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

• to be known. Target information is usually obtained experimentally by X-ray crystallography or NMR (nuclear magnetic resonance). When neither is available, computational methods such as homology modeling may be used to predict the three-dimensional structures of targets. Knowing the structure makes

• of glaucoma and was developed using structure-based tools (Figure 3) [7][8]. Protein structure determination All structure-based methods rely on the three-dimensional target structure. The most common way to determine a protein structure is by X-ray crystallography and NMR spectroscopy. Recently

• where the three-dimensional structures are known [35]. NCBI Basic Local Alignment Search Tool (BLAST) is one of the most popular bioinformatics sequence alignment tools used with sequence similarity searches [36]. Once a homologous protein structure for the sequence has been identified, building the

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

• Vladimir A. Stepchenko,
• Anatoly I. Miroshnikov,
• Frank Seela and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2016, 12, 2588–2601, doi:10.3762/bjoc.12.254

• not shown). Thus, both enzymes demonstrated severe restrictions on the bulkiness and three-dimensional structure of the substituent at the C-5 atom of the pyrimidines. The spatial organization of the very poor substrates 5-tert-butyluracil (15) and 5-phenyluracil (16) vs good substrates 5-ethyluracil

Synthesis of three-dimensional porous hyper-crosslinked polymers via thiol–yne reaction

• Mathias Lang,
• Alexandra Schade and
• Stefan Bräse

Beilstein J. Org. Chem. 2016, 12, 2570–2576, doi:10.3762/bjoc.12.252

• 650 m²/g. Those networks also showed a high thermal stability as well as insolubility in common organic solvents. Keywords: three-dimensional; porous hyper-crosslinked polymers; thiol–yne; Introduction The synthesis of different organic networks has been previously reported. Among them, especially

• ], gas separation [7] and catalysis [8][9][10]. For the synthesis of organic networks, many different reaction types such as condensation reactions [11][12], coupling reactions [3] and click reactions [5][13] have been reported. Herein we present the synthesis of porous, three-dimensional

NeoPHOX – a structurally tunable ligand system for asymmetric catalysis

• Jaroslav Padevět,
• Marcus G. Schrems,
• Robin Scheil and
• Andreas Pfaltz

Beilstein J. Org. Chem. 2016, 12, 1185–1195, doi:10.3762/bjoc.12.114

• -TBDMS gave somewhat lower enantioselectivities. In the hydrogenation of imine S4 none of the catalysts shown in Table 2 induced high enantioselectivity. Crystal structures of iridium NeoPHOX complexes The three dimensional structures of several threonine and serine-derived NeoPHOX iridium complexes were

Supramolecular chemistry at the interface of biology, materials and medicine

• Eric V. Anslyn and
• Steven C. Zimmerman

Beilstein J. Org. Chem. 2016, 12, 1101–1102, doi:10.3762/bjoc.12.105

• their own unique perspective and subarea. There is an enormous amount still to learn about the fundamental nature of noncovalent interactions and particularly how to design and synthesize molecules that complex other molecules or are able to assemble spontaneously into three-dimensional structures. Thus

Indenopyrans – synthesis and photoluminescence properties

• Andreea Petronela Diac,
• Ana-Maria Ţepeş,
• Albert Soran,
• Ion Grosu,
• Anamaria Terec,
• Jean Roncali and
• Elena Bogdan

Beilstein J. Org. Chem. 2016, 12, 825–834, doi:10.3762/bjoc.12.81

• interactions. Further edge-to-face H···π [44] and π–π interactions [45][46] (Table 4) between molecules from neighboring layers contribute to the three-dimensional crystal packing (Figure S6 in Supporting Information File 1). Conclusion Several indenopyrone derivatives were synthesized and characterized by NMR

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

• Maria C. Guimarães,
• Mariene H. Duarte,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76

• suggesting that these 2D MD´s can be advantageous over some three-dimensional descriptors. Keywords: conformational analysis; isoflurane; QSAR; theoretical calculations; volatile anesthetics; Introduction Quantitative structure–activity relationship (QSAR) studies try to find a correlation between chemical

• hydrophobicity to three-dimensional descriptors [2]. Indeed, the most popular QSAR methods are based on molecular descriptors generated from 3D molecular structures, such as the widely used techniques based on molecular field analysis [3][4]. The problem with most 3D-QSAR methods is that the bioactive

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• single path through the TSS to the product at a rate governed by the Eyring equation [9] and (b) a three-dimensional hypothetical PES exhibiting the features of a PTSB and a qualitative representation of the starting points for dynamics trajectories. The function z = 2x5 − 5x2 − 5xy + y2 + 2 was used to

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

• Eric V. Anslyn

Beilstein J. Org. Chem. 2016, 12, 362–376, doi:10.3762/bjoc.12.40

• much of the same concept is just a simple 96-well plate. a) LDA plot of the response from different wine varietals with array Z [103]. b) Three-dimensional LDA plot of the response from the SOX-peptides showing in vitro differentiation of nine MAP kinases [106]. c) LDA plot of data collected from 96

Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

• Giuseppina Raffaini,
• Fabio Ganazzoli and
• Antonino Mazzaglia

Beilstein J. Org. Chem. 2016, 12, 73–80, doi:10.3762/bjoc.12.8

• the cell periodicity, just as the ordering in arrays suggested in one case (Figure 2) for eight aCD molecules (see also Figure 4 for the starting arrangement of the sixty-four molecules that still display the previously assumed three-dimensional periodicity) yielded a more complicated bidimensional

Supramolecular polymer assembly in aqueous solution arising from cyclodextrin host–guest complexation

• Jie Wang,
• Zhiqiang Qiu,
• Yiming Wang,
• Li Li,
• Xuhong Guo,
• Duc-Truc Pham,
• Stephen F. Lincoln and
• Robert K. Prud’homme

Beilstein J. Org. Chem. 2016, 12, 50–72, doi:10.3762/bjoc.12.7

• associative forces including hydrogen bonding, coordinate bonding, electrostatic interactions and hydrophobic interactions is ubiquitous in nature. This is exemplified by the use of DNA and RNA complementarity [1][2] and polypeptide helix formation [3][4] to produce three-dimensional structures and materials

Determination of formation constants and structural characterization of cyclodextrin inclusion complexes with two phenolic isomers: carvacrol and thymol

• Miriana Kfoury,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2016, 12, 29–42, doi:10.3762/bjoc.12.5

• spectroscopy has been widely employed to investigate CD inclusion complexes [40][41]. It is one of the most complete spectroscopic techniques because it allows a clear distinction between inclusion and other possible external interaction processes. Moreover, it gives direct information on the three-dimensional

Organocatalytic and enantioselective Michael reaction between α-nitroesters and nitroalkenes. Syn/anti-selectivity control using catalysts with the same absolute backbone chirality

• Jose I. Martínez,
• Uxue Uria,
• Maria Muñiz,
• Efraím Reyes,
• Luisa Carrillo and
• Jose L. Vicario

Beilstein J. Org. Chem. 2015, 11, 2577–2583, doi:10.3762/bjoc.11.277

• biological systems [1]. As a consequence, the last decades have witnessed an enormous progress directed toward the development of synthetic methodology for the preparation of chiral molecules as single enantiomers with a well-defined three-dimensional arrangement. In this scenario, asymmetric catalysis

Smart molecules for imaging, sensing and health (SMITH)

• Bradley D. Smith

Beilstein J. Org. Chem. 2015, 11, 2540–2548, doi:10.3762/bjoc.11.274

• supramolecular community should build much larger synthetic hosts. How can this be done? One approach is to create covalently linked polymers that are programmed to fold up into three dimensional structures that mimic the topologies of proteins and nucleic acids. Perhaps a more facile fabrication strategy is to

Preparation of Pickering emulsions through interfacial adsorption by soft cyclodextrin nanogels

• Shintaro Kawano,
• Toshiyuki Kida,
• Mitsuru Akashi,
• Hirofumi Sato,
• Motohiro Shizuma and
• Daisuke Ono

Beilstein J. Org. Chem. 2015, 11, 2355–2364, doi:10.3762/bjoc.11.257

• three-dimensional spherical structure collapses and flattens during the drying process. The image appears to have a “deflated balloon” structure, indicating that CD nanogel particles can be fused together via interconnections after adsorption at the oil–water interface. The “deflated balloon” structures

Life lessons

• Jonathan R. Nitschke

Beilstein J. Org. Chem. 2015, 11, 2350–2354, doi:10.3762/bjoc.11.256

• space, going from a one-dimensional linear array (Figure 1a) [7] to a two-dimensional grid (Figure 1b) [8] to a three-dimensional tetrahedron (Figure 1c) [9], which turned out to be capable of binding white phosphorus (P4) and rendering it air-stable [10]! The work went well at Geneva – we were

Ru complexes of Hoveyda–Grubbs type immobilized on lamellar zeolites: activity in olefin metathesis reactions

• Hynek Balcar,
• Naděžda Žilková,
• Martin Kubů,
• Michal Mazur,
• Zdeněk Bastl and
• Jiří Čejka

Beilstein J. Org. Chem. 2015, 11, 2087–2096, doi:10.3762/bjoc.11.225

• article we discuss the immobilization of HGIIN+Cl− and HGIIN+PF6− (Figure 1) on zeolitic supports having MWW structure: MCM-22 (three-dimensional), MCM-56 (unilamellar), and MCM-36 (pillared) and the activity of corresponding catalysts (i) in RCM of (−)-β-citronellene and N,N-diallyl-2,2,2

• utilizes chemically selective hydrolysis of Ge–O bonds to form layers from three-dimensional zeolites [28]. Generally, two-dimensional zeolites possess BET areas above 500–600 m2/g, which is comparable with mesoporous molecular sieves. The surface of two-dimensional zeolites can be modified with various

Supramolecular chemistry: from aromatic foldamers to solution-phase supramolecular organic frameworks

• Zhan-Ting Li

Beilstein J. Org. Chem. 2015, 11, 2057–2071, doi:10.3762/bjoc.11.222

• favorite. Many years later at Fudan, I initiated a project to study the potential of its radical cation stacking in controlling the folded conformation of linear molecules and two- and three-dimensional supramolecular polymers and frameworks. My life in the small town of Odense was also memorable. Its calm

• Li+. Solution-phase supramolecular metal–organic frameworks (MOFs) Periodicity is the key feature of single crystals in which molecules arrange repeatedly in the three-dimensional space. Porous crystals such as metal–organic frameworks (MOFs) exhibit many unique properties mainly due to their large

Star-shaped tetrathiafulvalene oligomers towards the construction of conducting supramolecular assembly

• Masahiko Iyoda and
• Masashi Hasegawa

Beilstein J. Org. Chem. 2015, 11, 1596–1613, doi:10.3762/bjoc.11.175

• bonding, metal coordination, CT interaction, π···π stacking, van der Waals interaction, etc.) play an important role in the formation of the three-dimensional (3D) crystal structures [5]. For the construction of nanostructured objects, π···π, S···S, and other weak intermolecular interactions first

Structure and conformational analysis of spiroketals from 6-O-methyl-9(E)-hydroxyiminoerythronolide A

• Ana Čikoš,
• Irena Ćaleta,
• Dinko Žiher,
• Mark B. Vine,
• Ivaylo J. Elenkov,
• Marko Dukši,
• Dubravka Gembarovski,
• Marina Ilijaš,
• Snježana Dragojević,
• Ivica Malnar and
• Sulejman Alihodžić

Beilstein J. Org. Chem. 2015, 11, 1447–1457, doi:10.3762/bjoc.11.157

• -d6 and CDCl3 attest to their close spatial proximity (2.0–2.6 Å). Other characteristic observed nOe interactions are: very strong 4-H↔6-Me, 8-Me↔10-Me, 3-H↔4-Me, 5-H↔7-Hax, 5-H↔6-Me, 5-H↔10-Me correlations and a weak interaction between 4-Me and 5-H. To simplify the generation of the three

• -dimensional structure and avoid time-consuming molecular dynamic simulations, the starting model of 2 was created from the X-ray single crystal structure of tricyclic spiroketal (CSD entry: ERYTHR) [55], with replacement of the 6-hydroxy group by 6-methoxy. A two-step minimization process consisted of adding

Selected synthetic strategies to cyclophanes

• Sambasivarao Kotha,
• Mukesh E. Shirbhate and
• Gopalkrushna T. Waghule

Beilstein J. Org. Chem. 2015, 11, 1274–1331, doi:10.3762/bjoc.11.142

• -workers have reported the synthesis of chiral cyclophyne 58 through the Eglinton coupling reaction [95]. A tandem inter- and intramolecular Eglinton coupling reaction affords the enantiopure three-dimensional cyclophyne 58 with a large cavity size (Figure 7). Glaser–Hay coupling: In 2010, Collins and co

• derivative 159 (Scheme 24). To prepare π-conjugated three-dimensional molecules with potential isoelectronic properties and facile processibility, Kurata and co-workers [146] reported sexithiophene 163, a bridged cage shaped compound (Scheme 25). Its synthesis involves a Suzuki–Miyaura coupling reaction

Synthesis of photoresponsive cholesterol-based azobenzene organogels: dependence on different spacer lengths

• Yuchun Ren,
• Bin Wang and
• Xiuqing Zhang

Beilstein J. Org. Chem. 2015, 11, 1089–1095, doi:10.3762/bjoc.11.122

• . Obviously, the gel from ethanol mainly shows a similar flower-like morphology. When we focused on the isopropanol xerogel, we could see that there are many regularly three-dimensional network structures. In 1-butanol, the organogelator molecules in the gel phase were self-assembled into tightly staked rods

Quarternization of 3-azido-1-propyne oligomers obtained by copper(I)-catalyzed azide–alkyne cycloaddition polymerization

• Shun Nakano,
• Akihito Hashidzume and
• Takahiro Sato

Beilstein J. Org. Chem. 2015, 11, 1037–1042, doi:10.3762/bjoc.11.116

• gyromagnetic ratio, and τ the 90°–180° pulse distance (a), and the concentration dependency of apparent self-diffusion coefficient D for the oligoAPMe in DMSO-d6 at 30 °C (b). A typical example of the three-dimensional structure of oligoAPMe of n = 11 built with ChemBio3D software (version 13.0) (a), a rodlike

Terminal lipophilization of a unique DNA dodecamer by various nucleolipid headgroups: Their incorporation into artificial lipid bilayers and hydrodynamic properties

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2015, 11, 913–929, doi:10.3762/bjoc.11.103

• the three-dimensional structure of the latter, (ii) from the length of the lipophilic moiety and (iii) from the position of the lipid residue at the nucleoside. For the LONs 10 and 11 we observed that the elongation of the C-atom chain length from 5 to 17 does not necessarily lead to an enhancement of

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• µM, unbound peptide could not be detected anymore whereas single and unbound nanoparticles are observed (Figure 7c). The obtained assemblies show a highly ordered adsorption of nanoparticles on the surface of the fiber in a three dimensional manner, which was supported by stereo Cryo TEM