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

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• those observed for peptides and proteins (see above). Current and potential medical and biological applications As mentioned earlier, CDs are able to complex biomolecules. Unfortunately, the strength of this behavior depends of the molecular structure. For instance, the binding constants increased in

A self-assembled cyclodextrin nanocarrier for photoreactive squaraine

• Ulrike Kauscher and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2016, 12, 2535–2542, doi:10.3762/bjoc.12.248

• . Additionally hexyl alkane chains were introduced on both N-termini. Santos et al. showed that these lead to a higher intersystem crossing compared to shorter alkane chains [20][21]. The analytical data for AdSq (see Supporting Information File 1) are consistent with the molecular structure shown in Figure 1

Sydnone C-4 heteroarylation with an indolizine ring via Chichibabin indolizine synthesis

• Florin Albota,
• Mino R. Caira,
• Constantin Draghici,
• Florea Dumitrascu and
• Denisa E. Dumitrescu

Beilstein J. Org. Chem. 2016, 12, 2503–2510, doi:10.3762/bjoc.12.245

• spectroscopy, with further supporting X-ray structural elucidation of the representative compound 9d, which displays an interesting packing feature described below. The molecular structure and numbering scheme for 9d are shown in Figure 2a. Principal torsion angles that describe the molecular conformation

• , 12c was selected for X-ray structural elucidation. Figure 4 shows the molecular structure, whose conformation is partially stabilized by two significant intramolecular hydrogen bonds. These are found between C24–H24A···O14 and C25–H25B···O28, with remarkably short C···O distances of 2.787(2) and 2.912

• significant intramolecular distortion in the other. Sydnone-pyrroloazines hybrids 1, indolizine (2), sydnone 3, indolizines attached directly to C-4 of a sydnone 4, indolizines attached via a keto group to C-4 of a sydnone 5. The molecular structure of 9d with thermal ellipsoids drawn at the 50% probability

Synthesis, dynamic NMR characterization and XRD studies of novel N,N’-substituted piperazines for bioorthogonal labeling

• Constantin Mamat,
• Marc Pretze,
• Matthew Gott and
• Martin Köckerling

Beilstein J. Org. Chem. 2016, 12, 2478–2489, doi:10.3762/bjoc.12.242

• ). Molecular structure of compound 3a (ORTEP plot with 50% probability level). Molecular structure of compound 4b (ORTEP plot with 50% probability level). Superimposition fit of the two conformers, which exist in the ratio of 1:1 in the solid state structure of compound 4b (label A marks the atoms of the

Isosorbide and dimethyl carbonate: a green match

• Fabio Aricò and
• Pietro Tundo

Beilstein J. Org. Chem. 2016, 12, 2256–2266, doi:10.3762/bjoc.12.218

• applications, but also by its high reactivity and peculiar molecular structure [89]. Isosorbide has an open-book V-shaped configuration formed by two cis-connected tetrahydrofuran rings with an opening angle of 120°. The four oxygen atoms incorporated in the structure are in β-position to each other [61][62

Diastereoselective synthesis of 3,4-dihydro-2H-pyran-4-carboxamides through an unusual regiospecific quasi-hydrolysis of a cyano group

• Mikhail Yu. Ievlev,
• Oleg V. Ershov,
• Mikhail Yu. Belikov,
• Angelina G. Milovidova,
• Viktor A. Tafeenko and
• Oleg E. Nasakin

Beilstein J. Org. Chem. 2016, 12, 2093–2098, doi:10.3762/bjoc.12.198

• biological studies. The molecular structure of 2a with atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are drawn as small spheres of arbitrary radii. An exclusive approach to 3,4-dihydro-2H-pyran-4-carboxamides from non-pyran sources. Known approach to pyran

Bridgehead vicinal diallylation of norbornene derivatives and extension to propellane derivatives via ring-closing metathesis

• Sambasivarao Kotha and
• Rama Gunta

Beilstein J. Org. Chem. 2016, 12, 1877–1883, doi:10.3762/bjoc.12.177

• allyl groups and oxa-bowl/propellane hybrids. Since non-flattened molecules are implicated in biological systems, our results would be useful in drug design [42]. Retrosynthetic approach to propellane derivatives. The molecular structure of 1a, with displacement ellipsoids drawn at the 50% probability

From supramolecular chemistry to the nucleosome: studies in biomolecular recognition

• Marcey L. Waters

Beilstein J. Org. Chem. 2016, 12, 1863–1869, doi:10.3762/bjoc.12.175

• chemistry in college at UCSD (here’s how not to teach genchem: my textbook listed all compounds by their molecular formula, so, for example, acetic acid was C2H4O2. Thus, the fact that molecular structure has anything to do with reactivity was completely left out). I actually started out as a bioengineering

Synthesis and properties of fluorescent 4′-azulenyl-functionalized 2,2′:6′,2″-terpyridines

• Adrian E. Ion,
• Liliana Cristian,
• Mariana Voicescu,
• Masroor Bangesh,
• Augustin M. Madalan,
• Daniela Bala,
• Constantin Mihailciuc and
• Simona Nica

Beilstein J. Org. Chem. 2016, 12, 1812–1825, doi:10.3762/bjoc.12.171

• ; found: C, 83.4; H, 5.2; N, 10.8; MS (ESI+, m/z): 402 (100, MH+), 403 (30%). Molecular structure and numbering scheme of 4′-(1-azulenyl)-2,2′:6′,2″-terpyridine (4a, left) and 4′-(1-(4,6,8-trimethyl-azulenyl)-2,2′:6′,2″-terpyridine (4b, right). Packing diagram for 4a showing the π–π stacking and CH–π

Effect of the π-conjugation length on the properties and photovoltaic performance of A–π–D–π–A type oligothiophenes with a 4,8-bis(thienyl)benzo[1,2-b:4,5-b′]dithiophene core

• Ni Yin,
• Lilei Wang,
• Yi Lin,
• Jinduo Yi,
• Lingpeng Yan,
• Junyan Dou,
• Hai-Bo Yang,
• Xin Zhao and
• Chang-Qi Ma

Beilstein J. Org. Chem. 2016, 12, 1788–1797, doi:10.3762/bjoc.12.169

• molecular structure and properties of the conjugated molecules with BDT core, we report here a series of A–π–D–π–A-type conjugated molecules with a regioregular oligo(3-hexylthiophene) chain as the π-bridge unit. The optical and electrochemical properties of these compounds were systematically investigated

On the cause of low thermal stability of ethyl halodiazoacetates

• Magnus Mortén,
• Martin Hennum and
• Tore Bonge-Hansen

Beilstein J. Org. Chem. 2016, 12, 1590–1597, doi:10.3762/bjoc.12.155

• stability of diazo compounds is highly influenced by the α-substituents present in their molecular structure. A simplified illustration of the thermal stabilities for some selected classes of diazo compounds is shown in Figure 1. Aliphatic, non-stabilized diazo compounds are thermally labile and usually

Flow carbonylation of sterically hindered ortho-substituted iodoarenes

• Carl J. Mallia,
• Gary C. Walter and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2016, 12, 1503–1511, doi:10.3762/bjoc.12.147

• by Cross et al. (Figure 2) [18]. The molecular structure of 1 comprises of a palladium atom with near perfect square planar geometry with a slight out of plane displacement of Br and C(1) where the Br–Pd–C(1) angle is 170.9°. As a whole, the molecule has approximate Cs symmetry with the PPh3 ligands

• under the supervision of dedicated staff and all associated safety measures were taken. Parr autoclave was pressure tested at 80 bar before use. Steric interactions of the carbon monoxide coordination to the aryl complex intermediate. A) molecular structure of complex 1; B) ball and stick representation

Star-shaped and linear π-conjugated oligomers consisting of a tetrathienoanthracene core and multiple diketopyrrolopyrrole arms for organic solar cells

• Hideaki Komiyama,
• Chihaya Adachi and
• Takuma Yasuda

Beilstein J. Org. Chem. 2016, 12, 1459–1466, doi:10.3762/bjoc.12.142

• approximately 40–60 nm. Moreover, the PCEs of TTA-DPP4-based devices were higher than those of TTA-DPP2, presumably because of its larger absorption coefficient resulting from its star-shaped molecular structure with a two-dimensionally expanded π-conjugated backbone. Conclusion In this study, the first attempt

• highly different from that of the reported general polymer- and small-molecule-based OSCs. A star-shaped molecular structure containing a two-dimensionally extended π-conjugated system is a promising electronic system for designing photovoltaic organic materials, as a result of its excellent

Stereoselective synthesis of tricyclic compounds by intramolecular palladium-catalyzed addition of aryl iodides to carbonyl groups

• Jakub Saadi,
• Christoph Bentz,
• Kai Redies,
• Dieter Lentz,
• Reinhold Zimmer and
• Hans-Ulrich Reissig

Beilstein J. Org. Chem. 2016, 12, 1236–1242, doi:10.3762/bjoc.12.118

• the discovered aryl iodide addition to carbonyl groups may be limited it is attractive since only low catalyst loadings are required and interesting products are formed with high stereoselectivity. Molecular structure (ORTEP, [14]) of compound 12a (thermal ellipsoids at 50% probability). Molecular

• structure (ORTEP, [14]) of compound 14a (thermal ellipsoids at 50% probability). Molecular structure (ORTEP, [14]) of compound 15a (thermal ellipsoids at 50% probability). Molecular structure (ORTEP [14]) of compound 15b (thermal ellipsoids at 50% probability). Planned Heck reaction of A to compound B and

Synthesis of a deuterated probe for the confocal Raman microscopy imaging of squalenoyl nanomedicines

• Eric Buchy,
• Branko Vukosavljevic,
• Maike Windbergs,
• Dunja Sobot,
• Camille Dejean,
• Simona Mura,
• Patrick Couvreur and
• Didier Desmaële

Beilstein J. Org. Chem. 2016, 12, 1127–1135, doi:10.3762/bjoc.12.109

• confocal Raman microspectroscopy of cells had to wait until laser technology and mathematical image processing have made enough progress [24][25]. In contrast to fluorescence spectroscopy, Raman spectroscopy is label-free, as its scattering effect is unique for a specific molecular structure. Raman spectra

Towards the total synthesis of keramaphidin B

• Pavol Jakubec,
• Alistair J. M. Farley and
• Darren J. Dixon

Beilstein J. Org. Chem. 2016, 12, 1096–1100, doi:10.3762/bjoc.12.104

• murine leukemia cells (IC50 0.28 μg/mL) [1]. It is a member of the manzamine alkaloids and has an exquisite molecular structure comprising a 6,6,6,11,13 pentacycle possessing 4 stereogenic centres including one quaternary centre (Figure 1). In 1992, two years before its isolation, Baldwin and Whitehead

Antibacterial structure–activity relationship studies of several tricyclic sulfur-containing flavonoids

• Lucian G. Bahrin,
• Henning Hopf,
• Peter G. Jones,
• Laura G. Sarbu,
• Cornelia Babii,
• Alina C. Mihai,
• Marius Stefan and
• Lucian M. Birsa

Beilstein J. Org. Chem. 2016, 12, 1065–1071, doi:10.3762/bjoc.12.100

• fluorine atom in their molecular structure. This suggests that the activity against Gram negative bacteria is less dependent on the nature of the introduced heavier halogen (Cl, Br or I). Compound 1 was found to be slightly more potent against S. aureus in terms of bacteriostatic properties than the other

• properties against S. aureus, albeit they were less potent than 1. Moreover, the halogen atoms present in their molecular structure did not greatly influence the MBC values; six out of the seven new flavonoids leading to the same result (exception 5e, Table 5, entry 6). This also applies to the bactericidal

• molecular structure of tricyclic flavonoid 1. The syn and anti-isomers of flavanones 4. Molecular structures of 4d (left) and 4f (right). Ellipsoids represent 50% probability levels [24]. Molecular structure of 5a (left, both independent molecules) and 5b (right, one of two independent molecules

Cationic Pd(II)-catalyzed C–H activation/cross-coupling reactions at room temperature: synthetic and mechanistic studies

• Takashi Nishikata,
• Alexander R. Abela,
• Shenlin Huang and
• Bruce H. Lipshutz

Beilstein J. Org. Chem. 2016, 12, 1040–1064, doi:10.3762/bjoc.12.99

• acetonitrile, as confirmed by NMR. The facile formation of this species supports the intermediacy of a palladacycle in the catalytic cycle. The structure of the isolated palladacycle was confirmed by X-ray analysis [216]. An ORTEP plot for palladacycle 6 is shown in Figure 7. The molecular structure consists

Reactions of N,3-diarylpropiolamides with arenes under superelectrophilic activation: synthesis of 4,4-diaryl-3,4-dihydroquinolin-2(1H)-ones and their derivatives

• Larisa Yu. Gurskaya,
• Diana S. Belyanskaya,
• Dmitry S. Ryabukhin,
• Denis I. Nilov,
• Irina A. Boyarskaya and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2016, 12, 950–956, doi:10.3762/bjoc.12.93

• . Molecular structure of 2f (ellipsoid contours of probability levels are 50%). LUMO of species C1 and D1. Transformations of 3-aryl-N-(aryl)propiolamides 1 into 4-arylquinolin-2(1H)-ones 3 or 4,4-diaryl-3,4-dihydroquinolin-2(1H)-ones 2 in the presence of arenes through the formation of intermediate cations A

Separation and identification of indene–C₇₀ bisadduct isomers

• Bolong Zhang,
• Jegadesan Subbiah,
• David J. Jones and
• Wallace W. H. Wong

Beilstein J. Org. Chem. 2016, 12, 903–911, doi:10.3762/bjoc.12.88

• electron donor and an electron acceptor) with the film nanostructure being extremely important for the device performance. Molecular structure of IC60BA and IC70BA. a) Schlegel diagram of C70; b) illustrations of three regioisomers of IC70BA and their geometrical isomers. Chromatograms of IC70BA mixture

Bi- and trinuclear copper(I) complexes of 1,2,3-triazole-tethered NHC ligands: synthesis, structure, and catalytic properties

• Shaojin Gu,
• Jiehao Du,
• Jingjing Huang,
• Huan Xia,
• Ling Yang,
• Weilin Xu and
• Chunxin Lu

Beilstein J. Org. Chem. 2016, 12, 863–873, doi:10.3762/bjoc.12.85

• diffusion of diethyl ether into an acetonitrile solution of the copper complex at room temperature. Green-yellow single crystals of complex 2 suitable for an X-ray diffraction study were grown from acetonitrile solution and diethyl ether. The molecular structure of complex 2 in the solid state is depicted

• -ray diffraction study were grown from acetonitrile solution and diethyl ether. The molecular structure of complex 3 is depicted in Figure 2. Complex 3 crystallizes in the monoclinic space group C2/c. The Cu(I) complex contains two crystallographically equivalent Cu centers, which are doubly bridged by

• , which are comparable to the known Cu(I)–NHC complexes [36][37][38][39]. The Cu1–Cu2 separation is 2.7867(7) Å, showing a weak metal−metal interaction. The molecular structure of complex 4 is depicted in Figure 3. Complex 4 consists of the cation unit [Cu2(L3)2]2+ and two hexafluorophosphate anions

A modular approach to neutral P,N-ligands: synthesis and coordination chemistry

• Vladislav Vasilenko,
• Torsten Roth,
• Clemens K. Blasius,
• Sebastian N. Intorp,
• Hubert Wadepohl and
• Lutz H. Gade

Beilstein J. Org. Chem. 2016, 12, 846–853, doi:10.3762/bjoc.12.83

• [2a-PdCl2] and [2a-PdCl]2(BF4)2, and molecular structure of the dimer [2a-PdCl]22+. Anisotropic displacement ellipsoids set at the 50% probability level. Hydrogen atoms have been omitted for clarity. (B) Formation of Pd(allyl) complexes of ligands 2a, 5, and 7. Reaction conditions: (i) DCM, [Pd(cod

Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents

• Daniel Wiegmann,
• Stefan Koppermann,
• Marius Wirth,
• Giuliana Niro,
• Kristin Leyerer and
• Christian Ducho

Beilstein J. Org. Chem. 2016, 12, 769–795, doi:10.3762/bjoc.12.77

• ]. All bacteria, i.e., Gram-positive and Gram-negative congeners, have a cell wall as part of their cell envelope. While its thickness differs among bacteria – Gram-positive strains usually have a thicker cell wall relative to Gram-negative ones – the principle molecular structure remains identical

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

• conformation of the compounds in a data set is usually unknown and, therefore, geometry optimization is carried out in a receptor-free environment to generate the molecular structure and, subsequently, the 3D MD´s. While molecular conformation in vacuum is governed by intramolecular interactions, the