Derivatives of the triaminoguanidinium ion, 3. Multiple N-functionalization of the triaminoguanidinium ion with isocyanates and isothiocyanates

• Jan Szabo,
• Kerstin Karger,
• Nicolas Bucher and
• Gerhard Maas

Beilstein J. Org. Chem. 2014, 10, 2255–2262, doi:10.3762/bjoc.10.234

• range, and therefore, a complete assignment of most of these spectra was not possible. Due to the likely occurrence of several dynamic processes in solution (conformational changes with hindered rotation around single bonds, prototropic tautomerism in the guanidine moiety [1], dynamics of intra- and

Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

• Nattawut Yotapan,
• Chayan Charoenpakdee,
• Pawinee Wathanathavorn,
• Boonsong Ditmangklo,
• Hans-Achim Wagenknecht and
• Tirayut Vilaivan

Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

• Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany 10.3762/bjoc.10.224 Abstract DNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work

• insertion are suggestive of different interactions between the Nile red label and the duplexes. Keywords: click chemistry; deoxyribonucleic acid; DNA bulge; fluorescence; nucleic acids; solvatochromism; Introduction Fluorescent labels are important tools for investigating the structure and dynamics of

Syntheses of ¹⁵N-labeled pre-queuosine nucleobase derivatives

• Jasmin Levic and
• Ronald Micura

Beilstein J. Org. Chem. 2014, 10, 1914–1918, doi:10.3762/bjoc.10.199

• ][7][8]. To explore the binding process of preQ1 base to the RNA and to shed light on the dynamics underpinning this process advanced NMR spectroscopic methods exist for which 15N-labeled preQ1 base derivatives would be highly beneficial. Here, we report efficient routes for the synthesis of three

Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?

• Diogo Vila-Viçosa,
• Oscar Francesconi and
• Miguel Machuqueiro

Beilstein J. Org. Chem. 2014, 10, 1513–1523, doi:10.3762/bjoc.10.156

• several molecular dynamics and constant-pH molecular dynamics simulations in acetonitrile and water to evaluate the conformational space of the receptor and to understand the molecular detail of the receptor–mannoside interaction. The protonation states sampled by the receptor show that the positive

• reason for the higher activity in this solvent. This work also presents a new implementation of the stochastic titration constant-pH molecular dynamics method to a synthetic receptor of sugars and attests its ability to describe the protonation/conformation coupling in these molecules. Keywords

• performances when changing the solvent and to identify the molecular determinants behind the reported high affinities. Simulation methods, namely the so-called constant-pH molecular dynamics (CpHMD) methods, have been used to understand the molecular detail of several phenomena in the last years [15][16][17

Multichromophoric sugar for fluorescence photoswitching

• Stéphane Maisonneuve,
• Rémi Métivier,
• Pei Yu,
• Keitaro Nakatani and
• Juan Xie

Beilstein J. Org. Chem. 2014, 10, 1471–1481, doi:10.3762/bjoc.10.151

• set to 3.1 ps. The instrumental response function was recorded before each decay measurement with a fwhm (full width at half-maximum) of ~25 ps. The fluorescence data were analyzed using the Globals software package developed at the Laboratory for Fluorescence Dynamics at the University of Illinois at

Biantennary oligoglycines and glyco-oligoglycines self-associating in aqueous medium

• Svetlana V. Tsygankova,
• Alexander A. Chinarev,
• Alexander B. Tuzikov,
• Nikolai Severin,
• Alexey A. Kalachev,
• Juergen P. Rabe,
• Alexandra S. Gambaryan and
• Nicolai V. Bovin

Beilstein J. Org. Chem. 2014, 10, 1372–1382, doi:10.3762/bjoc.10.140

• thermodynamically unfavorable contact with water. It was demonstrated for biantennary oligoglycines that a concentration of 0.1 mg/mL is optimal for the study of the dynamics of tectomer growth on a mica surface. At higher concentrations the growth both in solution and on the surface proceeded so rapidly that the

• dynamics study was considered impossible. No tectomer structure was observed under acidic conditions (рН < 5), whereas under neutral and basic conditions the reaction proceeded similarly in terms of both the velocity and the morphology of formed tectomers. The oligoethylene glycol derivatives Н-Glyn-NH

• )10NHGly4-Н was capable of forming tectomers in neutral and basic solutions which were unchanged in an aqueous phase for a long time. Figure 5 demonstrates the dynamics of layer growth on mica with the characteristic formation of islet structures (texp = 0.5 min, Figure 5а), growing laterally (texp = 1 min

A new building block for DNA network formation by self-assembly and polymerase chain reaction

• Holger Bußkamp,
• Sascha Keller,
• Marta Robotta,
• Malte Drescher and
• Andreas Marx

Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

• geometric restriction of the branching unit, the enzymatic generation of complex DNA networks by PCR was feasible. The novel generated DNA networks were investigated by agarose gel electrophoresis, atomic force microscopy, dynamics light scattering, and electron paramagnetic resonance spectroscopy on

• Supporting Information File 1). This DH is variable at different angles because DNA networks were not expected to have spherical morphology in solution [47]. Furthermore, different DH values in the case of branched DNA samples were owed to the dynamics in solution. Comparing scattering intensity of linear

• properties of biological macromolecules, e.g., DNA [48][49][50][51][52][53]. Since the systems studied in the current investigation are diamagnetic, nitroxide labels had to be inserted enzymatically [54][55]. EPR spectra of nitroxide labels are sensitive to dynamics on the picosecond to microsecond

Unusual polymorphism in new bent-shaped liquid crystals based on biphenyl as a central molecular core

• Anna Kovářová,
• Svatopluk Světlík,
• Václav Kozmík,
• Jiří Svoboda,
• Vladimíra Novotná,
• Damian Pociecha,
• Ewa Gorecka and
• Natalia Podoliak

Beilstein J. Org. Chem. 2014, 10, 794–807, doi:10.3762/bjoc.10.75

• dielectric measurements. The dielectric spectroscopy data are unique and presented for the first time in the SmCG phase providing new information about the molecular dynamics. Keywords: bent-shaped; biphenyl core; liquid crystals; mesomorphic behaviour; SmCG phase; Introduction Achiral bent-shaped liquid

Staudinger ligation towards cyclodextrin dimers in aqueous/organic media. Synthesis, conformations and guest-encapsulation ability

• Malamatenia D. Manouilidou,
• Yannis G. Lazarou,
• Irene M. Mavridis and
• Konstantina Yannakopoulou

Beilstein J. Org. Chem. 2014, 10, 774–783, doi:10.3762/bjoc.10.73

• , (iv) structural characterization regarding conformation and dynamics, intra- and intermolecular interactions, self-inclusion and aggregation in water, and ultimately (iv) availability of the individual CD cavities for molecular inclusion. The later has become of critical importance since it has been

Thermodynamically stable [4 + 2] cycloadducts of lanthanum-encapsulated endohedral metallofullerenes

• Yuta Takano,
• Yuki Nagashima,
• M. Ángeles Herranz,
• Nazario Martín and
• Takeshi Akasaka

Beilstein J. Org. Chem. 2014, 10, 714–721, doi:10.3762/bjoc.10.65

• . However, 3b shows a specific absorption band around 700 nm as in the spectrum recorded by the HPLC system shown in Figure 3, indicating its [6,6]-structure. Temperature-dependent dynamics of the [4 + 2] adducts of endohedral metallofullerenes were studied for 4a by dynamic 1H NMR measurements. Although 4a

Cyclic phosphonium ionic liquids

• Sharon I. Lall-Ramnarine,
• Joshua A. Mukhlall,
• James F. Wishart,
• Robert R. Engel,
• Alicia R. Romeo,
• Masao Gohdo,
• Sharon Ramati,
• Marc Berman and
• Sophia N. Suarez

Beilstein J. Org. Chem. 2014, 10, 271–275, doi:10.3762/bjoc.10.22

• cations wherein the room temperature viscosities of the phosphonium salts are approximately one-half of those of their ammonium congeners [7][8][9][10][11]. This difference draws attention to the particular role that the cyclic alkyl functionality plays in IL fluid dynamics in contrast to two linear

• chains. This topic merits further exploration via molecular dynamics simulations [28] and physical studies such as NMR diffusion measurements, nuclear Overhauser effect spectroscopies, and quasi-elastic neutron scattering. As seen for instance for the cyclic ammonium salts, the viscosities of the cyclic

Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of ¹³C chemical shifts

• Simone Di Micco,
• Angela Zampella,
• Maria Valeria D’Auria,
• Carmen Festa,
• Simona De Marino,
• Raffaele Riccio,
• Craig P. Butts and
• Giuseppe Bifulco

Beilstein J. Org. Chem. 2013, 9, 2940–2949, doi:10.3762/bjoc.9.331

• the configurational assignment of plakilactone H. Molecular dynamics and Monte Carlo conformational search calculations were performed on all possible diastereoisomers of 2 (Figure 3) by using the MMFFs [24] force field (MacroModel software package [25]) in the presence of chloroform (continuum model

• absolute configuration at C-7 and C-8, we tried to elucidate the absolute configuration at C-4 and C-6 on plakilactone G (1). The first step was the conformational search of the four possible diastereoisomers (1a–d in Figure 5), obtained with a fixed 7R,8S configuration, by using molecular dynamics (400

• conformational space of plakilactones G and H (1 and 2), we performed Molecular dynamics and Monte Carlo calculations. Molecular dynamics calculations of 1 and 2 were performed at different temperatures (400 and 600 and 800 K for 5 ns (time-step of 1.5 fs) by using the MMFFs [24] force field (MacroModel software

Flow synthesis of phenylserine using threonine aldolase immobilized on Eupergit support

• Jagdish D. Tibhe,
• Hui Fu,
• Timothy Noël,
• Qi Wang,
• Jan Meuldijk and
• Volker Hessel

Beilstein J. Org. Chem. 2013, 9, 2168–2179, doi:10.3762/bjoc.9.254

• development of an enzymatic bioreaction and found that the dynamics of a biochemical reaction can be studied in a few seconds [35]. Although many promising routes have been developed for the synthesis of chiral α-amino alcohols, these often depend on the use of toxic and expensive chiral ligands coupled to

Structure elucidation of β-cyclodextrin–xylazine complex by a combination of quantitative ¹H–¹H ROESY and molecular dynamics studies

• Syed Mashhood Ali,
• Kehkeshan Fatma and
• Snehal Dhokale

Beilstein J. Org. Chem. 2013, 9, 1917–1924, doi:10.3762/bjoc.9.226

• , could be obtained. We calculated the peak intensity ratio from the inter-proton distances for the most stable conformations obtained by molecular dynamics studies in vacuum. The results show that highly accurate structural information can be deduced efficiently by the combined use of quantitative ROESY

• and molecular dynamics analysis. On the other hand, a ROESY spectrum with no spin diffusion can only compliment an averaged ensemble conformation obtained by molecular dynamics which is generally considered ambiguous. Keywords: β-cyclodextrin; inclusion complex; ROESY; simulation studies; xylazine

• here the study of the complexation of β-CD with xylazine (XZ) (Figure 1) in aqueous medium by NMR spectroscopy and molecular dynamics. Xylazine has two rings, one substituted benzene ring which can only partially penetrate the CD cavity due to the presence of two methyl groups and a heterocyclic ring

True and masked three-coordinate T-shaped platinum(II) intermediates

• Manuel A. Ortuño,
• Salvador Conejero and
• Agustí Lledós

Beilstein J. Org. Chem. 2013, 9, 1352–1382, doi:10.3762/bjoc.9.153

• at work in solution. Recently, ab initio molecular dynamics (AIMD) simulations of some representative T-shaped Pt(II) complexes (T5b, A2b and A11a), performed in explicit dichloromethane solvent, have provided a detailed description of the mechanism by which the equivalence of signals takes place

• [106]. Simulations showed that the dynamics of the agostic interaction in solution strongly depends on the complex. Contingent upon the strength of the agostic interaction and the flexibility of the ligand, several events related with the occupation of the fourth coordination site by an agostic bond

Photoionisation of the tropyl radical

• Kathrin H. Fischer,
• Patrick Hemberger,
• Andras Bodi and
• Ingo Fischer

Beilstein J. Org. Chem. 2013, 9, 681–688, doi:10.3762/bjoc.9.77

• Kathrin H. Fischer Patrick Hemberger Andras Bodi Ingo Fischer Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland Süd, 97074 Würzburg, Germany Molecular Dynamics Group, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland 10.3762/bjoc.9.77 Abstract We present a

A computational study of base-catalyzed reactions of cyclic 1,2-diones: cyclobutane-1,2-dione

• Nargis Sultana and
• Walter M. F. Fabian

Beilstein J. Org. Chem. 2013, 9, 594–601, doi:10.3762/bjoc.9.64

• rearrangements of biacetyl and benzil [11]. Car–Parrinello molecular dynamics simulations of the hydrolysis of formamide in basic solution indicated that the traditional view of attack by hydroxide anion rather than a first-solvation-shell water molecule is more likely; however, the more powerful electrophile

A new intermediate in the Prins reaction

• Shinichi Yamabe,
• Takeshi Fukuda and
• Shoko Yamazaki

Beilstein J. Org. Chem. 2013, 9, 476–485, doi:10.3762/bjoc.9.51

• . Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them. Keywords: DFT calculations; hemiacetal intermediate; hydrogen bond; Prins reaction

• to confirm the obtained TS characters, dynamical calculations of a classical trajectory calculation using the atom-centered density matrix propagation molecular dynamics (ADMP) model [35][36][37] on TSs were carried out. Geometries of the TSs at 2000 steps of 0.1 femtoseconds (10−15 seconds) were

New GABA amides activating GABA_A-receptors

• Peter Raster,
• Andreas Späth,
• Svetlana Bultakova,
• Pau Gorostiza,
• Burkhard König and
• Piotr Bregestovski

Beilstein J. Org. Chem. 2013, 9, 406–410, doi:10.3762/bjoc.9.42

• Peter Raster Andreas Spath Svetlana Bultakova Pau Gorostiza Burkhard Konig Piotr Bregestovski Institute of Organic Chemistry, University of Regensburg, D-93040 Regensburg, Germany Inserm-U1106, Brain Dynamics Institute, Mediterranean University, 13005 Marseille, France Institute for Bioengineering

Spin state switching in iron coordination compounds

• Philipp Gütlich,
• Ana B. Gaspar and
• Yann Garcia

Beilstein J. Org. Chem. 2013, 9, 342–391, doi:10.3762/bjoc.9.39

• [135][136]. The possibility of investigating spin fluctuation rates was established with the classical iron(II) complex [Fe(phen)2(NCS)2], polymorph I [135][136]. In another case, fast dynamics have been revealed in the HS regime of the ST coordination polymer [Fe(NH2trz)3](NO3)2 (NH2trz = 4-amino

A new synthetic protocol for coumarin amino acid

• Xinyi Xu,
• Xiaosong Hu and
• Jiangyun Wang

Beilstein J. Org. Chem. 2013, 9, 254–259, doi:10.3762/bjoc.9.30

• the dye BODIPY-Fl to study the dynamics of protein–protein interactions [2]. Wang and co-workers genetically incorporated 1a to a position near to amino acids, which can be phosphorylated to investigate how phosphorylation affects the fluorescence properties of 1a, and the variation in the

Presence or absence of a novel charge-transfer complex in the base-catalyzed hydrolysis of N-ethylbenzamide or ethyl benzoate

• Shinichi Yamabe,
• Wei Guan and
• Shigeyoshi Sakaki

Beilstein J. Org. Chem. 2013, 9, 185–196, doi:10.3762/bjoc.9.22

• -centered density-matrix-propagation molecular dynamics (ADMP) model [57][58][59] were also conducted. Relative energies (ΔEs) and Gibbs free ones (ΔGs) were obtained by single-point calculations of RB3LYP/6-311++G(d,p) {SCRF = PCM, solvent = water} on the RB3LYP/6-31(+)G(d) geometries and their ZPVE and

• . The trajectory calculation may give a different result, if the potential surface at the OH− addition step is shallow. In order to check this point, the ADMP molecular dynamics calculation was made starting from TS1(es) of the ester n = 16. After 800 femtoseconds, the resultant geometry is shown in the

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

• Jutta Erika Helga Köhler and
• Nicole Grczelschak-Mick

Beilstein J. Org. Chem. 2013, 9, 118–134, doi:10.3762/bjoc.9.15

• investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β

• certainly no longer displayed the highly ordered hydrogen bonds of β-CD and benzene occupied many different positions inside the cavity, before it left the β-CD finally at its O2/O3 side. Keywords: AM1; benzene; COSMO-RS; cyclodextrin; hydrogen bonds; inclusion complex; molecular dynamics; quantum

• ). The β-CD dimers are connected with hydrogen bonds on their O2/O3 sides (Figure 1). Investigations of such “flat energy hypersurfaces” due to hydrogen bonds and noncovalent interactions demand several theoretical methods to capture the entire network of forces on which they rely. Molecular dynamics

A bisazobenzene crosslinker that isomerizes with visible light

• Subhas Samanta,
• Harris I. Qureshi and
• G. Andrew Woolley

Beilstein J. Org. Chem. 2012, 8, 2184–2190, doi:10.3762/bjoc.8.246

• residues [24]. The end-to-end distance changes expected upon photoisomerization of the resulting crosslink were estimated by molecular dynamics methods. Figure 1 shows models of compound 2 in trans,trans, trans,cis, and cis,cis-isomeric states. These simulations indicate that the trans,trans and cis,cis

• -isomers (force constant 16). Molecular dynamics runs were performed in vacuo, essentially as described previously [36], with a distance-dependent dielectric constant, and 1–4 scale factors of 0.833 for electrostatic and 0.5 for van der Waals interactions, a step size of 1 fs and 300 K as the simulation

Hydrophobic analogues of rhodamine B and rhodamine 101: potent fluorescent probes of mitochondria in living C. elegans

• Laurie F. Mottram,
• Safiyyah Forbes,
• Brian D. Ackley and
• Blake R. Peterson

Beilstein J. Org. Chem. 2012, 8, 2156–2165, doi:10.3762/bjoc.8.243

• of mitochondria in vivo, including visualization of the dynamics of fusion and fission of these organelles in the germline of living animals. Results and Discussion Synthesis of fluorophores As shown in Scheme 1, the triarylmethane scaffolds of HRB 9 and HR101 10 were synthesized by condensation of

• here is the ability to examine mitochondrial fusion and fission dynamics in the germline of living C. elegans after acute treatment with the hydrophobic rhodamine analogues HRB 9 and HR101 10. In this tissue, genetically encoded proteins are unsuitable for imaging of mitochondria, because transgenes

• of the HRB 9 and HR101 10 fluorophores. Partition constants of fluorophores. Supporting Information Supporting Information File 336: Supplementary time-lapse confocal microscopy video showing dynamics of mitochondrial fusion and fission in a living adult C. elegans animal imaged after treatment with