Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation and Calculated Properties Supporting Information
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Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation and Calculated Properties Supporting Information Emma L. Schymanski a,b* , Christine M. J. Gallampois c, Martin Krauss a, Markus Meringer d, Steffen Neumann e, Tobias Schulze a, Sebastian Wolf e and Werner Brack a. a UFZ - Helmholtz Centre for Environmental Research, Department of Effect-Directed Analysis, Permoserstrasse 15, D-04318 Leipzig, Germany. *Corresponding Author: Ph: +41 58 765 5537. Fax: +41 58 765 5826. E-mail: [email protected] b Now at Eawag – Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland. c Department of Clinical and Experimental Medicine, Faculty of Health Science, Linköping University, SE-581 83 Linköping, Sweden. d DLR – German Aerospace Centre, Remote Sensing Technology Institute, Münchner Strasse 20, D- 82234 Oberpfaffenhofen-Wessling, Germany. e IPB – Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, Weinberg 3, D-06120 Halle (Saale), Germany. This document contains Supporting Information for the manuscript “Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation and Calculated Properties”, ordered according to the Table of Contents below. Table of Contents Glossary/Abbreviations .............................................................................................................. 2 Materials and Methods .............................................................................................................. 3 Analytical Method .................................................................................................................. 3 Conformational Energy Criteria ............................................................................................. 4 Conformational Energy - Results ................................................................................................ 6 Calculation on Validation Sets ................................................................................................ 6 Energy Distribution: Plausibility Criterion .............................................................................. 7 Unknowns – Additional Results .................................................................................................. 9 Unknown 1 ............................................................................................................................. 9 Unknown 2 ........................................................................................................................... 10 References ................................................................................................................................ 11 S-1 Glossary/Abbreviations APCI atmospheric pressure chemical ionisation BP boiling point BR blue rayon EDA effect-directed analysis CDK Chemistry Development Kit ChemAxon software for chemical calculations ChemBio3D software for chemical calculations GC/EI-MS gas chromatography-electron ionization-mass spectrometry KRI Kovat’s retention index LC/MSMS liquid chromatography-tandem mass spectrometry log Kow logarithm of the octanol-water partitioning coefficient LRI Lee retention index MetFrag software for metabolite fragmentation prediction MOLGEN-MS software combining structure generation and spectral interpretation MOLGEN-QSPR software combining structure generation and qualitative structure prediction relationships MOPAC software for structure minimization and energy calculation MS mass spectrometry MS (n) multi-dimensional mass spectrometry MV match value NIST National Institute of Science and Technology NMR nuclear magnetic resonance spectroscopy OpenBabel software package for chemical calculations PAHs polycyclic aromatic hydrocarbons RDB ring and double bond count RI retention index RP-HPLC reverse phase high performance liquid chromatography SPE solid phase extraction Wiley mass spectral database S-2 Materials and Methods Analytical Method GC-MS (Model 6890 N, detector MSD 5973, Agilent Technologies, Waldbronn, Germany) analysis was performed using a HP-5MS capillary column (30 m × 0.25 mm I.D., 0.25 µm film, 5 % phenyl methyl siloxane, Agilent Technologies). The temperature program was 70 °C (held for 4 min.), then 3 K/min. to 300 °C (held for 20 min.). A C 8-C36 alkane calibration mix (46827U, Supelco, Seelze, Germany) was used to calculate the Kovat’s Retention Index (KRI) for the samples and the EPA-PAHs (Mix 9, Dr. Ehrenstorfer, Augsburg, Germany) was used to calculate the Lee Retention Index (LRI). The spectra of all samples were recorded first without and then with addition of the standards to avoid the loss of peaks of interest. Retention indices (KRI and LRI) were calculated according to the standard equation 1. Analytical confirmation was also performed using liquid chromatography coupled with high resolution tandem mass spectrometry (LC/MSMS). The Agilent series 1200 HPLC system consisted of a degasser, a high-pressure binary SL pump, an autosampler, a column oven and a diode array detector operated from 210 nm to 250 nm (Agilent Technologies, Santa Clara, CA, USA). Chromatographic separation was achieved using an analytical reversed-phase column (LC-PAH, 250 x 2.1 mm, 5 µm particle size, Supelco, CA, USA) and a gradient elution (bi-distilled water and HPLC grade methanol from Merck, Darmstadt, Germany) at a flow of 0.2 mL/min with the following conditions: 0-50 min, 50-95 % of methanol; 50-65 min, 95 % of methanol, then re-equilibration of the phase. A volume of 5 µL was injected. The HPLC system was coupled to a LTQ Orbitrap XL hybrid instrument (Thermo Fisher Scientific, Bremen, Germany), consisting of a LTQ linear ion trap MS and an Orbitrap MS, equipped with an atmospheric pressure chemical ionization (APCI) source. The full scan mass range of m/z 140-600 was acquired in the Orbitrap with a resolution of R = 60 000. Tandem MS experiments were conducted by collision-inducted dissociation (CID), with the product ions transferred to the Orbitrap for the detection of high resolution fragments (R = 60 000). All data were processed using Xcalibur (Thermo Fisher Scientific, San Jose, USA). S-3 Conformational Energy Criteria All calculations for the 1698 molecules started with SD files (hereafter called SDFs) saved from MOLGEN-QSPR, containing explicit hydrogens and 3D coordinates. MOLGEN-QSPR and ChemBio3D settings are given elsewhere 2. For Obenergy calculations, obminimize 3 was used to minimise the energies using three force fields (obminimize –n 600 –sd –ff FF, where FF = Ghemical, MMFF94 or UFF), which were sent to Obenergy for calculation (obenergy –ff FF, where FF is the same as for obminimize). ChemAxon calculations included Dreiding and MMFF94 optimisations with the option “leconf” (least energy conformation) set to either “always” or “never”. MOPAC calculations were performed using the AM1 method 4. MOPAC7 was recompiled to raise the limits of heteroatoms. Files were first optimized using Obminimize (obminimize –n 2400 –sd –ff FF, where FF = Ghemical, MMFF94 or UFF) and then submitted to MOPAC with the settings: “AM1, GEO-OK, ECHO, MMOK, XYZ, BONDS, T=4800”. To simplify the display of the results, each combination of program and optimisation setting was given a code, which is summarised in Table S-1. The formulas used for more detailed calculations with MOLGEN and PubChem are given in Table S-2. Table S-1: Code and description of programs and settings used for energy calculations. Code Program and Optimisation Settings CADA ChemAxon Dreiding optimisation and energy calculation, leconf always CADN ChemAxon Dreiding optimisation and energy calculation, leconf never CAMA ChemAxon MMFF94 optimisation and energy calculation, leconf always CAMN ChemAxon MMFF94 optimisation and energy calculation, leconf never CB3D ChemBio3D MM2 optimisation and energy calculation MOGH MOPAC7 Obminimize Ghemical, AM1 calculation MO94 MOPAC7 Obminimize MMFF94, AM1 MOUF MOPAC7 Obminimize UFF, AM1 OBGH OpenBabel Obminimize Ghemical, Obenergy Ghemical OB94 OpenBabel Obminimize MMFF94, Obenergy MMFF94 OBUF OpenBabel Obminimize UFF, Obenergy UFF QSPR MOLGEN-QSPR simplified MM2 optimisation and energy calculation S-4 Table S-2: Formulas for energy calculations with PubChem and MOLGEN structures. No. Formula Source No. Formula Source No. Formula Source 1 C18H35NO [1] 45 C2H6S5 [1] 89 C4H7O2Cl [2] 2 C10H10O4 [1] 46 C3H8S3 [1] 90 C6H14O [2] 3 C12H10 [1] 47 C2H6S4 [1] 91 C5H11NO2 [2] 4 C8H7ClO2 [1] 48 C2H6S3 [1] 92 C5H12O2 [2] 5 C9H8Cl4 [1] 49 C3H5BrCl2 [1] 93 C6H16OSi [2] 6 C8H10S2 [1] 50 C3H4Cl2 [1] 94 C4H6O2 [2] 7 C7H5ClO2 [1] 51 C3H3Cl5 [1] 95 C9H21NO [2] 8 C10H16O [1] 52 C2H2Cl4 [1] 96 C2H6O2 [2] 9 C7H5Cl3O [1] 53 S8 [1] 97 C4H8NOCl [2] 10 C5H7Cl2NOS [1] 54 C9H16 [2] 98 C5H6 [2] 11 C4H11O2PS2 [1] 55 C8H17N [2] 99 C13H28 [2] 12 C7H6Cl2O [1] 56 C9H20O [2] 100 C8H17Cl [2] 13 C8H10S [1] 57 C7H14 [2] 101 C8H16O [2] 14 C7H7ClO [1] 58 C10H18 [2] 102 C4H12N2 [2] 15 C3H9O2PS2 [1] 59 C8H12 [2] 103 C3H3Cl3 [2] 16 C10H16 [1] 60 C6H12O2 [2] 104 C7H9Br [2] 17 C6H3Cl3O [1] 61 CN3F5 [2] 105 C4H4O3 [2] 18 C3H9O3PS [1] 62 C4H8N2O [2] 106 C9H22NP [2] 19 C3H9OPS3 [1] 63 C6H9OBr [2] 107 C2H7P [2] 20 C4H8O2S2 [1] 64 CH5SiBr [2] 108 C7H14O [2] 21 C5H8Cl2O2 [1] 65 C4H2N2FCl [2] 109 C5H13NO [2] 22 C3H6O2S3 [1] 66 C5H11Br [2] 110 C7H19N3 [2] 23 C3H7NOS2 [1] 67 C9H14 [2] 111 C6H12O [2] 24 C6H12Cl2O2 [1] 68 C6H11OBr [2] 112 C7H13N [2] 25 C4H9NOS [1] 69 C4H7SiCl3 [2] 113 C4H11NO [2] 26 C6H6O [1] 70 C2H3NO [2] 114 C6H10 [2] 27 C4H3Cl3O2 [1]