dataesr/scientific-paragraphs-categorization huggingface dataset:
Preparation of the Analytical Standards To obtain pure avarol and its monoacetylated derivative, we collected several specimens of Dysidea avara and obtained approximately 6. 8 g of freeze-dried material, which was then extracted with a 1:1 (v:v) mixture of dichloromethane and methanol (3 × 50 mL). A total of 1. 6 g of crude extract was obtained after filtration and evaporation of the solvent under reduced pressure. The crude extract was subjected to silica gel flash column chromatography using stepwise elutions with heptane and ethyl acetate. The fraction eluted with a mixture of heptane:ethyl acetate 7:3 (v:v) afforded pure avarol (Figure  1 ) (178 mg) after crystallisation from n-hexane/diethyl ether. The spectral data of the isolated compound (UV, MS, and 1 H and 13 C NMR) were in full agreement with published values  [39].
The 5′-monoacetylavarol (Figure  1 ) was obtained by partial acetylation of avarol following the protocol described in the literature  [40]. The structure of 5′-monoacetylavarol was verified by comparison with the spectral data (UV, MS, and 1 H and 13 C NMR) already published for this compound and the position of the acetyl group was confirmed by long-range heteronuclear correlations observable on NMR spectra (HMBC experiments) of 5′-monoacetylavarol. Both 1D and 2D NMR spectra were recorded in DMSO-d 6 on a Jeol EX 400 spectrometer using standard Jeol pulse sequence programs.
Data Analysis Mass spectrometric data acquisition and processing were performed using Xcalibur-Thermo Fisher Scientific software. All the chemical quantitative analyses were performed using Empower software. Differences in avarol and 5′-monoacetylavarol concentrations with time (fixed factor) were analyzed by means of a permutational analysis of variance (PERMANOVA) using the Euclidean distance, as implemented in the (Primer v. 6 package, Primer E Ltd. , Plymouth, UK). The null distribution of the test statistic in PERMANOVA is produced by permutation, thus relaxing the usual normality assumptions of analysis of variance  [67]. Pair-wise a posteriori comparisons were performed by the program, and the corresponding p-values were adjusted for multiple comparisons following the B-Y (Benjamini and Yekutieli) false discovery rate method  [68].
Cross-Correlation analyses were also performed to check for relationships between monthly concentrations of avarol and 5′-monoacetylavarol with temperature (Systat v. 12 package, Systat Software Inc. , Washington, WA, USA). In these analyses, the correlation was calculated by lagging one series with respect to the other. Positive time-lags indicate correlation of the first series of values with the values obtained in subsequent months of the second series, and the reverse is true for correlations at negative time-lags. The correlation at time-lag = 0 is the usual Pearson correlation. For the analysis of inter-individual variability of avarol and 5′-monoacetylavarol, the non-parametric Kruskal-Wallis test was applied since data did not comply with the assumptions of normality and homogeneity of variances.
Acknowledgments We would like to thank  J. González ,  M. Guardiola ,  M. C. Pineda ,  G. & M. Turon , for their help in the sampling. Financial support was provided by the projects BENTHOMICS ( CTM2010-22218-C02 ) from the  Ministerio de Economía y Competitividad of the Spanish Government (MICINN)  and  SGR2009-655  from the  Generalitat de Catalunya. SC was funded by a  Beatriu de Pinós Postdoctoral Fellowship of the Autonomous Government of Catalonia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
The NP core size information obtained from SAXS data allowed for calculation of the graing density of each different polymer used to coat the NPs. TGA experiments were performed using a Q500 V5. 3 Build 171 TGA apparatus (TA Instruments, USA). Typical samples comprised 1. 5 to 3 mg of dry NP powder. The samples were heated from 30 C to 600 C under air ow at an average heating rate of 10 C min À1. We employed the highresolution operation mode, in which the heating rate is automatically reduced over the temperature ranges exhibiting the largest mass variations, thus yielding more accurate results. The mass loss measured between 150 C and 450 C was used to deduce the polymer shell mass m TGA [weight%] relative to the total particle mass. 2. 2. 4 X-ray reectivity. The HE-XR measurements were performed using the High-Energy Micro Diffractometer at the ID15A beamline of the European Synchrotron Radiation Facility, using a 69.
Acknowledgements The authors are thankful to  Patrick Ilg  and  Martin Kröger  for the calculations of the 2D brushes and useful discussions. Marcus Textor ,  Dieter Schlüter  and  Nicholas D. Spencer  are acknowledged for discussions and support during the NP synthesis. Christian Roth  and  Martin Elsner  are acknowledged for the fabrication of the liquid cell. L. I. acknowledges nancial support from  MC-IEF-2009-252926  and  SNSF Ambizione  ( PZ00P2_142532/1 ). The authors thank the  ESRF  for support and provision of beam time and the  MPI-Stuttgart  for access to the  High Energy Micro-Diffraction  instrument (ID15A).
Related literature For general background to magnesium porphyrin species and their applications, see:  Ghosh et al. (2010). For related structures, see:  Belghith et al. (2012) ;  McArdle (1995) ;  McKee et al. (1984) ;  Choon et al. (1986) ;  McKee & Rodley (1988) ;  Gryz et al. (2007) ;  Imaz et al. (2005). For a description of the Cambridge Structural Database, see: Allen  (2002).
Refinement All H atoms were placed in geometrically idealized positions (C-H = 0. 93-0. 97 Å) and constrained to ride on their parent atoms, with U(H) = 1. 2Ueq  (C). The 18-crown-6 is disordered in two conformations A and B (A is the major conformation) with occupancy coefficients fixed at 80% and 20% respectively. For the atoms of conformation B, the DFIX and SIMU/ISOR restraints  (McArdle, 1995)  commands in the SHELXL97 software were used. The DFIX constraint instruction was used for some distances in the conformation A: C25A-O2A, C25A-O26A and C23A-C24A while the DANG constraint instruction was also used for the distance C28A-O3A. where P = (F o 2 + 2F c 2 )/3 (Δ/σ) max < 0. 001 Δρ max = 0. 46 e Å -3 Δρ min = -0. 28 e Å -3 Special details Geometry. All s. u. 's (except the s. u. in the dihedral angle between two l.
The target description In the present work, the RNA-uracil target is described via its molecular orbitals by employing the quantum chemical GAUSSIAN 03 program  [7]. In the latter, the target wave functions are computed at the Hartree-Fock level optimized at the MP2/6-31G(d) computational level, i. e. by including correlation calculations at the second order of perturbation theory MP2 and by using GAUSS-IAN-type orbitals added to a double-zeta valence shell and polarization orbitals on non-hydrogen atoms. Total-energy calculations are then performed in the gas phase with the Gaussian 09 software at the RHF/3-21G level of theory. The ionization potentials (IP's) calculated at the RHF/3-21G level are in good agreement with the experiments, with in particular a mean absolute error of about 0.
Acknowledgments This work has been developed as part of the activities planned in the  Programme de Coopération ECOS-Sud A09E04  as well as in the project  PICS 5921  (THEOS) of the  Centre National de la Recherche Scientifique , the project PICT 2145 of the  Agencia Nacional de Promoción Científica y Tecnológica  and the projects  PIP 1026  and  PIP 0033  from  CONICET.
Acknowledgements We would like to thank the  National Science Foundation of China  (No. 20802092 ) and the  Young Scholar Foundation of the Fourth Military Medical University (FMMU, China)  for financial support of this work. P. A. Wang  also thanks the  Centre National de la Recherche Scientifique (CNRS, France)  for a postdoctoral fellowship to work in the  Laboratoire de Catalyse Moléculaire in the ICMMO, Université Paris-Sud.
Molecular dynamics of CK2 complexes In order to investigate the molecular basis of the interaction of the CK2 ATP binding pocket with the 1f and 1c inhibitors, Molecular Dynamics (MD) simulation of CK2/1f and CK2/1c complexes    were performed. From the protein coordinates of the CK2/CX-4945 complex crystal structure (pdb: 3pe1)  [48]  (Fig. 8a ; see Computational methods) and 1f and 1c optimized geometries, two protein/inhibitor systems were constructed and 40 ns MD runs were obtained employing an explicit box of TIP3P water molecules. Initially, a CK2/CX-4945 MD simulation was carried out as control trajectory, finding that both global complex conformation and polar proteineinhibitor interactions observed in the crystal structure resulted stable during the simulation time scale. Fig. 8b  shows that the nitrogen atom of the A-ring forms a hydrogen bond with the backbone nitrogen atom of Val116 (localized at the hinge/aD region), while on the opposite end of the CX-4945 molecule, the carboxyl group from the C-ring interacts in a strong polar network involving the Lys68, Glu81, Asp175 and two water molecules (positions W1 and W2).
The W1 water molecule remained in its position throughout the 40 ns of the trajectory, while exchanges of water molecules at the W2 position were observed. We have also observed that the side chain (D-ring) of the ligand was more flexible than the rest of the molecule, although the global orientation was conserved. Finally, rotations of the His160 side chain occurred throughout the 40 ns, continually switching from the up to the down conformations. Similar MD results related to the CX-4945 binding mode were recently reported by Liu et al. using another initial structure (pdb: 3nga)  [49]. The MD simulation of the CK2/1f binding mode showed very similar results to those observed in the CX-4945 system (Fig. 8c ). The main difference resides in the lack of polar interactions between the carbon atoms of the A-ring and the hinge/aD region, which increases the average distance between this protein region and the inhibitor (Table  3 , distance A).
Computational methods The geometries of the 1f and 1c compounds were optimized using the ab initio quantum chemistry program Gaussian 03 and the HF/6-31G** basis set  [53]. RESP (restraint electrostatic potential) atomic charges of both inhibitors were calculated to generate the corresponding force field parameters. Molecular dynamics (MD) were performed by using the AMBER12 software package  [54]. The crystal structure of the CK2/ CX-4945 complex (pdb: 3pe1)  [48]  was used as starting structure for the MD simulations; having removed the sulfate ions and water molecules, except those water molecules located within 5 A of the ligand. The CK2/1f complex was built in silico by superposing the central ring atoms of the ligand with the corresponding atoms of the CX-4945 compound in the CK2/CX-4945 complex.
The ligand parameters were assigned with the general AMBER force field (GAFF) and the corresponding RESP charges with the Antechamber module of AMBER. The Amber99 force field parameters were used for all residues  [56]  excepted for the ligands. Computed energetic contributions of 1f and 1c corresponded to the electrostatic energy and Van der Waals contributions arising from bond, angle and dihedral terms in the force field.
Calorimetry Heat capacity versus temperature profiles were recorded with a VP-DSC differential scanning microcalorimeter (MicroCal Inc. , Northampton, MA) at a scan rate of 1uC/min. Protein samples were diluted to 0. 2-0. 4 mg/mL concentration, dialyzed against buffer A and degassed before the calorimetric experiment. The reference cell was filled with degassed buffer A. Both cells were kept under an excess pressure of 30 psi to avoid bubbling during the scan. At the end of each run, the solutions were cooled and subjected to a second heating cycle under the same conditions to determine the reversibility of the transitions. Thermograms were corrected by subtracting the instrumental baseline, obtained with both cells filled with buffer A, and normalized for protein concentration. The T m (temperature at which excess heat capacity reaches a maximum) and the denaturation enthalpy (DH) were determined with the ORIGIN software provided by MicroCal, after subtraction of a progress baseline connecting the pre-and post-transition traces.
Stability and Enzymatic Activity Measurements For the unfolding/refolding curves, native or unfolded Mt-NDPK was diluted at the final protein concentration of 10 mg/mL in 0-8 M urea or 0-5 M guanidinium hydrochloride (GuHCl), and 20 mM phosphate buffer, pH 7. 0 at 25uC and incubated for 16 hours. Fluorescence intensities of the single tryptophan residue Trp132 were measured at 335 nm (bandwidth of 5 nm) with an excitation at 295 nm (bandwidth of 5 nm). Data were normalized after linear fitting correction of the pre-and post-transition. Enzymatic activities were measured with the spectrophotometric assay, containing 1 mM ATP and 0. 2 mM 8-bromoinosine-59diphosphate as substrates  [23]. The errors associated with the kinetic parameters are less than 20%.
X-Ray Diffraction Data Collection Complete data sets were collected at 107 K on the ID23-2 beamline (ESRF, Grenoble), scaled with SCALA from CCP4 suite and processed with MOSFLM  [24]. The structures were solved by molecular replacement with MOLREP using the coordinates of the wild type Mt-NDPK (PDB id: 1k44)  [13]  as search model. Refinement was done using phenix. refine [25]  alternated with manual model building using COOT  [26]. Data collection and refinement statistics are gathered in Table  1. The surface areas and hydrogen bonds were calculated using PISA  [27]. The crystal structure was drawn using PYMOL  [28].
The D3 hexamer is very cooperative since each subunit has contacts with 3 other subunits. The hexamer is very stable even if all individual subunit-subunit interactions are rather weak. In presence of urea, the mutation of the negatively charged Asp 93 into the neutral Asn had a dramatic effect on the hexamer stability. : the c 1/2 of the wt hexamer decreased from 5. 2 M to less than 0. 5 M for the D93N mutant. Folded monomers presented a c 1/2 of 2. 5 M urea for the wt as well as for the mutant. The hexamer stability decrease was therefore not due to subunit destabilization (see also Figure  6 ). In the crystal structure of D93N mutant, no direct interaction of the Asn 93 exists with neighbouring subunit. Long-range ionic interactions may also be involved with charged residues. Based on these interactions, PROPKA software calculates a rough estimate for the free energy of unfolding.
When changing an amino acid residue, the interactions changes and so does the free energy of unfolding. The calculated DG for the Mt-NDPK hexamer was 142. 9 kcal/mol. It decreased to 124. 4 kcal/ mol for the mutant D93N, respectively. It appears that the stability calculated from PROPKA software actually corresponds qualita-tively with the measured T m or with the hexamer stability in urea as denaturant. The D93N mutation appears to decrease the protein stability because the negative charge of the Asp 93 interacts with distant protein charges and stabilizes the hexamer.
Acknowledgments The authors are grateful to  Prof. Anna Giartosio  for her help and interest in this project, to  Dr. Didier Thoraval  for help in the mutagenesis experiments, to  Prof. Martin Willemoe  ¨s, to  Prof. Mircea Podar  and to the late  Prof. O. Barzu  for carefully reading the manuscript, to  Dr. Roland Brosch  for sending the Mt-NDPK gene, to  Ms. Audrey Paulo  for her participation in preliminary experiments. The authors wish to acknowledge the editor and the three reviewers for their detailed and helpful comments. The authors wish to thank beamline staff of the  European Synchrotron Radiation Facility (ESRF, Grenoble, France)  for providing in using beamline ID23-2. The atomic coordinates and structure factors of the D93N mutant of Mt-NDPK have been deposited in the Protein Data Bank (accession codes 4anc, 4and).
3 , entry 4): The title compound was obtained as a side-product following the abovedescribed procedure for the preparation of (E)-4ad. It could not be isolated pure after column chromatography, but characteristic NMR spectroscopic data were obtained. 1 H NMR (400 MHz, CDCl 3 ) δ 4. 32 (d(AB system), J = 14. 0 Hz, 1H), 4. 29 (d(AB system), J = 14. 0 Hz, 1H), 4. 24 (d(AB system), J = 8. 9 Hz, 1H), 4. 21 (d(AB system), J = 8. 9 Hz, 1H), 3. 75 (s, 3H), 2. 10 (dd, J = 14. 5, 6. 8 Hz, 1H), 1. 95 (dd, J = 14. 5, 5. 0 Hz, 1H), 1. 81 (m, 1H), 0. 98 (d, J = 6. 7 Hz, 3H), 0. 95 (d, J = 6. 6 Hz, 3H); 13 C NMR (100 MHz, CDCl 3 ) δ 172. 5, 152. 9, 80.
Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis PRO (Agilent, 2012); program(s) used to solve structure: SIR2004 (Burla et al. , 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012).
This usual pitfall in natural product chemistry has been overcome during the last years with the increasing use of chiroptical data such as electronic or vibrational circular dichroism (ECD and VCD) and theoretical calculations  [16] [17] [18]. During the isolation process, renierin 1 , renierin 2, 18-dihydroreinirin 1  [2] , fulvinol  [3]  and fulvynes A-I  [13]  were also identified. Herein we report the complete structural characterization of 1 and 2 on the basis of 1D and 2D NMR and GC-MS/MS spectra. The absolute configurations of both compounds were determined by comparison of experimentally with theoretically calculated ECD spectra. Absolute configuration of the previously reported cladocroic acid was then addressed using the sign of the specific optical rotation of compound 2a  [15].
Computational Details Conformational analysis was performed using the conformer research algorithm implemented in the Conflex-Barista software  [19] [20] [21] [22]. All the Density Functional Theory (DFT) calculations were performed using the Gaussian 03 program package  [23]  at the B3LYP/6-311+G* level  [24]  using the integral equation formalism variant (IEFPCM)  [25]. TD-DFT was employed to calculate excitation energy (in eV) and rotatory strength R in dipole velocity (R vel ) and dipole length (R len ) forms on the most stable conformers (∆E < 2 kcal. mol -  ). The calculated rotatory strengths were simulated in ECD curve by using the corrected Gaussian function  [26] : ∆ε(E) = 1 2. 297×10 -39 1 √ 2π∆ ∑ 0 i ∆E i R i e E-∆E i 2∆ where ∆ is half the bandwidth at 1 e peak height and ∆E and R are the excitation energies and the rotatory strengths for transition i , respectively.
1 H NMR spectra of collected peaks were recorded to confirm that both compounds were successfully separated (Table  2 ). Finally, the length of the methyl ester derivatives alkyl chain was reliably determined by GC-MS. A fairly similar fragmentation pattern and the same molecular ion at m/z 318 were observed for compounds 1a and 2b. Identification of the fragments led to the conclusion that the alkyl chain contained 12 methylenes (Figure  S11 ). Comparing NMR data and the signs of the optical rotation, we concluded that compound 2a was cladocroic acid previously isolated from C. invurvata. Since the authors were unable to assign the absolute configuration  [15] , compound 2 can be first described as (2S * ,3R * )-cladocroic acid while compound 1 can be identified as (2S * ,3S * )-cladocroic acid.
Conclusions We report here the isolation of 3-epi-cladocroic acid (1) from the Mediterranean sponge Haliclona fulva, a new epimer of the known cladocroic acid (2) previously isolated from the marine sponge Cladocroce incurvata. The structural elucidation was conducted using extensive 1D and 2D NMR data analysis, in addition to GC-MS/MS. The absolute configuration of both compounds 1 and 2 was addressed by comparison of the sign of the Cotton effect observed on the experimentally and theoretically calculated ECD spectra acquired on their methyl ester derivatives 1a and 2a.
Acknowledgements Financial support was provided by the  French ANR Biodiversité 2006 (ECIMAR program ,  ANR-06-BDIV-001 ) and the  Conseil Régional PACA. The authors thank  M. Gaysinski  for recording the NMR spectra and  J-M Guigonis  for recording the HRESIMS spectra. J. Will Allwood  is deeply acknowledged for correcting the manuscript.
II. EXPERIMENTS AND DISCUSSION The single crystal was grown using the Czochralski method in a tetra-arc furnace  [12]. Powdered single crystals were used for NMR measurements at ambient pressure with an orientation H c. We used single crystal for NMR measurements under pressure with the field applied along H c. Pressure was applied by using a piston-cylinder cell used Daphne7474 as a pressuretransmitting medium. [13]  The pressure at low temperatures was estimated by using a Pb manometer. NMR was performed using a standard spin-echo method. Magnetization (M ) measurements was performed using a Magnetic Property Measurement System (MPMS:Quantum Design). Several NMR data at ambient pressure have already been reported in another paper  [11]. Figure  1  shows NMR spectra for (a) 60 K and 0 GPa, (b) 4.
Radiative transfer model In order to compute the line emission from the cores, we use the non-LTE Monte-Carlo 1D (spherical) radiative transfercode RATRAN  (Hogerheijde & van der Tak 2000). The C 18 O and H 13 CO + abundances computed with our chemical model at each radius and time step are used as an input of the radiative transfer code. We use the Einstein coefficients and energy levels from the Cologne Molecular Database for Spectroscopy (CDMS;  Müller et al. 2001). For both species the same collisional rates as for the main isotopologue are adopted. For C 18 O, we use the CO collisional rates with ortho and para H 2 of  Yang et al. (2010). Indirect measurements of the H 2 ortho-topara ratio in dense cores indicate ratios in the range 10 - 2  -10 -1  (Maret & Bergin 2007; Pagani et al. 2009 ), and we therefore assume that all H 2 is in para form.
For H 13 CO + we use the HCO + collisional rates with para H 2 of  Flower (1999). The H 13 CO + (1-0) line has an hyperfine structure that slightly broadens this line  (Schmid-Burgk et al. 2004 ). To take this effect into account, we add a 0. 133 km s -1 broadening in quadrature to the turbulent broadening, following  Tafalla et al. (2006). All molecular data files were retrieved from the Leiden Atomic and Molecular Database (LAMDA;  Schöier et al. 2005). The radiative transfer model is used to produce synthetic data cubes for both the C 18 O (1-0) and H 13 CO + (1-0) lines. These data cubes are then convolved with a 25 ′′ and 30 ′′ FWHM Gaussian respectively, i. e. the effective (after spatial smoothing, see § 2) resolution of our observations. Finally, the convolved data cubes are compared to the observations.
Acknowledgements. The authors are grateful to  Dimtri Semenov  for his help for testing our chemical model. We also thank  Robin Garrod  for providing us the the binding energies of molecular species on dust grains, and  Karin Öberg  and  Eric Herbst  for discussions on photodesorption. Finally, we thank  Malcolm Walmsley  for his comments on this manuscript that helped to improve it. This work was supported by  NSF  grant  AST-1008800.