019, 15, 52–59, doi:10.3762/bjoc.15.5

• dynamics of the radical cation of N-phenylphenothiazine was investigated by Wasielewski et al. This radical cation had a high reduction potential of about +2.1 V (vs SCE) [17] allowing the reduction of poorly oxidizing agents. The combination of both properties in one system is a remarkable feature for

• chemical redox dynamics between −2.1 V up to +2.1 V. One of the key problems in photochemistry, which was recently addressed by the development of the consecutive photoelectron transfer process (conPET) [5], is the need to push the frontiers by accessing high reduction potentials. While the classical

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• = −1.5 to −3.7 °C). Molecular dynamics simulation on the nucleoside and oligonucleotide level revealed the preference of the C1’-exo/C2’-endo alignment of the furanose ring. Moreover, the simulation of duplexes with complementary RNA disclosed a DNA/RNA-type duplex structure suggesting that this

• modification might be a substrate for RNase H. Keywords: DNA/RNA affinity; fluorinated cyclopropanes; fluorinated nucleic acids; molecular dynamics simulations; sugar modified nucleosides; Introduction A powerful strategy for the treatment of various disorders like cancer, viral and inherited diseases is the

• unit and possibly positively impact the duplex stability. Here we report on the synthesis of the two 6’F-bc4,3 pyrimidine analogs with the base T and C, their incorporation into DNA, their biophysical properties, as well as a structural analysis by molecular dynamics simulations of hybrid DNA and RNA

Dispersion-mediated steering of organic adsorbates on a precovered silicon surface

• Lisa Pecher,
• Sebastian Schmidt and
• Ralf Tonner

Beilstein J. Org. Chem. 2018, 14, 2715–2721, doi:10.3762/bjoc.14.249

• dynamics (Figure 1). The dominant interaction between molecule and surface changes with the distance: For surface–adsorbate distances at which there is no significant orbital overlap but already rather close contact, dispersion attraction dominates since the numerous rather weak interactions add up to a

A pyridinium/anilinium [2]catenane that operates as an acid–base driven optical switch

• Sarah J. Vella and
• Stephen J. Loeb

Beilstein J. Org. Chem. 2018, 14, 1908–1916, doi:10.3762/bjoc.14.165

• DB24C8 ring resides solely at the bis(pyridinium)ethane site and changes to colorless when the crown ether is shuttling (i.e., circumrotating) back and forth between the two recognition sites thus optically signalling the onset of the shuttling dynamics. Keywords: catenane; mechanically interlocked

Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH

• Femke Beiroth,
• Tomas Koudelka,
• Thorsten Overath,
• Stefan D. Knight,
• Andreas Tholey and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1890–1900, doi:10.3762/bjoc.14.163

• X-ray crystallography, studies in solution add valuable information in molecular recognition studies as they take molecular dynamics as well as solvent effects into consideration. In the latter respect, photoaffinity labeling has evolved as a useful tool for studies under physiological conditions [1