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

• This equation shows that any change in the reaction equilibrium (ratio of the equilibrium molalities ) must be equalised by the ratio of the equilibrium activity coefficients of the reacting agents, or in other words . The activity coefficients describe the molecular interactions among the reaction

Co-crystallization of an organic solid and a tetraaryladamantane at room temperature

• Fabian Rami,
• Jan Nowak,
• Felix Krupp,
• Wolfgang Frey and
• Clemens Richert

Beilstein J. Org. Chem. 2021, 17, 1476–1480, doi:10.3762/bjoc.17.103

• may be obtained from organic molecules chosen for their shape complementarity and ability to engage in specific molecular interactions [21][22]. Such co-crystals are a fascinating class of materials with applications very different from mere structure elucidation. Conclusion Taken together, the

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• knowledge of protein–protein interactions, common characterisation methods to characterise them, and their role in protein complex formation with some examples. A deep understanding of protein–protein interactions and their molecular interactions is important for a number of applications, including drug

• design. Protein–protein interactions and their discovery are thus an interesting avenue for understanding how protein complexes, which make up the majority of proteins, work. Keywords: characterisation methods; heterooligomeric complex; homooligomeric complex; molecular interactions; protein–protein

• ], therapeutic interventions [8], and are crucial for potential drug discoveries [9]. This minireview will give a short insight into the different characterisation methods to characterise PPIs. Moreover, it will provide an examination of the different molecular interactions of PPIs and their role in protein

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• Debabrata Maity Department of Chemistry, New York University, New York, NY 10003, USA 10.3762/bjoc.16.247 Abstract To understand the molecular interactions, present in living organisms and their environments, chemists are trying to create novel chemical tools. In this regard, peptide-based

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor. Keywords: molecular recognition; NMR; protein ligand interaction; protein surfaces; supramolecular chemistry; Introduction In

• be detected by its luminescence [77][78][79]. Overall, while crystal structures provide fantastic insight into molecular interactions of such supramolecular ligands, they do not necessarily reflect the binding situation in solution. Furthermore, to our knowledge no protein co-crystal structures with

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

Synthesis of C₃-symmetric star-shaped molecules containing α-amino acids and dipeptides via Negishi coupling as a key step

• Sambasivarao Kotha and
• Saidulu Todeti

Beilstein J. Org. Chem. 2019, 15, 371–377, doi:10.3762/bjoc.15.33

• the structural and chemical nature of protein–protein interactions, synthetic peptides and unnatural AAAs [8][9][10][11][12][13][14][15] can be useful as molecular tools. Moreover, C3-symmetric peptides are valuable in studying the molecular interactions involving proteins that are derived from

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

• Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom 10.3762/bjoc.15.12 Abstract Weak molecular interactions (WMI) are responsible for processes such as physisorption; they are essential for the structure and stability of interfaces, and

• attractive, weak molecular interactions (WMIs) that the molecules involved retain their integrity. This may mean one of three things: 1) that the geometries of the interacting molecules differ very little from the equilibrium geometries of the isolated species, e.g., an interacting molecule changes only its

• represent repulsive interactions, monotonically increasing PEFs represent attractive interactions. PEFs V int(r) describing realistic molecular interactions, also called effective potentials, are always a sum of elementary attractive and repulsive components, V int = V rep + V att, not all of them need be

One hundred years of benzotropone chemistry

• Arif Dastan,
• Haydar Kilic and
• Nurullah Saracoglu

Beilstein J. Org. Chem. 2018, 14, 1120–1180, doi:10.3762/bjoc.14.98

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• Uiso(H) = xUeq(C), where x = 1.2 for the aromatic, methylene and methine H atoms, and x = 1.5 for the methyl H atoms. All presented molecular interactions were found using the PLATON program [44]. The figures for this publication were prepared using ORTEP-3 and Mercury programs [45][46]. The CCDC

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• Raman bands of the native CD in comparison to the bands of the guest molecule [29]. In contrary, the spectrum of the host–guest complexes, where due to molecular interactions some changes in Raman spectra would be observed (shifting or decreasing of the peak intensity or broadening of characteristic

Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• variations provides the controllability to influence the precise rates in feedback loops. Essentially, this flexibly helped us enormously at the stage of (1) retrosynthetic screening, as well as (2) in studies correlating the molecular interactions to the behavior in networks at both regulatory as well as at

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• structures in food and in biomedical applications, as hydrogels, triggers the development of novel experiments and tools, such as optical tweezers, while making use of synchrotron radiation. Description of the details of molecular interactions occurring between complex materials such as polysaccharides and

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

• simulations are therefore a useful technique providing details of the molecular interactions of structural components in different environments (e.g., water or water/co-solvent mixtures) which are often encountered in formulations. In our previous work [24], the preliminary results of phase solidities of the

Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

• Katharina Koschek,
• Vedat Durmaz,
• Oxana Krylova,
• Marek Wieczorek,
• Shilpi Gupta,
• Martin Richter,
• Alexander Bujotzek,
• Christina Fischer,
• Rainer Haag,
• Christian Freund,
• Marcus Weber and
• Jörg Rademann

Beilstein J. Org. Chem. 2015, 11, 837–847, doi:10.3762/bjoc.11.93

• peptide–polymer distance. Thermodynamic properties. From a physical point of view, the significantly varying mean peptide–peptide and peptide–polymer distances are mainly attributed to molecular interactions between the involved atoms. For this reason we calculated non-bonded interaction energies between

Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

• Manuel Gensler,
• Christian Eidamshaus,
• Maurice Taszarek,
• Hans-Ulrich Reissig and
• Jürgen P. Rabe

Beilstein J. Org. Chem. 2015, 11, 817–827, doi:10.3762/bjoc.11.91

• direction of applied forces, the green fluorescent protein shows most-probable rupture forces between 100 pN and 550 pN at pulling speeds of 2 µm/s, but only one thermal pathway of denaturation [15]. Also the mechanical stability of the titin-telethonin complex is highly directed [16]. Instead molecular

• interactions in biological systems are characterized by a balanced interplay between mechanical stability and malleability. Already in 1999 Rief et al. compared the mechanical stability of the α-helical domain spectrin with refolding forces from domain I27 of the muscle protein titin in β-sheet conformation

Synthesis of carbohydrate-scaffolded thymine glycoconjugates to organize multivalency

• Anna K. Ciuk and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2015, 11, 668–674, doi:10.3762/bjoc.11.75

• ] photocycloaddition; carbohydrate scaffolds; multivalency; thymine glycoconjugates; Introduction Multivalency of molecular interactions is a fundamental principle in carbohydrate recognition. It influences the avidity and specificity of carbohydrate–protein interactions as well as it enables supramolecular changes

Synthesis of modified cyclic and acyclic dextrins and comparison of their complexation ability

• Kata Tuza,
• László Jicsinszky,
• Tamás Sohajda,
• István Puskás and
• Éva Fenyvesi

Beilstein J. Org. Chem. 2014, 10, 2836–2843, doi:10.3762/bjoc.10.301

• , followed by β-CD, G7 and α-CD. In general, it can be concluded that maltooligomers have to be considered as potential complexation and interacting agents in the future that may substitute CDs in certain systems. Systematic aggregation studies were performed to corroborate the existence of molecular

• interactions between G8 and ibuprofen as an example (Figure 1) using PCS technique. The size distribution function of G8 in 1% solution (Figure 1a) shows that G8 does not form aggregates in itself in distilled water, since the peak found at around 1.5 nm well corresponds to the dimension of a single

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

• Friedrich Malberg,
• Jan Gerit Brandenburg,
• Werner Reckien,
• Oldamur Hollóczki,
• Stefan Grimme and
• Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

• . One might assume that the terminal groups play a minor role in the interplay within the rotaxane and serve only to prevent the axle mechanically from dethreading. However, we clearly demonstrated the importance of such rotaxanes parts as the stopper groups also for intra-molecular interactions of the

N-Alkylated dinitrones from isosorbide as cross-linkers for unsaturated bio-based polyesters

• Oliver Goerz and
• Helmut Ritter

Beilstein J. Org. Chem. 2014, 10, 902–909, doi:10.3762/bjoc.10.88

• nitrones. We expected that the cycloaddition of 3a with 4 yields two diastereomers for each 4- and 5-substituted isoxazolidines, resulting in four isomers. The proposed molecular interactions are shown in Scheme 2. The model compounds 3a/b were reacted with an excess of dimethyl itaconate (4) obtaining

• . Synthesis of Z-configurated model compounds 3a/b from E-benzaldoxime and acrylates 2a/b. Proposed molecular interactions of nitron 3a and dimethyl itaconate (4). 1,3-Dipolaric cycloaddition of nitrones 3a/b with dimethyl itaconate (4). Synthetic route to bio-based dinitrones derived from isosorbide

Molecular assembly of amino acid interlinked, topologically symmetric, π-complementary donor–acceptor–donor triads

• M. B. Avinash,
• K. V. Sandeepa and
• T. Govindaraju

Beilstein J. Org. Chem. 2013, 9, 1565–1571, doi:10.3762/bjoc.9.178

• ). In order to gain further insights into the nature of molecular interactions, 1, 2 and 3 were subjected to circular dichroism (CD) spectroscopic studies. The CD spectra of 1 in DMSO show positive excitonic cotton effects, indicating a P-type helical assembly (Figure 3a). However, with increase in the

Conformational analysis and intramolecular interactions in monosubstituted phenylboranes and phenylboronic acids

• Josué M. Silla,
• Rodrigo A. Cormanich,
• Roberto Rittner and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2013, 9, 1127–1134, doi:10.3762/bjoc.9.125

• a way that the molecular interactions are characterized by quantum-mechanical delocalization from filled donor to formally unoccupied acceptor NBOs [19]. In addition to the NBO method, the quantum theory of atoms in molecules (QTAIM) [20] has been widely used to examine the electronic densities

A new family of four-ring bent-core nematic liquid crystals with highly polar transverse and end groups

• Kalpana Upadhyaya,
• Venkatesh Gude,
• Golam Mohiuddin and
• Rao V. S. Nandiraju

Beilstein J. Org. Chem. 2013, 9, 26–35, doi:10.3762/bjoc.9.4

• well as a strong dipole in the bent direction. If molecular interactions are strong enough then the molecular structure can promote polar biaxial nematic phases. In this study, we aimed to combine the lateral dipole in the form of a cyanobiphenyl moiety as one of the arms of the bent-core molecule

• contributes to a weakening of lateral interactions and hence does not promote the necessary molecular interactions to exhibit mesomorphism. The repulsion between the transverse polar chloro substituent in 1a–1c and the adjacent ester or imine linkages leads to a torque exercised on the wing of the bent

An easily accessible sulfated saccharide mimetic inhibits in vitro human tumor cell adhesion and angiogenesis of vascular endothelial cells

• Grazia Marano,
• Claas Gronewold,
• Martin Frank,
• Anette Merling,
• Christian Kliem,
• Sandra Sauer,
• Manfred Wiessler,
• Eva Frei and
• Reinhard Schwartz-Albiez

Beilstein J. Org. Chem. 2012, 8, 787–803, doi:10.3762/bjoc.8.89

• interference with the adhesion of melanoma (Figure 2) and endothelial cells (Figure 7) to the extracellular matrix protein. In order to investigate the molecular interactions of GSF in the RGD binding site of the integrin molecule in more detail we performed molecular dynamics (MD) simulation in explicit water

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32