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

• the composition of the photostationary state. Ground state energies might therefore not be directly related to the isomerization reaction without investigation of the exited state potential energy surface. However, the difference in Gibbs free energy (ΔG, Figure 3) between the E- and Z-isomers shows a

• the same level to confirm that a minimum had been reached and to extract free energy corrections, which were evaluated at 298.15 K. A stability analysis was performed to ensure that a stable wave-function was attained for all species. Conformational analyses of the stiff stilbene macrocycles were

• . The investigated SS-macrocycles (Z)-1a–d. The photoisomerization of the SS-macrocycles shows a clear correlation between the Z/E ratio in the photostable mixture and the linker length. The non-cyclic SS-diester 7 is included as a reference. Gibbs free energy differences (ΔG) between Z- and E-isomers

Recent advances on the transition-metal-catalyzed synthesis of imidazopyridines: an updated coverage

• Gagandeep Kour Reen,
• Ashok Kumar and
• Pratibha Sharma

Beilstein J. Org. Chem. 2019, 15, 1612–1704, doi:10.3762/bjoc.15.165

• Cu2O as a byproduct which was marked by the change of color from initial green to red. The theoretical study was carried out to check the feasibility of the reaction by calculating Gibbs free energy difference for each step (Scheme 42). The capability of copper to catalyze the cyanation reaction was

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

• individual reactions involved in the study are bimolecular processes. In order to avoid errors due to entropic effects when comparing all stationery points in an only energy diagram, a correction to free energy was made by substracting Strans contribution and considering a 1 M concentration [59]. Single

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

• environment. The calculated Gibbs free energy values of the complex formation reaction of these ligands with the bare metal cations suggest a spontaneous and energy-favorable process for all metal cations in the gas phase and only for Na+, Mg2+, Lu3+ cations in water environment. For one of the studied

• by the negative Gibbs free energy values (ΔG1 and ΔG78). The combination of implicit/explicit solvent treatment seems useful in the modeling of the p-sulfonatocalix[4]arene (and thiacalix[4]arene) complexes with metal cations and in the prediction of the thermodynamic parameters of the complex

• 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

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

• where the guest benzyl group engages in aromatic stacking with the host anthracene sidewalls. Furthermore, the affinities followed a rough linear free energy relationship with electron density on the benzyl group, with highest affinity achieved when the benzylammonium contained a withdrawing p-CN group

New standards for collecting and fitting steady state kinetic data

• Kenneth A. Johnson

Beilstein J. Org. Chem. 2019, 15, 16–29, doi:10.3762/bjoc.15.2

• a two-step binding mechanism could lead to increased enzyme specificity. Most notably, Fersht argued that because a two-step binding sequence has the same net free energy change as a corresponding one-step mechanism, a two-step binding sequence could not lead to greater enzyme specificity [5]. This

• to the observed kcat/Km values for the correct and incorrect substrates. Figure 6 shows three possible scenarios for the effect of the conformational change on kcat and kcat/Km. In this figure, we show free energy profiles computed from different combinations of rate constants for a minimal three

• -step reaction where product release is fast after the chemistry step. In each figure, the slow step in the pathway defines kcat and is identified as the step with the largest local barrier (relative to the local minimum) in the free energy profile. On the other hand, the specificity constant, kcat/Km

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

• attributed to the conformational restriction of the sugar [62][64]. The Gibbs free energy of duplex formation corresponded well with the observed Tm values. CD spectroscopy Circular dichroism of ON1–7 paired with DNA or RNA was recorded to further analyze their helical conformation and to compare it with

Organometallic vs organic photoredox catalysts for photocuring reactions in the visible region

• Aude-Héloise Bonardi,
• Frédéric Dumur,
• Guillaume Noirbent,
• Jacques Lalevée and
• Didier Gigmes

Beilstein J. Org. Chem. 2018, 14, 3025–3046, doi:10.3762/bjoc.14.282

• mechanisms. From a single or triplet state of the photoredox catalyst, an electron is transferred. According to Rehm–Weller, an electron can be transferred from the electron donor to the electron acceptor in the excited state if the free energy change ∆Get is negative. ∆Get can be calculated from the

• carbazole of A3, the absorption at 470 nm is around 800 M−1·cm−1 where for A3 almost no absorption is observed. Main characteristics of A3 have been resumed in Table 8. The A3 component can be used both as electron donor and electron acceptor. Indeed, the free energy change (calculated with the Rehm–Weller

1,8-Bis(dimethylamino)naphthyl-2-ketimines: Inside vs outside protonation

• A. S. Antonov,
• A. F. Pozharskii,
• P. M. Tolstoy,
• A. Filarowski and
• O. V. Khoroshilova

Beilstein J. Org. Chem. 2018, 14, 2940–2948, doi:10.3762/bjoc.14.273

• ) preventing charge delocalisation. The protonation results in the formation of the N–H···N bonded cation 1H+, the removal of the electrostatic and steric strain and thus a considerable free energy gain (Scheme 1) [5]. This is also a reason why the vast majority of DMAN derivatives are protonated to the

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

• of these effects [47]. To resolve this issue we performed benchmark calculations for standard metathesis catalyst GrI, as well as newly developed catalyst featuring a labile carbodicarbene ligand (as a model of 1–3-GrII) [48]. In the case of GrI we found the Gibbs free energy of initiation in the M06

• Gibbs free energy difference for the symmetric dimer A. In the case of carbene 3, the Gibbs free energy of dimerization could not be estimated due to instability of the monomer during geometry optimization. Thus, the results indicate higher stability of dimers for all examined NHC, which are in

• ) are 0.4–3.1 kcal/mol lower compared to carbene dissociation (∆G3). We can speculate that the positive charge of carbenes 1–3 lowers the Ru–C bond strength, making it easier to dissociate than for neutral carbenes. Interestingly, the estimate of the Gibbs free energy of initiation for complex 3-GrI

A challenging redox neutral Cp*Co(III)-catalysed alkylation of acetanilides with 3-buten-2-one: synthesis and key insights into the mechanism through DFT calculations

• Andrew Kenny,
• Alba Pisarello,
• Arron Bird,
• Paula G. Chirila,
• Alex Hamilton and
• Christopher J. Whiteoak

Beilstein J. Org. Chem. 2018, 14, 2366–2374, doi:10.3762/bjoc.14.212

• inconsistent with the calculated mechanism. As demonstrated in this work, experimentally functionalisation of the acetanilide with 3-buten-2-one requires significantly harsher reaction conditions compared to the equivalent benzamide functionalisation. From initial comparison of the two free energy surfaces

• M06/def2-TZVP [38][39][40][41]. Frequencies calculations approximated the ZPE correction and entropic contributions to the free energy term as well as confirming all intermediate were true with no imaginary modes and all transition states had the correct critical frequency of decomposition (imaginary

Dynamic light scattering studies of the effects of salts on the diffusivity of cationic and anionic cavitands

• Anthony Wishard and
• Bruce C. Gibb

Beilstein J. Org. Chem. 2018, 14, 2212–2219, doi:10.3762/bjoc.14.195

• -solubilizing group. Although its pKa may not be optimal for deprotonation at neutral or physiological pH, its small size and relatively high free energy of hydration (−373 kJ mol−1) ensure that ion-pairing effects are not strong. This was further confirmed by 1H NMR spectroscopy (Supporting Information File 1

• solution of crystalline alkali halides and the difference between the absolute free energy (or heat) of hydration of the corresponding anion and cation [27][28]. As a result, in the words of Fajans, “in the case of alkali halides, the solubility in a number of salts with the same cation (anion) and

Applications of organocatalysed visible-light photoredox reactions for medicinal chemistry

• Michael K. Bogdos,
• Emmanuel Pinard and
• John A. Murphy

Beilstein J. Org. Chem. 2018, 14, 2035–2064, doi:10.3762/bjoc.14.179

• equations can be used for predicting whether PET from an excited state photocatalyst to a substrate is spontaneous: In both cases ΔGPET is the free energy change during PET, F is the Faraday constant and E0,0 is the energy of the excited state. From these equations one can conclude that for PET to take

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173

• complex formation was calculated as a difference between free energy of calix[4]arene + ADP/ATP complex and isolated calix[4]arene and ADP/ATP dianion. The complex structures corresponding to the minimum energy as well as supramolecular binding motif of ADP and ATP are presented in Figure 4. As can be

Rational design of boron-dipyrromethene (BODIPY) reporter dyes for cucurbit[7]uril

• Mohammad A. Alnajjar,
• Jürgen Bartelmeß,
• Robert Hein,
• Pichandi Ashokkumar,
• Mohamed Nilam,
• Werner M. Nau,
• Knut Rurack and
• Andreas Hennig

Beilstein J. Org. Chem. 2018, 14, 1961–1971, doi:10.3762/bjoc.14.171

• accordance with the anticipated PET mechanism [31][45]. Further, the change in free energy, ∆G, associated with PET was calculated using the Rehm–Weller equation [46]. Therefore, we used a reduction potential of −1.55 V for the 1,3,7,9-tetramethyl-BODIPY core acceptor of 1, 2, and 5 [47] and of −1.81 V for

DFT calculations on the mechanism of copper-catalysed tandem arylation–cyclisation reactions of alkynes and diaryliodonium salts

• Tamás Károly Stenczel,
• Ádám Sinai,
• Zoltán Novák and
• András Stirling

Beilstein J. Org. Chem. 2018, 14, 1743–1749, doi:10.3762/bjoc.14.148

• copper(III)-catalysed carboarylation–ring closure reactions leading to the formation of functionalised heterocycles. We have performed DFT calculations along selected routes and compared their free energy profiles. The calculations considered two viable options for the underlying mechanism which differ

• the free energy level of the intermediate: 17.6 kcal/mol. There are two reasons behind this choice: i) the preceding and subsequent barriers were computed to be very close in energy to that of this structure; ii) one of the participants of this step is the solvent EtOAc molecule, i.e., the solvent

• Scheme 2 and Scheme 3) the ring formation takes place with an activation free barrier of 22.6 kcal/mol (TSrcA). Along this path this is the rate determining step. The calculations revealed that once the ring is formed, the aryl transfer spontaneously occurs and a significant amount of free energy is

A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene

• Liu-Pan Yang,
• Song-Bo Lu,
• Arto Valkonen,
• Fangfang Pan,
• Kari Rissanen and
• Wei Jiang

Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134

• large amplitude conformational responses to the electronic substituents on the guests. Instead of a linear free-energy relationship, ZB4 follows a parabolic free-energy relationship. This is explained by invoking the influence of secondary C–H···O hydrogen bonds on the primary cation···π interactions

• conformer III (C2h symmetry) [37] to be the most favored conformation for all complexes. Obviously the conformational network of ZB4 shows no response to the electronic substituents on the guests. This is quite different from TA4. In addition, there has been a linear free energy relationship between

• follow a parabolic rather than a linear free energy relationship. A closer look at four representative crystal structures suggested that the parabolic free energy relationship may be caused through influencing the major interactions in the host–guest complexes by tuning the weak C–H∙∙∙O hydrogen bonds

Cobalt-catalyzed C–H cyanations: Insights into the reaction mechanism and the role of London dispersion

• Eric Detmar,
• Valentin Müller,
• Daniel Zell,
• Lutz Ackermann and
• Martin Breugst

Beilstein J. Org. Chem. 2018, 14, 1537–1545, doi:10.3762/bjoc.14.130

• in more detail employing density functional theory. A complete free energy profile on the B3LYP-D3BJ/def2-QZVP/COSMO//B3LYP-D3BJ/def2-TZVP potential energy surface is depicted in Figure 1 (black line), while the free-energy profile on the M06-L surface is summarized in Supporting Information File 1

• the experimental data depicted in Scheme 2, the turnover-limiting step for this transformation is the insertion of 2a with an overall barrier of 25.5 kcal mol−1. The initial C–H cobaltation occurs with a smaller activation free energy of 15.5 kcal mol−1. These values are also in good qualitative

• reaction additionally with B3LYP without dispersion correction and the dispersion-corrected M06-L functional under otherwise identical conditions as a first starting point. Independent of the computational method, the overall reaction free energy for the transformation of Scheme 2 is almost identical

Steric “attraction”: not by dispersion alone

• Ganna Gryn’ova and
• Clémence Corminboeuf

Beilstein J. Org. Chem. 2018, 14, 1482–1490, doi:10.3762/bjoc.14.125

• between the slightly different (perfectly π-stacked and shifted by ≈1.2 Å in long and short axis) geometries. This contribution is therefore vital when exploring the free-energy landscape. While the energetic consequences are less pronounced for the sp3-rich systems, the absence of charge penetration

[3 + 2]-Cycloaddition reaction of sydnones with alkynes

• Veronika Hladíková,
• Jiří Váňa and
• Jiří Hanusek

Beilstein J. Org. Chem. 2018, 14, 1317–1348, doi:10.3762/bjoc.14.113

• found Taran’s suggestion as the most plausible because of the lowest activation free energy (ΔG‡ = 25.4 kcal·mol−1) and due to the observed 1,4-regiocontrol. Intrinsic reaction coordinate (IRC) calculations also showed concerted but asynchronous formation of the pyrazole ring, through initial C–C bond

• and IR measurements performed for the most active Cu(OTf)2 have shown that this salt coordinates to the sydnone oxygen carrying a negative charge which leads to an energy decrease of the sydnone LUMO and an increase of its electrophilicity. Also computed activation free energy (ΔG‡ = 25.4 kcal·mol−1

• . Quantum calculations [92] and IR measurements performed for Cu(OAc)2 also show that the Lewis acid character of this salt is less pronounced and formation of the 1,3-diphenylpyrazole necessitates a much higher activation free energy (ΔG‡ = 41.4 kcal·mol−1) than for the uncatalyzed reaction. Formation of

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

• intramolecular interactions (b). Thermal Z→E isomerization half-lives τ (standard deviations in parentheses) of azobenzenes 4–7 in various solvents. Computational results for (Z)-azobenzenes 4–7. ΔG is the free energy of the most stable Z-conformer relative to the corresponding open (Z)-conformation (method in

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• geometric calculations of the MDs were performed using the program VMD 1.9.2 [36]. Moreover, the molecular mechanics/generalized Born surface area (MM/GBSA) method [49], was used for a theoritical estimation of the binding free energy ΔGGB of the inclusion complex. The calculations were performed using

• 10,000 complex frames. Generalized Born ESURF calculated using 'LCPO' surface areas. The ΔGGB value includes the terms ΔGgas (van der Waals contribution from MM and the electrostatic energy as calculated by the MM force field) and ΔGsolv (the electrostatic contribution to the solvation free energy

• calculated by GB model and nonpolar contribution to the solvation free energy calculated using 'LCPO' surface areas) ΔGGB = ΔGgas + ΔGsolv as described by Miller et al. [50]. The entropy term T∙ΔS was also calculated from normal mode analysis with constant temperature using the respective module of the Amber

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• artificial cleaving agents that have enzyme-like catalytic properties but are more robust. pH-Rate profiles, linear free energy relationships and kinetic heavy atom isotope effects are the experimental approaches that are, together with construction of multifunctional cleaving agents, most extensively used

• obtained [29][32]. Linear free energy relationships are, in turn, used to determine the position of transition state on the reaction coordinate [33]. The polar property of either entering or departing nucleophile or non-departing groups is altered in a systematic manner and the effect on reaction rate is

• compared to the effect on the equilibrium of the reaction. In this manner, information about charge distribution in the transition state is obtained; whether the transition state is early (close to starting materials) or late (close to products). A free energy relationship is in principle a plot of

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• in turn, is affected by the nature of the C2', C3' and C5' substituents [80][81]. Codée and coworkers elaborated on the mechanism and stereochemistry of this reaction by calculating the energies of different oxocarbenium conformers using a free energy surface (FES) mapping method [80][81]. These

One-pot three-component route for the synthesis of S-trifluoromethyl dithiocarbamates using Togni’s reagent

• Azim Ziyaei Halimehjani,
• Martin Dračínský and
• Petr Beier

Beilstein J. Org. Chem. 2017, 13, 2502–2508, doi:10.3762/bjoc.13.247

• ) provided the rates of rotation around the N–C bond at all temperatures and the Eyring plot (Figure 2) allowed to determine the enthalpy and entropy of activation. The entropy of activation is small (−4.2 cal/K) and the free energy of activation (15.8 kcal/mol at 300 K) is dominated by the enthalpic term