Oxidation of [3]naphthylenes to cations and dications converts local paratropicity into global diatropicity

• Abel Cárdenas,
• Zexin Jin,
• Yong Ni,
• Jishan Wu,
• Yan Xia,
• Francisco Javier Ramírez and
• Juan Casado

Beilstein J. Org. Chem. 2025, 21, 277–285, doi:10.3762/bjoc.21.20

• , 2000 scans at a resolution better than 4 cm−1 were accumulated to optimize the signal-to-noise ratio. Theoretical methods Quantum chemistry was addressed with the Gaussian 09 suite of programs [28]. DFT calculations were performed at the (U)B3LYP[29][30] level, using the 6-311G* basis set [31]. This

pKalculator: A pK_a predictor for C–H bonds

• Rasmus M. Borup,
• Nicolai Ree and
• Jan H. Jensen

Beilstein J. Org. Chem. 2024, 20, 1614–1622, doi:10.3762/bjoc.20.144

• . As molecular complexity increases, this task becomes more challenging. This paper introduces pKalculator, a quantum chemistry (QM)-based workflow for automatic computations of C–H pKa values, which is used to generate a training dataset for a machine learning (ML) model. The QM workflow is

• quantum chemistry (QM)-based workflow for the automatic computation of C–H pKa values in DMSO. The computed C–H pKa values are then used to generate training data for an ML model using LightGBM [6]. The QM-based workflow and the ML model are freely available under the MIT license. Methods Datasets We

• pharmaceutical intermediates that undergo selective borylation to compare our QM workflow and ML model with experimentally determined reaction sites. The quantum chemistry-based workflow Following work by Ree et al. [12][13][14][15], we present a fully automated QM-based workflow for computing C–H pKa values. A

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

• potentially the roles specific active site residues play during catalysis [23][24][27]. Conclusion In the current work we performed gas-phase quantum chemistry calculations for the competing reaction pathways leading to IEs A and B as well as hydropyrene and hydropyrenol. In the former two reactions there is

• calculations and then chose the lowest energy conformer as representative of each carbocation intermediate in the mechanism. Hence, each intermediate state is represented by a single conformer, which is the lowest energy conformer found. Quantum chemistry calculations Optimizations and subsequent frequency

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

• Benjamin Jeffries,
• Zhong Wang,
• Robert I. Troup,
• Anaïs Goupille,
• Jean-Yves Le Questel,
• Charlene Fallan,
• James S. Scott,
• Elisabetta Chiarparin,
• Jérôme Graton and
• Bruno Linclau

Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182

• relates to the difference in Gibbs energy of the free ligand conformations of this solute in the respective solvents. Quantum chemistry calculations of Gibbs energies in octanol and water thus provide theoretical estimations of lipophilicities. Such estimations require systematic conformational analyses

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• ; chemical structure representation; chemical structure models; language of chemistry; quantum chemistry; Introduction This article originally arose out of our discussions for the 2020 Beilstein Bozen Meeting “Models of Convenience” [1], which had to be postponed due to Covid-19 pandemic. It essentially

• 3D ball-and-sticks model only represents one of several possible conformations of clozapine but that all these conformations are inherent in the 2D-line structure. The dichotomy, really that between fundamental quantum chemistry and the common bonding models, which is made evident in Figure 1 and

• approximation for computational quantum chemistry has long attained the status of a bonding model to such an extent that many chemists outside the theoretical community are unaware that it is an approximation. Molecular-orbital bonding models based on the LCAO approximation discuss chemical bonds in terms of

In silico rationalisation of selectivity and reactivity in Pd-catalysed C–H activation reactions

• Liwei Cao,
• Mikhail Kabeshov,
• Steven V. Ley and
• Alexei A. Lapkin

Beilstein J. Org. Chem. 2020, 16, 1465–1475, doi:10.3762/bjoc.16.122

• , reaction conditions, and so on [23]. In order to achieve accurate and efficient reaction prediction, a mechanism-based method was chosen to direct quantum chemistry calculations and predictions, see Figure 1. For the Pd(II)-catalysed C–H activation reactions, there are two main commonly accepted mechanisms

Preparation of 2-phospholene oxides by the isomerization of 3-phospholene oxides

• Péter Bagi,
• Réka Herbay,
• Nikolett Péczka,
• Zoltán Mucsi,
• István Timári and
• György Keglevich

Beilstein J. Org. Chem. 2020, 16, 818–832, doi:10.3762/bjoc.16.75

• double bond migration pathways were elucidated by quantum chemical calculations. Keywords: chlorophosphonium salts; isomerization; 2-phospholene oxides; 3-phospholene oxides; quantum chemistry; Introduction P-Heterocyclic derivatives are valuable targets in synthetic organophosphorus chemistry [1][2][3

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

• temperature. Computational details: All calculations were carried out using the TURBOMOLE version 7.2 quantum chemistry package [67]. Geometry optimizations of all compounds in different conformers were carried out using DFT with PBE approximation to the exchange-correlation (XC) functional and employing 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

• 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

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

• structure of compound 2 was obtained by editing the DTB structure. First, we computed General Amber Force Field parameters for molecules of compound 1 and 2 in Antechamber software. Charges were calculated by restrained electrostatic potential method (RESP) based on a wave function calculated using quantum

• chemistry at the HF/6-31G*//HF/6-31G* level. Compound 1 molecule was manually docked into the SERCA binding site for thapsigargin using UCSF CHIMERA 1.10.2 (University of California, San Francisco) software by two approaches. In the first one, the molecule was docked so that the spatial orientation of the

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

• Dominic Bernhard,
• Fabian Dietrich,
• Mariyam Fatima,
• Cristóbal Pérez,
• Hannes C. Gottschalk,
• Axel Wuttke,
• Ricardo A. Mata,
• Martin A. Suhm,
• Melanie Schnell and
• Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

Are dispersion corrections accurate outside equilibrium? A case study on benzene

• Tim Gould,
• Erin R. Johnson and
• Sherif Abdulkader Tawfik

Beilstein J. Org. Chem. 2018, 14, 1181–1191, doi:10.3762/bjoc.14.99

• of dispersion correction models. Note, this is different to seamless approaches like MP2, RPA or other quantum chemistry methods which include dispersion forces automatically. Common van der Waals corrections can be broadly divided into three categories, as will be detailed below. Substantial effort

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• sound models of the interaction potential for water to be used in molecular simulations. In particular, the role of many-body interactions beyond the two-body interactions, which are often not explicitly taken into account by empirical force fields, can be accurately described by quantum chemistry

• electron correlation effects. Efficient quantum chemistry approaches for describing intermolecular interactions between water molecules may therefore describe higher-body interactions on an uncorrelated Hartree–Fock level without a serious loss in accuracy. Keywords: dispersion; many-body effects; water

• . These commonly depend on a number of empirical parameters that are determined either by a fit to experimentally known liquid or bulk properties, or by fitting to energies from ab initio quantum chemistry methods. The most popular potentials for water are the TIP3P [2], TIP4P [2][3] and TIP5P [4][5

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• Marton Bojtar Peter Zoltan Janzso-Berend David Mester Dora Hessz Mihaly Kallay Miklos Kubinyi Istvan Bitter Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1521 Budapest, Hungary MTA-BME Lendület Quantum Chemistry Research Group, Department of

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• of qA inside DNA disqualifies it for use as a base–base FRET donor. In order to maintain the base-analogue properties and achieve improved photophysical properties, we used quantum chemistry-supported design and developed a series of four, second generation, quadracyclic adenine analogues, qAN1–qAN4

Complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives

• Leonid S. Kikot',
• Catherine Yu. Kulygina,
• Alexander Yu. Lyapunov,
• Svetlana V. Shishkina,
• Roman I. Zubatyuk,
• Tatiana Yu. Bogaschenko and
• Tatiana I. Kirichenko

Beilstein J. Org. Chem. 2017, 13, 2056–2067, doi:10.3762/bjoc.13.203

• , Odesa 65080, Ukraine Department of X-ray Diffraction Studies and Quantum Chemistry, SSI ‘‘Institute for Single Crystals’’, National Academy of Sciences of Ukraine, Nauky Ave. 60, Kharkiv 61001, Ukraine Department of Inorganic Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody Sq., 61122

Theoretical simulation of the infrared signature of mechanically stressed polymer solids

• Matthew S. Sammon,
• Milan Ončák and
• Martin K. Beyer

Beilstein J. Org. Chem. 2017, 13, 1710–1716, doi:10.3762/bjoc.13.165

• ][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74]. A variety of theoretical approaches have been developed to model external force using methods of quantum chemistry [9][75][76

New approach toward the synthesis of deuterated pyrazolo[1,5-a]pyridines and 1,2,4-triazolo[1,5-a]pyridines

• Aleksey Yu. Vorob’ev,
• Vyacheslav I. Supranovich,
• Gennady I. Borodkin and
• Vyacheslav G. Shubin

Beilstein J. Org. Chem. 2017, 13, 800–805, doi:10.3762/bjoc.13.80

• position 3a to position 2 in cycloadduct 10 (path a) with the formation of intermediate 11 which, on further oxidation, gives product 8. Intermediate 11 is the most stable isomer among other dihydro intermediates according to quantum chemistry calculations by the M-06-2X 6-31G+(d,p) method (Figure 2) and

Creating molecular macrocycles for anion recognition

• Amar H. Flood

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

• With accurate values for the 1:1 stabilities of various anion complexes deconvoluted from a veritable stew of other equilibria, quantum chemistry can be used to get an accurate picture of binding. First, we learn how to bring experiment and theory into agreement, then delve deeper into the origins of

Solving the puzzling competition of the thermal C²–C⁶ vs Myers–Saito cyclization of enyne-carbodiimides

• Anup Rana,
• Mehmet Emin Cinar,
• Debabrata Samanta and
• Michael Schmittel

Beilstein J. Org. Chem. 2016, 12, 43–49, doi:10.3762/bjoc.12.6

• and Discussion The proper description of organic reactions involving diradical intermediates and transition state structures remains a difficult task in quantum chemistry [27][28][29][30][31][32][33][34][35]. Singlet diradicals have two electronic configurations that can only be treated accurately by

Efficient CO₂ capture by tertiary amine-functionalized ionic liquids through Li⁺-stabilized zwitterionic adduct formation

• Zhen-Zhen Yang and
• Liang-Nian He

Beilstein J. Org. Chem. 2014, 10, 1959–1966, doi:10.3762/bjoc.10.204

• the reaction mixture after CO2 absorption in the absence or presence of water. Influence of the ratio of LiNTf2/neutral ligands (PEG150MeTMG and PEG150MeBu2N) on the CO2 capacity of the coordinating mixtures. The quantum chemistry calculations (enthalpy changes) of the reaction between CO2 and

Host–guest complexes of mixed glycol-bipyridine cryptands: prediction of ion selectivity by quantum chemical calculations, part V

• Svetlana Begel,
• Ralph Puchta and
• Rudi van Eldik

Beilstein J. Org. Chem. 2013, 9, 1252–1268, doi:10.3762/bjoc.9.142

• ; quantum chemistry; selective ion complexation; Introduction The present report continues a series of contributions from our group dealing with quantum chemical investigations of the selective complexation of alkali and alkaline-earth metal cations by supramolecular species, predominantly cryptands and

Utilizing the σ-complex stability for quantifying reactivity in nucleophilic substitution of aromatic fluorides

• Magnus Liljenberg,
• Tore Brinck,
• Tobias Rein and
• Mats Svensson

Beilstein J. Org. Chem. 2013, 9, 791–799, doi:10.3762/bjoc.9.90

• accuracy since they do not take the relevant TS or solvation into account. Quantum chemistry methods exploring the PES on the other hand can, with sufficient modeling and appropriate level of theory, yield very accurate results and do not rely on predetermined experimental data. However, this procedure is

High-spin intermediates of the photolysis of 2,4,6-triazido-3-chloro-5-fluoropyridine

• Sergei V. Chapyshev,
• Denis V. Korchagin,
• Patrik Neuhaus and
• Wolfram Sander

Beilstein J. Org. Chem. 2013, 9, 733–742, doi:10.3762/bjoc.9.83

• is based on comparison of their zero-field splitting (ZFS) parameters derived from experimental EPR spectra and calculated by quantum chemistry methods. The most accurate theoretical estimations are obtained at the PBE/DZ level of theory, which overestimates the experimental ZFS values of nitrenes by

New reactive intermediates in organic chemistry

• Götz Bucher

Beilstein J. Org. Chem. 2013, 9, 613–614, doi:10.3762/bjoc.9.67

• exponential increase in computing power available to researchers, much of the mechanistic work nowadays is done using the tools of quantum chemistry. In particular, the various flavours of density functional theory have proven valuable in this respect, but high-level correlated methods such as CCSD(T) also