Physical Chemistry
Summary:
Physical chemistry is an interdisciplinary science at the frontier between chemistry and physics, whose topics go beyond the classical areas of the respective individual sciences. While preparative chemistry focuses on questions of the methodology of chemical synthesis of known and new substances, physical chemistry attempts to describe the properties of substances and their transformation by applying concepts of physics to objects of chemistry by means of theoretical and experimental methods. Along with organic and inorganic chemistry, physical chemistry therefore represents one of the three key disciplines of "classical" chemistry, since it provides the theoretical basis for technical chemistry and process engineering. Its knowledge is also an integral part of many other disciplines and is used, for example, for description and understanding in biology and medicine, meteorology as well as the earth sciences. Due to this great interdisciplinarity and the use of numerous physicochemical methods in almost all areas of chemistry, a complete description of physical chemistry as profile is hardly possible, which is why this article explicitly makes no claim to do so.
Methods Profiles
EPR spectroscopy
What is it?
- Electron Paramagnetic Resonance spectroscopy belongs together with NMR (Nuclear Magnetic Resonance) spectroscopy to the group of magnetic resonance methods
- measures the resonant microwave absorption of a paramagnetic sample in an external magnetic field (i.e measurement needs unpaired electrons)
For what?
- provides information about the electronic/atomic structure and the chemical environment (e.g. local environmental polarity) of the sample
- for the characterization of molecular dynamics on the time scale of approx. 10 ps-1 μs (allows e.g. conclusions to be drawn about local nanoviscosity)
- for distance measurements in the range of about 1-8 nm
What kind of data is generated?
- almost exclusively proprietary file formats (e.g. .spe or .DTA/.DSC) of the "Bruker Corporation" company
- transfer into open file formats (e.g. .txt or .csv) either via Bruker software on the measuring device itself or via tools like SpinToolbox
- analysis of data using Bruker software or e.g. EasySpin as open-source toolbox for MATLAB
How to do it FAIR?
- documentation of all research data and metadata is carried out digitally using an suitable ELN (possibly in addition to a manual laboratory notebook in paper form)
- experimental conditions (e.g. sample concentration, solvent etc.) and measurement parameters (e.g. frequency, temperature) are noted in the ELN
- observations, deviations from planned measurement protocol or other peculiarities during measurement with no digital output (i.e. no data files) are added manually to the ELN entry of the experiment
- obtained unprocessed raw files from measurements are uploaded to ELN in open file formats and attached directly to the respective ELN experiment entry, including metadata with data on the instrument (e.g. manufacturer, type, etc.), measurement conditions & parameters
- metadata related to the obtained data, such as temperature or solvent of measurement, follow common metadata standards
- research data are processed, analysed and compared with open non-proprietary software tools
- simultaneously with publication as a research article in a scientific journal, the underlying research data is published in an open data repository and linked to the article (incl. semantically richly annotated raw and processed data in open data formats for reuse)
- an unique persistent identifier (e.g. DOI) is generated for each dataset as well as for the journal publication
Methods Data Format Overview
| Analytical method | Exemplary proprietary file extensions | Typical size of propietary file | Converter to open file format | Recommendation for open file extension* | File format | File size of open format |
|---|---|---|---|---|---|---|
| NMR spectroscopy | .fid | <1-50 MB | MNova Topspin | .jdx .zip | JCAMP-DX NMReDATA | ~1 MB |
| EPR spectroscopy | .spe .DTA/.DSC | <1 MB | SpinToolbox | .txt .csv | text file, comma-separated values | <1 MB |
| IR spectroscopy | .ispd .icIR | <1 MB | .dx | JCAMP-DX | <1 MB | |
| Raman spectroscopy | .dpt .spc .icRaman .sps .acs | <1 MB | proprietary software | .dx | JCAMP-DX | <1 MB |
| UV/VIS spectroscopy | .dsw .str .bsk .bkn .ksd .jws .jwb .str8 .spc .sre | <1 MB | proprietary software | .csv | comma-separated values | <1 MB |
| Fluorescence spectroscopy | .fds .fs2f .jws .opj | <1 MB | proprietary software | .dx | JCAMP-DX | <1 MB |
| Mass spectrometry | .raw .d .baf | ~250 MB | Proteowizard | .mzML | mzML | ~250 MB |
| Single crystal XRD | .raw | <1 MB | proprietary software | .cif | crystallographic information file | <1 MB |
| Powder XRD | .raw | <1 MB | proprietary software | .xyd | text file | <1 MB |
| Gas chromatography | .gcd .d | ~2 MB | proprietary software | .txt | text file | <1 MB |
| HPLC | .xls | <1 MB | proprietary software | .csv | comma-separated values | <1 MB |
| Cyclic voltammetry | .nox .pssession | ~8 MB | proprietary software | .txt | text file | <1 MB |
| Differential scanning calorimetry (DSC) | .ngb-dsu .ngb-taa | <1 MB | proprietary software | .csv | comma-separated values | <1 MB |
| Isothermal titration calorimetry (ITC) | ??? | ??? | ??? | ??? | ??? | ??? |
| Physisorption | .smp | <1 MB | proprietary software | .csv | comma-separated values | <1 MB |
| Dynamic light scattering (DLS) | .apkw .xlsx | <1 MB | proprietary software | .csv | comma-separated values | <1 MB |
| Atomic force microscopy (AFM) | ??? | ??? | ??? | ??? | ??? | ??? |
| Transmission electron microscopy (TEM) | ??? | ??? | ??? | ??? | ??? | ??? |