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

• 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

Comparative study of thermally activated delayed fluorescent properties of donor–acceptor and donor–acceptor–donor architectures based on phenoxazine and dibenzo[a,j]phenazine

• Saika Izumi,
• Prasannamani Govindharaj,
• Anna Drewniak,
• Paola Zimmermann Crocomo,
• Satoshi Minakata,
• Leonardo Evaristo de Sousa,
• Piotr de Silva,
• Przemyslaw Data and
• Youhei Takeda

Beilstein J. Org. Chem. 2022, 18, 459–468, doi:10.3762/bjoc.18.48

• concentration of the cyclohexane solution and the molar absorption coefficient ε were not determined. As is clearly seen from Figure 2, the absorption spectra were not affected by the dielectric constant of the solvents. In contrast, the emission peaks of the PL spectra drastically red-shifted from cyclohexane

• agree very well with those obtained from the measurement in Zeonex® (Table 2), which has a similar dielectric constant as toluene (≈2.3), the solvent used in the calculations. A comparison with results from steady-state PL spectra (Table 1), however, show that the predicted peak matches measurements

• made with cyclohexane, but appear to be blue shifted with respect to measurements in toluene. Considering that cyclohexane has only a slightly lower dielectric constant (≈2.0) than toluene, it is reasonable that calculations would produce similar predictions, which makes the red-shifted experimental

Electron-rich triarylphosphines as nucleophilic catalysts for oxa-Michael reactions

• Susanne M. Fischer,
• Simon Renner,
• A. Daniel Boese and
• Christian Slugovc

Beilstein J. Org. Chem. 2021, 17, 1689–1697, doi:10.3762/bjoc.17.117

• effects of chloroform have been considered for calculation of the Gibbs free energy (ΔG) of zwitterion formation and were calculated by the conductor-like screening model (COSMO) [53][54] with a dielectric constant of 4.8 and a radius of 3.17. Our best estimate for the calculation of zwitterion energies

Naphthalonitriles featuring efficient emission in solution and in the solid state

• Sidharth Thulaseedharan Nair Sailaja,
• Iván Maisuls,
• Jutta Kösters,
• Alexander Hepp,
• Andreas Faust,
• Jens Voskuhl and
• Cristian A. Strassert

Beilstein J. Org. Chem. 2020, 16, 2960–2970, doi:10.3762/bjoc.16.246

• ) character (n–π*) of the excited state. Due to sterical hindrance, the two adjacent phenyl rotors restrict their molecular rotation in solution. The increasing push–pull (D–A) character progressively enhances the coupling with solvent molecules and sensitivity to changes in the dielectric constant when going

• mixture (Table 2). All the compounds exhibited an up-down tendency in intensity upon increasing the water fraction. Compounds H, Me and t-Bu showed a progressive red-shift with growing water content, owing to the increased solvent polarity and dielectric constant favoring the CT character of the emissive

• decrease in the dielectric constant. In summary, our straightforward synthetic strategy enables the realization of molecules which can go from deep blue to red emission and highly luminescent materials in solution and in the solid state, which are potentially interesting for optoelectronic and bioimaging

Controlled decomposition of SF₆ by electrochemical reduction

• Sébastien Bouvet,
• Bruce Pégot,
• Stéphane Sengmany,
• Erwan Le Gall,
• Eric Léonel,
• Anne-Marie Goncalves and
• Emmanuel Magnier

Beilstein J. Org. Chem. 2020, 16, 2948–2953, doi:10.3762/bjoc.16.244

• chemically and physiologically, it is non-flammable, has a high density and a high dielectric constant (2.5 times greater than that of air) [2][3][4][5]. These properties explain that this compound is widely used industrially as an electrical insulating gas in circuit breakers or in electrical substations [6

• electrochemistry. Having a dielectric constant relatively high (ε = 38), acetonitrile allows a good dissociation of several salts providing the conductivity of the medium. The concentration of SF6 in the following studies was then around 1.7 × 10−2 M. We then turned our attention to the determination of the

Rearrangement of o-(pivaloylaminomethyl)benzaldehydes: an experimental and computational study

• Csilla Hargitai,
• Györgyi Koványi-Lax,
• Tamás Nagy,
• Péter Ábrányi-Balogh,
• András Dancsó,
• Gábor Tóth,
• Judit Halász,
• Angéla Pandur,
• Gyula Simig and
• Balázs Volk

Beilstein J. Org. Chem. 2020, 16, 1636–1648, doi:10.3762/bjoc.16.136

• close dielectric constant (ε = 4.7 for CHCl3 and 8.9 for DCM) [28], the similar polarity index (P = 2.7 for CHCl3 and 3.1 for DCM) [29][30][31], and the very close dipole moment (1.15 for CHCl3, 1.14 for DCM) [32], the conformation of the compounds should be almost the same in the NMR solvent and in the

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• molecular layers [107]. The complex models used to describe charge transport in organic materials with differing degrees of disorder is well described by Liu, Noh, and co-workers [108]. The relative permittivity or dielectric constant (εr(ω)), which influences the screening of the charge carriers within the

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

• electron transfer (ΔGet) and the reorganization energy λ depict additional parameters affecting ket. Knowledge about redox potentials and excitation energy provides information about ΔGet needed for Equation 8 [72]. The dielectric constant ε and refractive index n of the surrounding matrix contribute to

A green, economical synthesis of β-ketonitriles and trifunctionalized building blocks from esters and lactones

• Daniel P. Pienaar,
• Kamogelo R. Butsi,
• Amanda L. Rousseau and
• Dean Brady

Beilstein J. Org. Chem. 2019, 15, 2930–2935, doi:10.3762/bjoc.15.287

• therefore an excellent nucleophile and is usually generated from nitriles using metal amides or other strong bases [14][15]. Under our reaction conditions at rt, we propose that the presence of a catalytic amount of IPA increases the dielectric constant of the solvent as a whole, thereby increasing the

Probing of local polarity in poly(methyl methacrylate) with the charge transfer transition in Nile red

• Aydan Yadigarli,
• Qimeng Song,
• Sergey I. Druzhinin and
• Holger Schönherr

Beilstein J. Org. Chem. 2019, 15, 2552–2562, doi:10.3762/bjoc.15.248

• , respectively, were obtained for NR. An effective local dielectric constant of 5.9–8.3 for PMMA thin films was calculated from the solvatochromic plot and the fluorescence maximum of NR observed in the PMMA films. The fluorescence band of NR in the rigid PMMA films shifted to the red by 130 cm−1 with increasing

• particular, the spatial distribution of the dielectric constant measured for thin PMMA films was described using NR as a reported dye [15]. Because NR is (i) a photostable dye, (ii) possesses convenient optical properties, such as excitation with visible light, and fluorescence, which does not overlay with

• dielectric constant for thin PMMA films was mapped by analyzing the position of the fluorescence of NR employed as a reporter dye [15]. Besides polarity, the Young’s modulus of the polymer matrix was found to be related to the fluorescence lifetimes (τf) of NR [21]. Furthermore, the spectral position of NR

Effect of ring size on photoisomerization properties of stiff stilbene macrocycles

• Sandra Olsson,
• Óscar Benito Pérez,
• Magnus Blom and
• Adolf Gogoll

Beilstein J. Org. Chem. 2019, 15, 2408–2418, doi:10.3762/bjoc.15.233

• calculated in MacroModel 9.9 with the OPLS3e force field, CHCl3 as solvent and dielectric constant 9.1 [48][49]. Redundant conformer elimination in MacroModel was used to reduce the number of conformations to 10–20 structures [50]. Synthesis Synthesis of 6-methoxyindan-1-one (3) Compound 2 (2.523 g, 14.0

Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors

• Christoph W. Grathwol,
• Nathalie Wössner,
• Sören Swyter,
• Adam C. Smith,
• Enrico Tapavicza,
• Robert K. Hofstetter,
• Anja Bodtke,
• Manfred Jung and
• Andreas Link

Beilstein J. Org. Chem. 2019, 15, 2170–2183, doi:10.3762/bjoc.15.214

• ) and CC2 calculations make use of the resolution-of-identity approximation [73]. ADC(2) calculations were also done using the continuum solvent model COSMO as previously described [54][55][74][75][76]. A dielectric constant of 62.14 and a refractive index of 1.3379 were used, which corresponds to a

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

• order to evaluate if complex disintegration is mostly affected by the dielectric constant or by proton/acceptor affinity of the solvent we have analyzed the complexes in MeOH/H2O (1:1) mixture that has a similar dielectric constant to DMSO (ε(DMSO) = 46.7, ε(MeOH/H2O 1:1) ≈ 52). CD spectra of [1(LysOMe

• )2] (Figure 5f). This is in contrast to results in DMSO and indicate that DMSO is more disintegrative for noncovalent complexes based on electrostatic interactions, than the MeOH/H2O (1:1) mixture, which has a similar dielectric constant. We find this result quite nonintuitive and worth attention in

• complexes in MeOH/H2O (1:1) mixture, that have a similar dielectric constant to DMSO, reveal that in DMSO the complexes dissociate to a much higher extend. We find this result quite nonintuitive and worth attention in the context of formation of supramolecular complexes in polar environment, for which DMSO

Synthesis, photophysical and electrochemical properties of pyridine, pyrazine and triazine-based (D–π–)₂A fluorescent dyes

• Keiichi Imato,
• Toshiaki Enoki,
• Koji Uenaka and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2019, 15, 1712–1721, doi:10.3762/bjoc.15.167

• , OUK-2 and OUJ-2, respectively, estimated from DFT calculation at the B3LYP/6-31G(d,p) level of theory [47]), Δf is the orientation polarizability, ε is the static dielectric constant, and n is the refractive index of the solvent. The Lippert–Mataga plots (Figure 3) for the three dyes show high

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

• structures possessing less elaborate hydrogen bond networks (compare ΔH1/ΔH78 for reaction 2 with those of reactions 1 and 3 in Table 1). Generally, increasing the polarity of the medium (higher dielectric constant) attenuates the energies of complex formation although the enthalpies remain negative. Adding

• density (SMD) scheme as encoded in the Gaussian 09 program package. Single-point calculations in water (with dielectric constant ε ≈ 78) at both levels of theory M062X/6-31G(d,p)//M062X/6-31G(d,p) and M062X/6-311++G(d,p)//M062X/6-31G(d,p) were performed on each fully optimized gas-phase structure. The

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

• of the respective reactant or product of the reaction in the gas phase was subjected to a single point calculation in water (with dielectric constant ε = 78). The difference between the gas-phase and SMD energies yielded the solvation energy, ∆Esolvε ≈ ∆Gsolvε, of the molecule/complex. Solvation free

• energies of the products and reactants were used to calculate the free energy of the complex formation in condensed medium (water): The fully optimized structure of some molecules and complexes in the gas phase was also re-optimized in water (with a dielectric constant ε = 78). The ∆G values derived from

• Gibbs free energies ΔG1 and ΔG78 (in kcal/mol) for the complex formation reaction with hydrated metal cation are shown. ΔG1 refers to reaction free energy in the gas phase, whereas ΔG78 refers to reaction free energies in an environment characterized by an effective dielectric constant of 78 (water

Conformational signature of Ishikawa´s reagent using NMR information from diastereotopic fluorines

• Laize A. F. Andrade,
• Lucas A. Zeoly,
• Rodrigo A. Cormanich and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2019, 15, 506–512, doi:10.3762/bjoc.15.44

• dipole moments and, consequently, the conformer populations are expected to change with the solvent polarity [29]. Indeed, the 1H NMR outcomes in C6D12 (dielectric constant ε = 2.2), CDCl3 (ε = 4.8) and C5D5N (ε = 12.4) solutions are informative on the rotation of H–C2–C1–F and conformational equilibrium

• probing the conformations of 1. An intermediate conformational behavior is calculated in chloroform solution, because this solvent has a larger dielectric constant than cyclohexane and a smaller value than pyridine, but the experimental 3JH,F(1) obtained in CDCl3 suggests that the conformers population in

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• energy corrections, and solvation energies were calculated using the implicit solvent method SMD [67] with a dielectric constant ε = 4. A) 2D representation of ThDP (blue) and the residues included in the active site models, and B) optimized structure of model B with an empty active site. Asterisks mark

The influence of the cationic carbenes on the initiation kinetics of ruthenium-based metathesis catalysts; a DFT study

• Magdalena Jawiczuk,
• Angelika Janaszkiewicz and
• Bartosz Trzaskowski

Beilstein J. Org. Chem. 2018, 14, 2872–2880, doi:10.3762/bjoc.14.266

• transition states). In the second step we performed solvation energy calculations using the Poisson–Boltzmann self-consistent polarizable continuum method as implemented in Jaguar v.7.9 (Schrodinger, 2013) to represent dichloromethane, using the dielectric constant of 8.93 and the effective radius 2.33 Å

• . The solvation calculations were performed using the M06-D3/LACVP** level of theory and the gas-phase optimized structures. We also used the same polarizable continuum method to estimate the solvation energies in water (dielectric constant of 80.73 and the effective radius 1.40 Å) and these results are

London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding

• Andreas H. Heindl,
• Raffael C. Wende and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106

• become weaker with increasing dielectric constant of the solvent [35]. This fact becomes obvious when comparing the half-lives of azobenzene 4 in non-polar toluene or TBME with polar DMSO. In contrast to toluene, the half-life of 4 decreased almost by 50% in DMSO due to the weakening of intramolecular

Liquid-assisted grinding and ion pairing regulates percentage conversion and diastereoselectivity of the Wittig reaction under mechanochemical conditions

• Kendra Leahy Denlinger,
• Lianna Ortiz-Trankina,
• Preston Carr,
• Kingsley Benson,
• Daniel C. Waddell and
• James Mack

Beilstein J. Org. Chem. 2018, 14, 688–696, doi:10.3762/bjoc.14.57

• , so it is important to continue understanding the rules governing the system. In a mechanochemical reaction, the reactants are added into a vessel along with one or more grinding balls and the vessel is shaken at high speeds to facilitate a chemical reaction. The dielectric constant of the solvent

• the reaction in comparison to completely solvent-free conditions. Finally, we observed that there was an effect of the dielectric constant of the solvent used in LAG on the stereochemistry of the product [27]. Although previously we were able to generate high yields of Wittig products under liquid

• important to note that under traditional solution-based conditions, benzyl benzoate has never been reported as a product in the Wittig reaction. Under mechanochemical conditions, the side-product formation appears to be hindered when utilizing a LAG solvent with a high dielectric constant. These results

Gram-scale preparation of negative-type liquid crystals with a CF₂CF₂-carbocycle unit via an improved short-step synthetic protocol

• Tatsuya Kumon,
• Shohei Hashishita,
• Takumi Kida,
• Shigeyuki Yamada,
• Takashi Ishihara and
• Tsutomu Konno

Beilstein J. Org. Chem. 2018, 14, 148–154, doi:10.3762/bjoc.14.10

• protocol for the synthesis of multicyclic molecules having a CF2CF2-containing cyclohexadiene or cyclohexane framework in a mesogenic structure. These molecules are promising candidates for vertical alignment (VA)-mode liquid crystal (LC) display devices owing to their large negative dielectric constant

What contributes to an effective mannose recognition domain?

• Christoph P. Sager,
• Deniz Eriş,
• Martin Smieško,
• Rachel Hevey and
• Beat Ernst

Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255

• described, the various approaches explored by nature to optimize selectivity and affinity of carbohydrate–lectin interactions offer interesting therapeutic perspectives for the development of carbohydrate-based drugs. Keywords: carbohydrate–lectin interactions; desolvation penalty; dielectric constant

• such as binding sites with minimal solvent-exposed surface areas, increased number of ligand interactions, “shared” desolvation costs, and multivalency. Degree of solvent exposure in the binding site (Figure 2). Because of the electrostatic character of H-bonds, the dielectric constant ε becomes

• Å2 for G, 262 Å2 for H, and 310 Å2 for I. The decreased dielectric constant ε in the deep cavities of H and I, as well as the resulting occlusion of the ligand from surrounding water molecules, leads to a more stable hydrogen-bond network and thus to higher affinities. Furthermore, the binding site

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

• dielectric constant, as would be expected from an electrostatic interaction between the polar alkoxy group and the amide moiety (Figure 4). A somewhat similar situation has been recently reported by Siebler et al. for the C-terminal amide in dimethylamido N-acetylproline, where the conformational equilibrium

• solvent dielectric constant, ε. The trans/cis ratios were determined from the 1H and 19F NMR spectra at 298 K. Solvent set: C6D6, CDCl3, CD2Cl2, CD3OD, CD3CN, D2O. For details see Table S1 in Supporting Information File 1. Mean residue molar circular dichroism (Δε) of peptides 8–10 in methanol (left) and

Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and ³J_HH coupling constant analyses

• Weslley G. D. P. Silva,
• Carolyne B. Braga and
• Roberto Rittner

Beilstein J. Org. Chem. 2017, 13, 925–937, doi:10.3762/bjoc.13.94

• introduced. Using the IEF−PCM implicit solvent model, small changes in the populations of conformers of 1 are observed when the solvent dielectric constant (ε) is increased. However, these slight variations do not affect the total populations of conformers a, b and c, and thus, it is an indicative that the

• studied media. In isolated phase, the conformer 3-trans-Ia represents 45.6% of the conformational equilibrium of 3, but when the dielectric constant of the medium is increased, this geometry is destabilized and has its population decreased to 34.8%. The same tendency is observed for 4-trans-Ia, which has

• investigated through experimental 3JHH coupling constant obtained from 1H NMR spectroscopy and the corresponding calculated ones (Table 6). For the compound 3, the experimental data show that the 3JHaHb1,obs and 3JHaHb2,obs coupling constants vary when the dielectric constant of the solvent (ε) is increased