Enantioselective regiospecific addition of propargyltrichlorosilane to aldehydes catalyzed by biisoquinoline N,N’-dioxide

• Noble Brako,
• Sreerag Moorkkannur Narayanan,
• Amber Burns,
• Layla Auter,
• Valentino Cesiliano,
• Rajeev Prabhakar and
• Norito Takenaka

Beilstein J. Org. Chem. 2024, 20, 3069–3076, doi:10.3762/bjoc.20.255

• % yield with 61:39–92:8 enantiomeric ratios. Furthermore, possible mechanisms of propargyl–allenyl isomerization of propargyltrichlorosilane were computationally investigated. Keywords: α-allenic alcohol; computational chemistry; Lewis base catalysis; organocatalysis; propargyltrichlorosilane

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• field of computational chemistry and biochemistry: 1. AMBER [56]: AMBER (https://ambermd.org/) is the acronym for "Assisted Model Building with Energy Refinement", and it is an open-source software widely employed for molecular modelling and simulation. It is known for its stability, user-friendly

• the field of computational chemistry and bioinformatics. It is extensively used to model and simulate the dynamic behaviour of various molecular systems, including proteins, nucleic acids, lipids, and small molecules. GROMACS provides various tools for system preparation, simulation setup, and post

Allostreptopyrroles A–E, β-alkylpyrrole derivatives from an actinomycete Allostreptomyces sp. RD068384

• Marwa Elsbaey,
• Naoya Oku,
• Mohamed S. A. Abdel-Mottaleb and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2024, 20, 1981–1987, doi:10.3762/bjoc.20.174

• , Japan Computational Chemistry Lab, Department of Chemistry, Faculty of Science, Ain Shams University, 11566 Abbassia, Cairo, Egypt 10.3762/bjoc.20.174 Abstract Five new β-alkylpyrrole derivatives, allostreptopyrroles A–E (1–5), were isolated from the culture broth of Allostreptomyces RD068384. Their

Regioselective alkylation of a versatile indazole: Electrophile scope and mechanistic insights from density functional theory calculations

• Pengcheng Lu,
• Luis Juarez,
• Paul A. Wiget,
• Weihe Zhang,
• Krishnan Raman and
• Pravin L. Kotian

Beilstein J. Org. Chem. 2024, 20, 1940–1954, doi:10.3762/bjoc.20.170

• Pengcheng Lu Luis Juarez Paul A. Wiget Weihe Zhang Krishnan Raman Pravin L. Kotian Department of Discovery Chemistry, BioCryst Pharmaceuticals Inc., Discovery Center of Excellence, 2100 Riverchase Center Building 200, Suite 200 Birmingham, AL, 35244, USA Department of Computational Chemistry and

Hetero-polycyclic aromatic systems: A data-driven investigation of structure–property relationships

• Sabyasachi Chakraborty,
• Eduardo Mayo Yanes and
• Renana Gershoni-Poranne

Beilstein J. Org. Chem. 2024, 20, 1817–1830, doi:10.3762/bjoc.20.160

• on a range of electronic molecular properties of PASs. Keywords: computational chemistry; database; dataset; π-conjugated; polycyclic aromatic hydrocarbons; polycyclic aromatic systems; Introduction Polycyclic aromatic systems (PASs) – molecules made up of fused aromatic rings – are among the most

Biphenylene-containing polycyclic conjugated compounds

• Cagatay Dengiz

Beilstein J. Org. Chem. 2023, 19, 1895–1911, doi:10.3762/bjoc.19.141

• phenomenon is a result of non-radiative deactivation was corroborated by detailed computational chemistry studies. In continuation of the aforementioned work by Wagner and co-workers [49], they have synthesized also "v" and "z"-shaped POAs, wherein biphenylene groups are angularly incorporated into the 1,4

Thienothiophene-based organic light-emitting diode: synthesis, photophysical properties and application

• Recep Isci and
• Turan Ozturk

Beilstein J. Org. Chem. 2023, 19, 1849–1857, doi:10.3762/bjoc.19.137

• absorption and emission maxima of 411 and 520 nm, respectively, with a mega Stokes shift of 109 nm and fluorescence quantum yields both in the solid state (41%) and in solution (86%). The optical properties were supported by computational chemistry using density functional theory for optimized geometry and

• . The high thermal stability is profitable for the preparation of stable and durable OLED devices. Computational chemistry Ground-state geometry optimization of DMB-TT-TPA (8) was performed using density functional theory (DFT) calculations with the Gaussian 16 software at the B3LYP/6-31G (d,p) level

Quinoxaline derivatives as attractive electron-transporting materials

• Zeeshan Abid,
• Liaqat Ali,
• Sughra Gulzar,
• Faiza Wahad,
• Raja Shahid Ashraf and
• Christian B. Nielsen

Beilstein J. Org. Chem. 2023, 19, 1694–1712, doi:10.3762/bjoc.19.124

• compound with the donor polymer PM6 to create BHJ nanoparticles and employed it in the hydrogen evolution reaction. This approach substantially reduced trap density, increasing the hydrogen evolution rate by 2–3 times compared to conventional inorganic/organic hybrid photocatalysts [30]. Computational

• chemistry offers a cost-effective and time-efficient means of screening and selecting promising candidates for experimental exploration. Bhattacharya et al. employed density functional theory (DFT) approach to explore structural modulation for tuning the optoelectronic properties of Qx13. Their designed

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B

• Moe Nakano,
• Rintaro Gemma and
• Hajime Sato

Beilstein J. Org. Chem. 2023, 19, 1503–1510, doi:10.3762/bjoc.19.107

• , computational chemistry including DFT [5][6][7][8][9], QM/MM [10][11][12][13][14][15][16] and QM/MM MD [14][15][16][17] calculations have been used for the biosynthetic studies of terpene/terpenoids [18]. Terpene-forming reactions, which involve various types of carbocation species stabilized by

Total synthesis: an enabling science

• Bastien Nay

Beilstein J. Org. Chem. 2023, 19, 474–476, doi:10.3762/bjoc.19.36

• [12], as illustrated in this thematic issue with the synthesis of pheromones [16]. This requires permanent technological progress. Thus, the recent boom of artificial intelligence, machine learning, and computational chemistry for retrosynthetic analyses and beyond foreshadows a renewed interest in

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

• reactions that involve the same or a similar change in chemical bonding, e.g., by using group contribution methods [32][33][34][35]. And, one should not overlook the use of computational chemistry as a means to obtain the desired property values. Finally, there is a close relationship between equilibrium

Experimental and theoretical studies on the synthesis of 1,4,5-trisubstituted pyrrolidine-2,3-diones

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Nguyen Ngoc Tri,
• Luc Van Meervelt,
• Nguyen Tien Trung and
• Wim Dehaen

Beilstein J. Org. Chem. 2022, 18, 1140–1153, doi:10.3762/bjoc.18.118

• Nguyen Tran Nguyen Vo Viet Dai Nguyen Ngoc Tri Luc Van Meervelt Nguyen Tien Trung Wim Dehaen Department of Chemistry, University of Science and Education, the University of Da Nang, Ton Duc Thang 459, 550000 Da Nang, Viet Nam Laboratory of Computational Chemistry and Modelling, Faculty of Natural

Enzymes in biosynthesis

• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 1131–1132, doi:10.3762/bjoc.18.116

• novel products [7]. An alternative approach is offered by computational chemistry, which is ideally performed in combination with experimental verification of the computational results, e.g., through the enzymatic conversion of isotopically labelled compounds [8]. This thematic issue will cover all

The enzyme mechanism of patchoulol synthase

• Houchao Xu,
• Bernd Goldfuss,
• Gregor Schnakenburg and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 13–24, doi:10.3762/bjoc.18.2

• results from these experiments are contradictory. The present work reports on a reinvestigation of patchoulol biosynthesis by isotopic labelling experiments and computational chemistry. The results are in favour of a pathway through the neutral intermediates germacrene A and α-bulnesene that are both

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• an attempt at resolving this problem by means of the electronic circular dichroism (ECD) technique. We recorded an ECD spectrum of both compounds and compared it with simulated spectra, generated for both possible diastereomers (2-(R) and 2-(S)) using computational chemistry software. Unfortunately

Synthesis of purines and adenines containing the hexafluoroisopropyl group

• Viacheslav Petrov,
• Rebecca J. Dooley,
• Alexander A. Marchione,
• Elizabeth L. Diaz,
• Brittany S. Clem and
• William Marshall

Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224

• supplementary publication nos. CCDC #1998565−1998569. Computational chemistry Computational optimization of 8a and 8b structures was performed with Gaussian 9 software. Density functional theory at the B3LYP level, with a 6-311g++ basis set (Co phase) was employed. Reaction of purine (2) and 1 A mixture of 1.2

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• ] and MDTraj [39]) which are available as computational chemistry analysis tools in Galaxy [6], and these were used to analyze the molecular dynamics trajectories. The root-mean-square deviation (RMSD) is calculated to measure the stability and conformation of a set of selected atoms. The RMSD is a

• . Acknowledgements We would like to acknowledge the Galaxy community, the Galaxy Europe team, and the Galaxy computational chemistry team on GitHub. We thank the University of Cape Town eResearch (for support and use of the ilifu data centre) and the Centre for High Performance Computing (for the use of their GPU

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• mechanism studies using computational chemistry methods. The probable reaction mechanisms were studied by hybrid DFT QM/MM molecular dynamics simulations [11] where the possible transition state (TS) structures were localized. The observation of the possible TS structure opens the opportunities for the in

• synthesized. We performed docking studies of these compounds into the active site of GlfT2 by computational chemistry methods. Although the docking study showed good binding affinities of the prepared compounds towards the GlfT2 active site, their biological evaluation revealed a very poor effect on the

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• particular, in situ kinetic studies by spectroscopic methods [31] correlated to computational chemistry approaches [32] might reveal specific interaction between reactants and catalysts as well as solvent effects at work in such a complex system that should provide an understanding of the underlying reason

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

• transition metal coordination sphere; the energy of a new M–C bond formed and the thermodynamic stability of organometallic product. With new developments in computational chemistry, mechanistic studies using density functional theory (DFT) provide valuable insights into the reactivity of organometallic

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

Synthesis and characterization of bis(4-amino-2-bromo-6-methoxy)azobenzene derivatives

• David Martínez-López,
• Amirhossein Babalhavaeji,
• Diego Sampedro and
• G. Andrew Woolley

Beilstein J. Org. Chem. 2019, 15, 3000–3008, doi:10.3762/bjoc.15.296

• absorption wavelengths of possible derivatives. Based on these considerations, we carried out the synthesis and photochemical characterization of compounds 4 and 5. Results and Discussion Computational chemistry Calculations were performed using density functional theory (DFT) methods (B3LYP/6-31+G**) to

Pigmentosins from Gibellula sp. as antibiofilm agents and a new glycosylated asperfuran from Cordyceps javanica

• Soleiman E. Helaly,
• Wilawan Kuephadungphan,
• Patima Phainuphong,
• Mahmoud A. A. Ibrahim,
• Kanoksri Tasanathai,
• Suchada Mongkolsamrit,
• Janet Jennifer Luangsa-ard,
• Souwalak Phongpaichit,
• Vatcharin Rukachaisirikul and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2968–2981, doi:10.3762/bjoc.15.293

• , Narathiwat 96000, Thailand Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, 61519, Egypt National Centre for Genetic Engineering and Biotechnology (BIOTEC), NSTDA, 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120

Dyes in modern organic chemistry

• Heiko Ihmels

Beilstein J. Org. Chem. 2019, 15, 2798–2800, doi:10.3762/bjoc.15.272

• theoretical and computational chemistry [20]. In the same way, essential dye properties, such as aggregation [21][22] or solvatochromism [23], are still in the focus of current physical organic research. The analytical sciences also depend very much on the availability of appropriate dyes with characteristic

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

• progress made in experiments and theory/computational chemistry, there is still a need for improvement and benchmarking [7]. Many aromatic solute–solvent complexes have been studied in the gas phase (cf. [8][9][10] and references therein). Studied systems involving methanol as attached solvent molecule