Tailored charge-neutral self-assembled L₂Zn₂ container for taming oxalate

• David Ocklenburg and
• David Van Craen

Beilstein J. Org. Chem. 2024, 20, 3007–3015, doi:10.3762/bjoc.20.250

• Information Supporting Information File 2: Synthetic protocols, characterization data, NMR spectra, guest binding investigations, data fitting, and computational modeling details. Funding The authors are grateful for financial support by the Fonds der Chemischen Industrie (FCI) through a Liebig grant and the

Research progress on the pharmacological activity, biosynthetic pathways, and biosynthesis of crocins

• Zhongwei Hua,
• Nan Liu and
• Xiaohui Yan

Beilstein J. Org. Chem. 2024, 20, 741–752, doi:10.3762/bjoc.20.68

• CsCCD2 that exhibits broader substrate specificity and higher catalytic efficiency through computational modeling. Heterologous expression of the S323A mutant of CsCCD2 in yeast led to a 4-fold enhancement in the production of 1, with a crocetin (1) titer of 107 mg/L in a 5-liter fed-batch fermentation

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• stability, etc. Emerging research methods on bioinformatics, computational modeling, deep learning, protein engineering, and high-throughput screening will accelerate the pace of enzyme discovery to provide a broader platform of tools for employing chemoenzymatic strategies [64][87][88][89]. More

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• fluoroprolines in peptide and protein degradation is lacking though. 8 The potency of computational modeling in the design of proteins containing fluoroprolines The conformational consequences of the fluorination of the 4-position of proline have been well studied using computational methods. The latter provided

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• tackle increasingly complex glycan synthesis problems owing to the advent of a number of enabling computational modeling technologies. Linear Code is used to represent reaction rules of glycan synthesis thereby bringing both human-readability and computer-parsability to the glycoinformatics space. The

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 others [14][16] provides a foundation for further investigation into the binding of glycopeptide antigens to antibodies using computational modeling. Molecular dynamics (MD) simulations and analysis thereof are a well-known ingredient of the in-silico process for mechanistic screening of

One-pot synthesis of oxazolidinones and five-membered cyclic carbonates from epoxides and chlorosulfonyl isocyanate: theoretical evidence for an asynchronous concerted pathway

• Esra Demir,
• Ozlem Sari,
• Yasin Çetinkaya,
• Ufuk Atmaca,
• Safiye Sağ Erdem and
• Murat Çelik

Beilstein J. Org. Chem. 2020, 16, 1805–1819, doi:10.3762/bjoc.16.148

• isocyanate; computational modeling; cyclic carbonates; density functional theory; oxazolidinone; Introduction Oxazolidinones (1), five-membered heterocyclic rings containing an ester group adjacent to a nitrogen atom, are important compounds in synthetic and pharmaceutical chemistry because of their

Experimental and computational electrochemistry of quinazolinespirohexadienone molecular switches – differential electrochromic vs photochromic behavior

• Eric W. Webb,
• Jonathan P. Moerdyk,
• Kyndra B. Sluiter,
• Benjamin J. Pollock,
• Amy L. Speelman,
• Eugene J. Lynch,
• William F. Polik and
• Jason G. Gillmore

Beilstein J. Org. Chem. 2019, 15, 2473–2485, doi:10.3762/bjoc.15.240

• cyclic voltammetry and 1H NMR analyses, in concert with computational modeling. These results are compared to those for the symmetric parent PSHD, which due to symmetry possesses only a single possible regioisomer upon either electrochemical or photochemical ring-opening. Density functional theory

• . Computational modeling Predicted ground-state reduction potentials were computed based on the energy difference of the ground-state molecule (S0) and its one electron-reduced (D0) radical anion and our published correlation of this energy difference with experimental reduction potentials (vs SCE in acetonitrile

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• , fungicidal and tumorstatic effects [32]. A key player in the biosynthesis of cyclooctatin 5 is the bacterial diterpene synthase CotB2. Different research teams have investigated CotB2 by means of biochemical [30][31][38], biophysical [33][34][35], structural biology [36][37][38][39] and computational

• modeling approaches [35][37][39][40], revealing a rather unusual reaction mechanism. Given the diverse bioactivities of cyclooctatin 5, CotB2 is of biotechnological relevance as well. Cyclooctatin 5 can be manufactured biotechnologically in E. coli in milligram scales [26][30], which is important for an

Design of indole- and MCR-based macrocycles as p53-MDM2 antagonists

• Constantinos G. Neochoritis,
• Maryam Kazemi Miraki,
• Eman M. M. Abdelraheem,
• Ewa Surmiak,
• Tryfon Zarganes-Tzitzikas,
• Beata Łabuzek,
• Tad A. Holak and
• Alexander Dömling

Beilstein J. Org. Chem. 2019, 15, 513–520, doi:10.3762/bjoc.15.45

• HSQC NMR spectra of 15N-labeled MDM2 and computational modeling studies. Acknowledgements This research has been supported to (AD) by the National Institute of Health (NIH) (2R01GM097082-05), the European Lead Factory (IMI) under grant agreement number 115489, the Qatar National Research Foundation

Detection of therapeutic radiation in three-dimensions

• John A. Adamovics

Beilstein J. Org. Chem. 2017, 13, 1325–1331, doi:10.3762/bjoc.13.129

• been experimentally determined by computational modeling and vibrational spectra to be twisted much like a three-bladed propeller [20]. We found that numerous other aromatic aldehydes gave good results while highly hindered aryl aldehydes, such as pentamethylbenzaldehyde, 2-fluorenecarboxaldehyde, 9

Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications

• Vinila N. Viswanathan,
• Arun D. Rao,
• Upendra K. Pandey,
• Arul Varman Kesavan and
• Praveen C. Ramamurthy

Beilstein J. Org. Chem. 2017, 13, 863–873, doi:10.3762/bjoc.13.87

• stability with onset decomposition temperature of >410 °C. Computational modeling of the three polymers was performed to gain insight into the molecular energy levels along with band gaps using density functional theory (DFT) at the B3LYP/6-31G (d,p) level as implemented in Gaussian-09 software [37]. For

• computational modeling of the polymers, the alkyl chains were replaced by methyl groups and only two repeating units of monomers were used to keep the calculations simple. The ground-state potential energy of all optimized structures in their stable local minima was obtained to find the HOMO and LUMO. The

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

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

• QM methods and other parts with MM methods, for example, in enzymes where the active site can be modeled with QM and the remaining structure with MM methods. Predictive models for the SNAr reaction This paper is a continuation of our work on the predictive computational modeling of the synthetically

Toward an integrated route to the vernonia allenes and related sesquiterpenoids

• Da Xu,
• Michael A. Drahl and
• Lawrence J. Williams

Beilstein J. Org. Chem. 2011, 7, 937–943, doi:10.3762/bjoc.7.104

• intrinsic change, should that become necessary or desirable. Table 1 summarizes the ground state computational modeling of several C–C fragmentation substrates. The Gaussian suite of programs, with the B3LYP functional and the 6-31G(d,p) basis set, was used to generate these data [49][50][51][52][53][54][55