Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles

• Ido Azuri,
• Anna Hirsch,
• Anthony M. Reilly,
• Alexandre Tkatchenko,
• Shai Kendler,
• Oded Hod and
• Leeor Kronik

Beilstein J. Org. Chem. 2018, 14, 381–388, doi:10.3762/bjoc.14.26

• for the mixed-polymorph TNT crystal, taken from [16], as captured by a data analysis program. All other spectra are computed for: (O) the orthorhombic structure and (M) the monoclinic structure, calculated with and without TS-vdW interactions. Colored horizontal lines appearing below various

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• /RNA helical axis. The other techniques mentioned in the Introduction (VCD, FDCD, and CPL) will be treated more shortly because of their relatively less widespread use in the context of interest. The particular aspects of data analysis and interpretation will be discussed for each method, while general

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• /min, continuing with a linear gradient of 5–70% ACN over 25 min, flow rate: 20.0 mL/min. UV-detection occurred at 220 nm. Data analysis was performed with an EZChrom Elite-Software (Version 3.3.2 SP2, Agilent Technologies, Santa Clara, CA, USA). The fractions containing pure peptide were combined

Binding abilities of a chiral calix[4]resorcinarene: a polarimetric investigation on a complex case of study

• Marco Russo and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2698–2709, doi:10.3762/bjoc.13.268

• region only) and their 1:1 complex (purple). Possible depiction of the 1:1 and 1:2 complexes of 12. Binding constants for CAP anions with guests 6–12. Supporting Information Supporting Information File 396: Mathematical details on the derivation of the equations used for polarimetric data analysis, and

The effect of milling frequency on a mechanochemical organic reaction monitored by in situ Raman spectroscopy

• Patrick A. Julien,
• Ivani Malvestiti and
• Tomislav Friščić

Beilstein J. Org. Chem. 2017, 13, 2160–2168, doi:10.3762/bjoc.13.216

• reaction component xn (Figure 3). It is important to note that the herein presented approach to data analysis assumes that the Raman spectra of individual reactants or products are not significantly affected by the degree of crystallinity or changes in the composition of the reaction mixture. While Raman

Synthesis and enzymatic ketonization of the 5-(halo)-2-hydroxymuconates and 5-(halo)-2-hydroxy-2,4-pentadienoates

• Tyler M. M. Stack,
• William H. Johnson Jr. and
• Christian P. Whitman

Beilstein J. Org. Chem. 2017, 13, 1022–1031, doi:10.3762/bjoc.13.101

• equation. The initial rates were determined in triplicate, averaged, plotted versus initial substrate concentration, and fit to determine kcat and Km. Nonlinear regression data analysis was performed using Mathematica (Wolfram Research, Inc., Mathematica, Version 8.0, Champaign, IL 2010). The 4-OT

Use of costic acid, a natural extract from Dittrichia viscosa, for the control of Varroa destructor, a parasite of the European honey bee

• Kalliopi Sofou,
• Demosthenis Isaakidis,
• Apostolos Spyros,
• Anita Büttner,
• Athanassios Giannis and
• Haralambos E. Katerinopoulos

Beilstein J. Org. Chem. 2017, 13, 952–959, doi:10.3762/bjoc.13.96

• experiments which were performed in five replicates. In both cases the solvent was allowed to evaporate before covering the vials. The mortality of mites was recorded under a stereoscope binocular set after 5, 8, and 12 hours. Data analysis. All graphs and statistical analysis (one way ANOVA followed by the

Synthesis of multi-lactose-appended β-cyclodextrin and its cholesterol-lowering effects in Niemann–Pick type C disease-like HepG2 cells

• Keiichi Motoyama,
• Rena Nishiyama,
• Yuki Maeda,
• Taishi Higashi,
• Yoichi Ishitsuka,
• Yuki Kondo,
• Tetsumi Irie,
• Takumi Era and
• Hidetoshi Arima

Beilstein J. Org. Chem. 2017, 13, 10–18, doi:10.3762/bjoc.13.2

• of Filipin III area to cell area by the fluorescence microscope and BZ-II analyzer. Data analysis Quantitative data was expressed as the mean ± standard error of the mean (S.E.M.), while the statistical comparisons were made using the Scheffe's test. A p-value < 0.05 was considered statistically

The in situ generation and reactive quench of diazonium compounds in the synthesis of azo compounds in microreactors

• Faith M. Akwi and
• Paul Watts

Beilstein J. Org. Chem. 2016, 12, 1987–2004, doi:10.3762/bjoc.12.186

• the azo compound. However, highly alkaline conditions are usually avoided as they lead to diazonium salt decomposition. In the regression summary of the statistical data analysis (Table 2) of the observed data, it is seen from the p-values (0.067 and 0.084) associated with the estimated coefficients

• . The wavelength used for quantification of the 2-naphthol was 349 nm. Data analysis The total volume of samples collected (tvscollected) was calculated by multiplying the total flow rate of the reactant solutions (tfrABC) by the total sample collection time (tcollection). The reaction time was

• calculated by dividing the total reaction space volume i.e. the total volume of the two LTF-MS plates, the PTFE tubing used to join the two mixers and also that leading to the final outlet: the point of sample collection by the total flow rate of reactant solutions (tfrABC). For purposes of data analysis

Beta-hydroxyphosphonate ribonucleoside analogues derived from 4-substituted-1,2,3-triazoles as IMP/GMP mimics: synthesis and biological evaluation

• Tai Nguyen Van,
• Audrey Hospital,
• Corinne Lionne,
• Lars P. Jordheim,
• Charles Dumontet,
• Christian Périgaud,
• Laurent Chaloin and
• Suzanne Peyrottes

Beilstein J. Org. Chem. 2016, 12, 1476–1486, doi:10.3762/bjoc.12.144

• acids. Thus, nucleoside phosphonate analogues 1a–q (Scheme 2) were isolated as their sodium salts with yields ranging from 21 to 77% over three steps. Structures of all final compounds were unambiguously confirmed on the basis of NMR (1H, 13C and 31P) and MS (MS and HRMS) data analysis (see Supporting

Strecker degradation of amino acids promoted by a camphor-derived sulfonamide

• M. Fernanda N. N. Carvalho,
• M. João Ferreira,
• Ana S. O. Knittel,
• Maria da Conceição Oliveira,
• João Costa Pessoa,
• Rudolf Herrmann and
• Gabriele Wagner

Beilstein J. Org. Chem. 2016, 12, 732–744, doi:10.3762/bjoc.12.73

• done with the program PCGamess (version 7.1) [40][41], using B3LYP/6-31G** for neutral compounds and B3LYP/6-31++G** for anions. Zero-point energies and basis set superposition errors were not included since no high precision numerical results were needed. Data analysis and visualization was done with

Polydisperse methyl β-cyclodextrin–epichlorohydrin polymers: variable contact time ¹³C CP-MAS solid-state NMR characterization

• Isabelle Mallard,
• Davy Baudelet,
• Franca Castiglione,
• Monica Ferro,
• Walter Panzeri,
• Enzio Ragg and
• Andrea Mele

Beilstein J. Org. Chem. 2015, 11, 2785–2794, doi:10.3762/bjoc.11.299

• , while for times longer than 250 μs the value of the increment was progressively increased. All the experiments were performed at 298 K. The data analysis was performed using the OriginPro software (9.0 version). The NMR spectra were deconvoluted using OriginPro software (9.0 version). Each peak was

Bromotyrosine-derived alkaloids from the Caribbean sponge Aplysina lacunosa

• Qun Göthel,
• Thanchanok Sirirak and
• Matthias Köck

Beilstein J. Org. Chem. 2015, 11, 2334–2342, doi:10.3762/bjoc.11.254

• aplysinin B (3), together with 15 known compounds (4–18) were isolated from the sponge Aplysina lacunosa collected from Stirrup Cay, Bahamas. The structures of the isolated compounds were identified on the basis of MS and NMR data analysis. The 13C NMR assignment of spirocyclohexadienylisoxazoline moieties

Cholesterol lowering effects of mono-lactose-appended β-cyclodextrin in Niemann–Pick type C disease-like HepG2 cells

• Keiichi Motoyama,
• Yumi Hirai,
• Rena Nishiyama,
• Yuki Maeda,
• Taishi Higashi,
• Yoichi Ishitsuka,
• Yuki Kondo,
• Tetsumi Irie,
• Takumi Era and
• Hidetoshi Arima

Beilstein J. Org. Chem. 2015, 11, 2079–2086, doi:10.3762/bjoc.11.224

• cells was detected by a KEYENCE Biozero BZ-8000, a fluorescence microscope. The fluorescence intensities were determined by a BZ-II analyzer (Keyence, Osaka, Japan). Data analysis The experimental results are shown as means ± S.E.M. Significance levels for comparisons between samples were determined

Cross-metathesis of polynorbornene with polyoctenamer: a kinetic study

• Yulia I. Denisova,
• Maria L. Gringolts,
• Alexander S. Peregudov,
• Liya B. Krentsel,
• Ekaterina A. Litmanovich,
• Arkadiy D. Litmanovich,
• Eugene Sh. Finkelshtein and
• Yaroslav V. Kudryavtsev

Beilstein J. Org. Chem. 2015, 11, 1796–1808, doi:10.3762/bjoc.11.195

• data analysis undertaken in the present study makes it possible to outline the cross-metathesis scenario for the mixtures of PCOE and PNB in the presence of the Gr-1 catalyst. Contrary to the situation with a corresponding monomer mixture, where this catalyst first initiates vigorous polymerization of

Azobenzene-based inhibitors of human carbonic anhydrase II

• Leander Simon Runtsch,
• David Michael Barber,
• Peter Mayer,
• Michael Groll,
• Dirk Trauner and
• Johannes Broichhagen

Beilstein J. Org. Chem. 2015, 11, 1129–1135, doi:10.3762/bjoc.11.127

• purification, crystallization and binding data analysis. P.M. collected X-ray datasets of 1a–i and solved the structures. M.G. collected hCAII X-ray dataset and solved the structure. J.B., D.M.B and D.T. wrote the manuscript with input from all authors.

Adsorption mechanism and valency of catechol-functionalized hyperbranched polyglycerols

• Stefanie Krysiak,
• Qiang Wei,
• Klaus Rischka,
• Andreas Hartwig,
• Rainer Haag and
• Thorsten Hugel

Beilstein J. Org. Chem. 2015, 11, 828–836, doi:10.3762/bjoc.11.92

• Inverse Optical Lever Sensitivity (InvOLS) of the functionalized cantilever was determined from the indentation slope and the spring constant calibrated with the thermal noise method according to [30]. The tip velocity was 1 µm/s and the standard dwell time was 1 s. Data analysis The data handling and

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

• constant velocities between 100 nm/s and 10 µm/s using a grid of different spots on the surface. Force–distance curves were processed as described in [27]. In short, signals were fitted according to the wormlike-chain model using Hooke, a Python-based force spectroscopy data analysis program [56]. Most

Probing multivalency in ligand–receptor-mediated adhesion of soft, biomimetic interfaces

• Stephan Schmidt,
• Hanqing Wang,
• Daniel Pussak,
• Simone Mosca and
• Laura Hartmann

Beilstein J. Org. Chem. 2015, 11, 720–729, doi:10.3762/bjoc.11.82

• internal reflections and a Zeiss AxiocamHRm camera were used to image the RICM patterns. To conduct the JKR measurements of the adhesion energies, both the contact radius and the particle radius were measured. Image processing and data analysis were done using the image analysis software ImageJ (public

Fluoride-driven ‘turn on’ ESPT in the binding with a novel benzimidazole-based sensor

• Kai Liu,
• Xiaojun Zhao,
• Qingxiang Liu,
• Jianzhong Huo,
• Bolin Zhu and
• Shihua Diao

Beilstein J. Org. Chem. 2015, 11, 563–567, doi:10.3762/bjoc.11.61

• ). Synthesis of sensor BIP. Possible binding mode between BIP and fluoride. Supporting Information Supporting Information File 242: Data analysis of QP after the addition of fluoride. Acknowledgements Authors thank the Tianjin Science & Technology Development Fund Planning Project for Colleges and

Effects of RAMEA-complexed polyunsaturated fatty acids on the response of human dendritic cells to inflammatory signals

• Éva Rajnavölgyi,
• Renáta Laczik,
• Viktor Kun,
• Lajos Szente and
• Éva Fenyvesi

Beilstein J. Org. Chem. 2014, 10, 3152–3160, doi:10.3762/bjoc.10.332

• , USA). Fluorescence intensities were measured with FACSCalibur (BD Biosciences). Data analysis was performed with the FlowJo software (Tree Star, Ashland, OR, USA). Determination of GPR120 expression levels GPR120 expression levels were measured by real-time quantitative PCR (Q-PCR). Total RNA was

Synthesis of uniform cyclodextrin thioethers to transport hydrophobic drugs

• Lisa F. Becker,
• Dennis H. Schwarz and
• Gerhard Wenz

Beilstein J. Org. Chem. 2014, 10, 2920–2927, doi:10.3762/bjoc.10.310

• were measured at room temperature by a BrukerBioSpin spectrometer Magnet System 400 MHz Ultra shield plus (1H: 400 MHz, 13C: 100.6 MHz). The chemical shifts are given in parts per million (ppm) in relation to the corresponding solvent signal. The data analysis was performed with SpecManager included in

Preparation and evaluation of cyclodextrin polypseudorotaxane with PEGylated liposome as a sustained release drug carrier

• Kayoko Hayashida,
• Taishi Higashi,
• Daichi Kono,
• Keiichi Motoyama,
• Koki Wada and
• Hidetoshi Arima

Beilstein J. Org. Chem. 2014, 10, 2756–2764, doi:10.3762/bjoc.10.292

• . Korsmeyer–Peppas’s model where Mt/M∞ is fraction of drug release at time t, kP is the release rate constant, and n is the release exponent. Data analysis Data were given as the mean ± S.E. The statistical significance of mean coefficients for the studies was performed by analysis of variance followed by

Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers

• Michael Kurlemann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 2428–2440, doi:10.3762/bjoc.10.253

• before use. The data were analysed using NanoAnalyse Data Analysis version 2.36 (TA Instruments, Waters Corp., Milford, Massachusetts, USA), Microsoft® Excel version 14.07113.5005 as part of Microsoft® Office Professional Plus 2010 (Microsoft Corp., Redmond, Washington, USA) and OriginPro 9.1.0G

The effect of permodified cyclodextrins encapsulation on the photophysical properties of a polyfluorene with randomly distributed electron-donor and rotaxane electron-acceptor units

• Aurica Farcas,
• Ana-Maria Resmerita,
• Pierre-Henri Aubert,
• Flavian Farcas,
• Iuliana Stoica and
• Anton Airinei

Beilstein J. Org. Chem. 2014, 10, 2145–2156, doi:10.3762/bjoc.10.222

• Edinburgh FLS 980 photoluminescence spectrometer with 1 cm quartz cells. A 375 nm pulsed diode laser (EPL-375, maximum average power: 5 mW, pulse width: 73.2 ps) was used as a light source. Decay data analysis was performed by the deconvolution procedure with multiexponential decay models. The quality of