Catalysing (organo-)catalysis: Trends in the application of machine learning to enantioselective organocatalysis

• Stefan P. Schmid,
• Leon Schlosser,
• Frank Glorius and
• Kjell Jorner

Beilstein J. Org. Chem. 2024, 20, 2280–2304, doi:10.3762/bjoc.20.196

• physicochemical descriptors. A prominent early example are Hammett parameters, developed in 1937 [26][27], that relate substituent parameters to the equilibrium constant of the deprotonation of a substituted benzoic acid. The derived substituent parameters are used to gain insight into the mechanism of reactions

Cyclodextrins permeabilize DPPC liposome membranes: a focus on cholesterol content, cyclodextrin type, and concentration

• Ghenwa Nasr,
• Hélène Greige-Gerges,
• Sophie Fourmentin,
• Abdelhamid Elaissari and
• Nathalie Khreich

Beilstein J. Org. Chem. 2023, 19, 1570–1579, doi:10.3762/bjoc.19.115

• ) was able to form two types of soluble complexes, with molar ratios of 1:1 and 1:2 (CHOL/DOM-β-CD). The latter (1:2 inclusion complex) occurred much more easily than that of the 1:1 complex showing a much higher equilibrium constant. At low CDs concentration, the formation of the 1:1 inclusion complex

• dominated with low equilibrium constant (109 M−1) suggesting that the unstable complex would rapidly decompose into its components. With time elapsing and with increasing CDs concentration, the 1:1 inclusion complex was transformed into the more stable 1:2 complex with greater equilibrium constant (5.68

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

• . Thus, attention must be paid to the identification of the substances, specification of the reaction(s), the conditions of reaction, the definition of the equilibrium constant(s) and standard states, the use of standard nomenclature, symbols, and units, and uncertainties. This document contains a

• general discussion of various aspects of these equilibrium measurements as well as STRENDA (Standards for Reporting Enzymology Data) recommendations regarding the measurements and the reporting of results. Keywords: enzyme-catalyzed reactions; equilibrium constant; standards; thermodynamics; Perspective

• the apparent equilibrium constant K′ and the standard transformed molar Gibbs energy of reaction (ΔrG'°) for biochemical reactions [11]. STRENDA does not aim at policing authors who report data on enzyme kinetic or on equilibrium measurements. The aim is to aid these researchers by providing

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• effect of the nucleotide on the reaction equilibrium. For this, we applied the thermodynamic activity-based framework that uses the equilibrium constant Ka, which is independent of concentration. It is expressed via the law of mass action, and exemplarily for the reaction from ADP to ATP it reads as

Shift of the reaction equilibrium at high pressure in the continuous synthesis of neuraminic acid

• Jannis A. Reich,
• Miriam Aßmann,
• Kristin Hölting,
• Paul Bubenheim,
• Jürgen Kuballa and
• Andreas Liese

Beilstein J. Org. Chem. 2022, 18, 567–579, doi:10.3762/bjoc.18.59

• of product and substrates was calculated for each sample and converged to the equilibrium constant under the given conditions. The equilibrium constant for the first reaction (one-to-one) was insensitive to pressure. For the second reaction (aldolase), the calculated equilibrium constant is shown in

• reaction was, like the aldolase reaction, positively influenced by pressure. This was shown by the ratio of product to substrates (with the equilibrium constant K as the asymptote), as well as conversion, selectivity, and yield (Table 6). While the conversion, selectivity, and yield depend on the ratio of

• substrates, the equilibrium constant can also be used for other ratios. Conclusion An epimerase and an aldolase were investigated to continuously produce N-acetylneuraminic acid under high pressure. Both enzymes were successfully immobilized with high stability and used to catalyze a reaction starting from N

Methodologies for the synthesis of quaternary carbon centers via hydroalkylation of unactivated olefins: twenty years of advances

• Thiago S. Silva and
• Fernando Coelho

Beilstein J. Org. Chem. 2021, 17, 1565–1590, doi:10.3762/bjoc.17.112

• promote the enolization of carbonyl compounds [43] allowed the use of simple ketones as substrates in the intramolecular hydroalkylation of olefins. As discussed before, these are problematic substrates because of the low equilibrium constant between the keto and enol forms. Che’s group used [IPrAuCl

Kinetics of enzyme-catalysed desymmetrisation of prochiral substrates: product enantiomeric excess is not always constant

• Peter J. Halling

Beilstein J. Org. Chem. 2021, 17, 873–884, doi:10.3762/bjoc.17.73

• the equilibrium constant where the enzymatic reaction was not completely irreversible [2]. A limitation of the enzymatic resolution is that the maximum yield of the desired enantiomer is the 50% contained in the starting racemate. This is one reason for the current greater interest in enzymatic

• favoured product are completely absent. In most of the applications the overall reaction is significantly reversible, with an equilibrium constant that is not enormously larger than 1. And in many cases there is a noticeable formation of the less favoured enantiomer, with product ee values of 0.98 or less

• rate constants equal to the equilibrium constant of the overall reaction, which the enzyme is of course unable to change. A different combination of rate constants must equal the equilibrium constant for the isomerisation of one product enantiomer into the other, which is necessarily 1 (in an achiral

Efficient synthesis of piperazinyl amides of 18β-glycyrrhetinic acid

• Dong Cai,
• ZhiHua Zhang,
• Yufan Meng,
• KaiLi Zhu,
• LiYi Chen,
• ChangXiang Yu,
• ChangWei Yu,
• ZiYi Fu,
• DianShen Yang and
• YiXia Gong

Beilstein J. Org. Chem. 2020, 16, 798–808, doi:10.3762/bjoc.16.73

• agent [12]. Piperazinyl amide fragments have the ability to form several hydrogen bonds, modulate the acid–base equilibrium constant and change the octanol–water partition coefficient [13]. They are considered as the basic motif for designing many biologically active molecules [14][15]. Some piperazinyl

The reaction of arylmethyl isocyanides and arylmethylamines with xanthate esters: a facile and unexpected synthesis of carbamothioates

• Narasimhamurthy Rajeev,
• Toreshettahally R. Swaroop,
• Ahmad I. Alrawashdeh,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Seegehalli M. Anil,
• Kuppalli R. Kiran,
• Chandra,
• Paris E. Georghiou,
• Kanchugarakoppal S. Rangappa and
• Maralinganadoddi P. Sadashiva

Beilstein J. Org. Chem. 2020, 16, 159–167, doi:10.3762/bjoc.16.18

• favor of 4cB. The resulting calculated equilibrium constant of 2.042, corresponding to a 67.1/32.9 ratio of the rotamers (4cB/4cA), was in good agreement with the experimentally by 1H NMR (CDCl3) observed ratio of 65/35. Significantly, the single crystal of 4c, which afforded the crystal structure shown

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

• this case, kcat and kcat/Km can be approximated as follows (Note Ki = ki/k−i): Note that kcat is not simply defined by k3; rather, the equilibrium constant for the conformational change step defines the fraction of the bound substrate that is in the FS state (K2/(1 + K2)). An unfavorable equilibrium

• constant for the conformational change (K2) could reduce both kcat and kcat/Km. Case 2 We next consider the case shown in Figure 6B where the conformational change is rate-limiting. Here it can be seen that the rate of the conformational change governs both kcat and kcat/Km. This model mimics the standard

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

• transition metal complexes” [106]. In this mechanism, the catalyst is the most important component: it determines the equilibrium constant between the active and dormant species which is directly linked to the distribution of chain lengths [107]. As photoredox catalysts for ATRP applications, copper(II

Some mechanistic aspects regarding the Suzuki–Miyaura reaction between selected ortho-substituted phenylboronic acids and 3,4,5-tribromo-2,6-dimethylpyridine

• Piotr Pomarański,
• Piotr Roszkowski,
• Jan K. Maurin,
• Armand Budzianowski and
• Zbigniew Czarnocki

Beilstein J. Org. Chem. 2018, 14, 2384–2393, doi:10.3762/bjoc.14.214

• isomers (syn)-7 and (anti)-8 we analyzed signals having chemical shifts of 3.50 ppm, 3.57 ppm and 3.64 ppm, respectively. In the case of derivative (syn)-10 and (anti)-9 the observed signals of the chemical shifts are at 3.76 and 3.74 ppm. We are able to calculate the value of the equilibrium constant and

The hydrolysis of geminal ethers: a kinetic appraisal of orthoesters and ketals

• Sonia L. Repetto,
• James F. Costello,
• Craig P. Butts,
• Joseph K. W. Lam and
• Norman M. Ratcliffe

Beilstein J. Org. Chem. 2016, 12, 1467–1475, doi:10.3762/bjoc.12.143

• orthoesters are in fact delicately poised between stepwise and concerted processes; depending upon the substituent, both mechanisms are operational for aryl dimethyl orthoformates [21]. Stage 2 sees reaction of B with H2O to afford 2-hydroxy-1,3-dioxolane C (i.e., k2) with the overall equilibrium constant K2

Creating molecular macrocycles for anion recognition

• Amar H. Flood

Beilstein J. Org. Chem. 2016, 12, 611–627, doi:10.3762/bjoc.12.60

• signature for the TBA+ cation’s α proton showed a lower diffusion coefficient at 1 equiv when it forms the larger ion pair complex MC·Cl−·TBA+. Ultimately, any accurate assessment of an equilibrium constant requires inclusion of all the equilibria. There are a few tricks [25]. Some of the less stable

Base metal-catalyzed benzylic oxidation of (aryl)(heteroaryl)methanes with molecular oxygen

• Hans Sterckx,
• Johan De Houwer,
• Carl Mensch,
• Wouter Herrebout,
• Kourosch Abbaspour Tehrani and
• Bert U. W. Maes

Beilstein J. Org. Chem. 2016, 12, 144–153, doi:10.3762/bjoc.12.16

• the basicity of the pyridine nitrogen and not that much on the acidity of the methylene hydrogen. While the thermodynamical equilibrium constant between the imine and enamine tautomers predicts whether or not a substrate can be oxidized (see Supporting Information File 1), it does not provide an

Comparison of the catalytic activity for the Suzuki–Miyaura reaction of (η⁵-Cp)Pd(IPr)Cl with (η³-cinnamyl)Pd(IPr)(Cl) and (η³-1-t-Bu-indenyl)Pd(IPr)(Cl)

• Patrick R. Melvin,
• Nilay Hazari,
• Hannah M. C. Lant,
• Ian L. Peczak and
• Hemali P. Shah

Beilstein J. Org. Chem. 2015, 11, 2476–2486, doi:10.3762/bjoc.11.269

• ) and Cp (2.2 mg, 0.00375 mmol) were added to a vial. C6D6 (0.5 mL) was added and the solution was transferred to a J. Young tube and sealed. The mixture was heated to 60 °C and allowed to equilibrate over 36 hours. At this time, an NMR spectrum was recorded at room temperature. The equilibrium constant

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• solubility at all β-CD concentrations studied (0–10 mM). From the equilibrium constant calculation, the inclusion complex is still a binary complex (1:1), even in the presence of ethanol. The results from our theoretical study confirm that the binding mode is binary complex and the presence of ethanol as co

• [50]. The stoichiometry and formation constant (the equilibrium constant, Kbapp) can be obtained from phase solubility diagrams constructed by assessing the effect of the CD concentration on the apparent solubility of α-MGS. Figure 2 shows the α-MGS solubility increasing exponentially with ethanol

• , Ktint, could be determined according to Equation 8, and subsequently ρb and ρt were calculated using nonlinear regression and found to be 0.27 and 0.22 M−1, respectively. The equilibrium constant for binary complex formation (α-MGS/β-CD) was higher than that for ternary complex formation (α-MGS/β-CD

First principle investigation of the linker length effects on the thermodynamics of divalent pseudorotaxanes

• Andreas J. Achazi,
• Doreen Mollenhauer and
• Beate Paulus

Beilstein J. Org. Chem. 2015, 11, 687–692, doi:10.3762/bjoc.11.78

• , 298.15 K) and equilibrium constant K for the systems from the double mutant cycle.a Acknowledgements Support by the German Research Foundation (DFG) through the Collaborative Research Center (CRC) 765 'Multivalency as chemical organization and action principle: new architectures, functions and

Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

• Christine Beuck and
• Elmar Weinhold

Beilstein J. Org. Chem. 2014, 10, 2293–2306, doi:10.3762/bjoc.10.239

• demonstrate that the presented cross-linked DNA with an ethylene-linked A/T base pair analog at the target position is a useful tool to determine the base-flipping equilibrium constant of a base-flipping enzyme which lies mostly on the extrahelical side for M.TaqI. Keywords: DNA base flipping; DNA cross-link

• association equilibrium with the dissociation constant KD,init, followed by flipping of the target base with the equilibrium constant Kflip (Figure 6a) [55][56][69]. The binding affinity of base-flipping enzymes is often determined using DNA with the fluorescent base analog 2-aminopurine (2AP) at the target

• combination of equations (1) and (2): We used the duplex 1I6S-Et-S4U2 containing a locked A/T base pair analog at the target position within the double-stranded 5’-TCGA-3’ recognition site of the DNA adenine-N6 MTase M.TaqI to determine the equilibrium constant Kflip for the base flipping step. The

Photoswitchable precision glycooligomers and their lectin binding

• Daniela Ponader,
• Sinaida Igde,
• Marko Wehle,
• Katharina Märker,
• Mark Santer,
• David Bléger and
• Laura Hartmann

Beilstein J. Org. Chem. 2014, 10, 1603–1612, doi:10.3762/bjoc.10.166

• functionalization was monitored by SPR. Photoswitching of the glycooligomers was realized either ex situ prior to surface functionalization or in situ by direct irradiation of the functionalized chip. The equilibrium constant KD was obtained by fitting the obtained binding values at the turning point between

3-Pyridinols and 5-pyrimidinols: Tailor-made for use in synergistic radical-trapping co-antioxidant systems

• Luca Valgimigli,
• Daniele Bartolomei,
• Riccardo Amorati,
• Evan Haidasz,
• Jason J. Hanthorn,
• Susheel J. Nara,
• Johan Brinkhorst and
• Derek A. Pratt

Beilstein J. Org. Chem. 2013, 9, 2781–2792, doi:10.3762/bjoc.9.313

• to calibrate the spectrometer response, linear regression plots (Absorbance versus [ArOH]) in CCl4 were preliminarily recorded in the range 1–10 mM. Deviation from linearity was observed only in the case of 7b, allowing the determination of its self-association equilibrium constant as Kself = 121

Advancements in the mechanistic understanding of the copper-catalyzed azide–alkyne cycloaddition

• Regina Berg and
• Bernd F. Straub

Beilstein J. Org. Chem. 2013, 9, 2715–2750, doi:10.3762/bjoc.9.308

Damage of polyesters by the atmospheric free radical oxidant NO₃^•: a product study involving model systems

• Catrin Goeschen and
• Uta Wille

Beilstein J. Org. Chem. 2013, 9, 1907–1916, doi:10.3762/bjoc.9.225

• the reaction outcome and mechanic considerations, were avoided. It should also be noted that NO2• is in equilibrium with its dimer dinitrogen tetroxide, N2O4. In solution the NO2•/N2O4 equilibrium constant favours the dimer [15], and N2O4 can be oxidized with O3 to give N2O5. Gas-phase kinetic studies

Influence of cyclodextrin on the solubility and the polymerization of (meth)acrylated Triton^® X-100

• Melanie Kemnitz and
• Helmut Ritter

Beilstein J. Org. Chem. 2012, 8, 2176–2183, doi:10.3762/bjoc.8.245

• , and fluorescence studies, were used to determine the equilibrium constant [4][5][6][7][8][9][10][11][12]. The results also differ in the stoichiometry of the formed complexes [4][7][9][10][11]. Host/guest ratios of 1:1 [4][7], 2:1 [9] and the coexistence of 1:1 and 2:1 [10][11] complexes of β-CD and

• Triton® X-100 are reported in literature. In our previous paper, the coexistence of a 1:1 and 2:1 complex with an extraordinary high (K1 = 1.71 × 105 M−1) and a lower equilibrium constant (K2 = 260 M−1) was described [12]. Due to the fact that the tert-octyl group represents the preferred binding site of

Molecular solubilization of fullerene C₆₀ in water by γ-cyclodextrin thioethers

• Hai Ming Wang and
• Gerhard Wenz

Beilstein J. Org. Chem. 2012, 8, 1644–1651, doi:10.3762/bjoc.8.188

• CD rings. For the back process, the first dissociation step should be slow and rate determining, because of the necessary cleavage of these intermolecular hydrogen bonds. These assumptions lead to an apparent equilibrium constant K′ in which the CD concentration is only present in first order. The