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enllacos_rmn

Enllaços sobre espectroscòpia de rmn

Cursos on-line

Wikibooks

Llocs wiki

  • NMR Wiki, is an open non-profit online NMR project (started on Nov 8th 2007). The goal of this site is to provide a collaborative informational resource to Spectroscopists, Chemists, Biologists and others using magnetic resonance techniques.
  • SeRMN wiki, el nostre wiki 8-) per tot allò que afecta al funcionament del SeRMN.

Blogs on NMR

(Per ordre alfabètic del cognom de l'autor)

  • Carlos Cobas' Blog, un dels autors inicials del programa Mestre-C (actualment Mnova) i fundador de la companyia Mestrelab Research SL. El blog està dedicat principalment al processament i interpretació dels espectres de rmn.
  • Glen Facey's Blog, del servei de rmn de la Universitat d'Otawa. Tracta aspectes instrumentals, i com que tenen espectròmetres Bruker ens podem aprofitar.
  • Solid-State NMR Literature Blog pel grup d'en Rob Schurko a la University of Windsor.
  • Ryan's Blog on NMR Software, a ACD/Labs. Especialitzat en l'aplicació dels espectres de rmn a l'elucidació estructural i identificació dels components de mescles complexes.
  • Stan's NMR Blog , tracta una mica de tot: la història de la rmn, les persones que la van protagonitzar, els fonaments químico-físics de la rmn, etcètera.

Calculadores on-line

Per RMN

Ús general

  • UnitConversion.org is the ultimate resource for unit conversion. Use our free online unit converters to easily convert between different units of measurement. Simply select the appropriate unit converter from the lists below.

Basses de dades de desplaçaments químics

Solvents residuals

  • The Solvent Chemical Shift Finder. The solvent chemical shift finder is an experimental database of over 100 different solvents and reagents which might appear in an NMR spectrum. For further details consult the references,
    • I. C. Jones, G. J. Sharman, J. Pidgeon. Spectral Assignments and Reference Data. 1-H and 13-C NMR data to aid the identification and quantification of residual solvents by NMR spectroscopy Magn. Reson. Chem., 2005, 43, 497-509.
    • H. E. Gottlieb, V. Kotlyar, A. Nudelman. NMR Chemical Shifts of Common Laboratory Solvents as Trace Impurities J. Org. Chem., 1997, 62, 7512-7515.

Compostos orgànics

  • nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The nmrshiftdb2 software is open source, the data is published under an open content license. Please consult the documentation for more detailed information. nmrshiftdb2 is the continuation of the NMRShiftDB project with additional data and bugfixes and changes in the software.
  • Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds,which includes 6 different types of spectra under a directory of the compounds. The six spectra are as follows, an electron impact Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), a 1H nuclear magnetic resonance (NMR) spectrum, a 13C NMR spectrum, a laser Raman spectrum, and an electron spin resonance (ESR) spectrum.
  • NMR misinterpretation. Basic Misinterpretations, Typos and other Sad Events in NMR-Spectroscopy. What is presented on this page? This page holds examples of strange interpretation of NMR-data, either caused by missing basic knowledge about this method or caused by typos or caused by any other reason. What is intended with this page? The sole intention of this page is to promote massive application of computer programs to verify structural and spectral data. In NMR-Spectroscopy we are in the lucky situation, that we have already algorithms available which allow us to check our analytical data in a(n) (semi-)automatic way. Routine application of these programs would increase the quality of the chemical literature in an easy and efficient manner.

Predicció de desplaçaments químics

  • nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The nmrshiftdb2 software is open source, the data is published under an open content license. Please consult the documentation for more detailed information. nmrshiftdb2 is the continuation of the NMRShiftDB project with additional data and bugfixes and changes in the software.
  • NMRdb is a web-based approach implementing a new java applet that enables to assign a chemical structure to the corresponding NMR spectrum by simply drawing lines between atoms and automatically characterized signals. Includes: NMR Simulator, NMR Resurrector, NMR Assigner and NMR Predictor.
  • NMRPREDICT-Server. És un cul de sac sobre bases de dades i programes de predicció d'espectres de 13C. Per exemple,
    • Spectral Similarity Search, entra els desplaçaments químics dels teus pics a l'espectre de 13C i et trobarà estructures amb espectres semblants.
    • Aquest enllaç està estretament relacionat amb el programa comercial del mateix nom NMRPredict
  • ACD/Labs i-Lab. Reduce the need for labor intensive experimental testing and literature searches, by using the online ACD/I-Lab prediction engine to predict physicochemical properties, NMR spectra and chemical shifts, and ADME toxicities. The browser-based I-Lab software also assesses prediction reliability and includes searchable content databases. I-Lab predictions are made using the same advanced algorithms that power our full desktop software suites, giving you the same highly accurate predictions without the need for individual software installations. A site license allows unlimited predictions for all of your organization’s users, while the I-Lab for Intranets API can be implemented on servers behind your own firewalls. How It Works: Predictions are generated from structures, input in a variety of forms. Draw a structure in the I-Lab interface, paste a structure from ACD/ChemSketch, upload a SMILES string, or look up a compound in the built-in dictionary. Select a module to predict the property or spectra of interest, or generate a systematic name or structure for the molecule. Generate a report by saving the results to a PDF. Available prediction modules: Physicochemical Properties, ADME Properties, Toxicity Properties, NMR Spectra and Chemical Shifts Nomenclature. I-Lab is also available for individual users as a credit-based system.

Predicció de propietats químiques

  • OSIRIS Property Explorer. The OSIRIS Property Explorer is an integral part of Actelion's inhouse substance registration system. It lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid. Prediction results are valued and colour coded. Properties with high risks of undesired effects like mutagenicity or a poor intestinal absorption are shown in red. Whereas a green color indicates drug-conform behaviour.

Metabolòmica

BioCyc

The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. Furthermore, BioCyc PGDBs include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc website provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions.

BioCyc contains 2988 databases as of June 11th (version 17.1). The most comprehensive databases are part of Tier 1 Databases and they are required to have received at least one year of literature-based curation by scientists. Currently they are:

  • EcoCyc Escherichia coli K-12 substr.MG1655. SRI International.
  • MetaCyc Metabolic pathways and enzymes from over 2063 organisms. SRI International.
  • HumanCyc 250 metabolic pathways. SRI International.
  • AraCyc Arabidopsis thaliana S. Rhee, Department of Plant Biology, Carnegie Institution, USA.
  • YeastCyc Saccharomyces cerevisiae. SGD Curators, Stanford U., USA.
  • LeishCyc Leishmania major. Friedlin Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia.

Find below a more detailed description of the most relevant databases for biomedical studies.

  • MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 2097 pathways from more than 2460 different organisms [more], and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary [def] and secondary [def] metabolism, as well as associated compounds, enzymes, and genes.
  • HumanCyc is a bioinformatics database that describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. For example, HumanCyc has tools for analysis of human metabolomics and gene-expression data.
  • MouseCyc is a database of curated biochemical pathways data for the laboratory mouse that can be integrated with functional and phenotypic data from MGI.

ExPASy

ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. (see Categories in the left menu). On this portal you find resources from many different SIB groups as well as external institutions.

MetaboHunter

MetaboHunter is a web server application for semi-automatic assignment of 1D NMR spectra of metabolites. MetaboHunter provides tools for metabolite identification based on spectra or peak lists with three different search methods and with possibility for peak drift in a user defined spectral range. The assignment is performed by comparison with two major publically available databases (HMDB, MMCD) of NMR metabolite standard measurements. In this work we present the Web tool with detailed testing of the methods provided in the Supplementary data.

  • MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures. Dan Tulpan et al., BMC Bioinformatics 2011, 12:400 PDF Supplementary data

Taules de desplaçaments químics

Taules periòdiques

Fonaments de la rmn

Programari d'interés

  • rNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks.
  • SPINUS (Structure-based Predictions In NUclear magnetic resonance Spectroscopy) is an on-going project for the development of structure-based tools for fast prediction of NMR spectra. SPINUS - WEB currently accepts molecular structures via a Java molecular editor, and estimates 1H NMR chemical shifts and coupling constants. The predictions are obtained from ensembles of previously trained feed-forward neural networks, and corrected with data from an additional memory.
  • PLT for Windows. PLT is a program for drawing chemical structures and creating hard copy on printers and other Windows-supported output devices.
  • AcornNMR Periodic Table. This is an Excel spreadsheet which calculates resonant frequencies for all magnetically active nuclei. Just enter your proton frequency (in cell B5) and all others are calculated from it.

Altres llocs web d'interés

  • Print Free Graph Paper. Save yourself money and a trip to the store! Print graph paper free from your computer. All graph paper files are optimized PDF documents requiring Adobe Reader for viewing. Available formats: Cartesian, Engineering, Polar, Isometric, Logarithmic, Hexagonal, Probability, and Smith; in Letter or Din a4 paper size; in inches or millimeters measuring units, and several chart spacing.
  • Martindales Center conté un munt d'enllaços d'interès per RMN i MRI, però no he tingut temps de comprovar la seva vàlua i utilitat.
  • Organic Chemistry Portal. The Organic Chemistry Portal offers an overview of recent topics, interesting reactions, and information on important chemicals for organic chemists.
  • eMolecules empowers researchers to explore uncharted chemical and biological space and deliver more efficient drug discovery programs. Our promise to drug discovery researchers is that we will aim to facilitate:
    • exploration of unchartered chemical and biological space with our database of over 8 million compounds available from our global network of trusted suppliers.
    • evaluation of the best source of molecules for their projects based upon suppliers' availability, delivery time and pricing data which we normalize, update and curate monthly.
    • expedition of their drug discovery programs by reducing the barriers, time and costs associated to acquiring molecules.
enllacos_rmn.txt · Last modified: 2017/01/01 19:55 by miquel