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 characterisation 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
Quantum Mechanical (QM) calculations
What is it?
- Quantum Mechanical calculations are one of the major computational tools to elucidate molecular properties on a first-principles basis
- solving the Schrödinger equation provides the electronic energy of a molecule/molecular system, from which properties can be derived as higher-order derivatives. Descriptors can also be computed from orbital/density data which is equally available
For what?
- calculated molecular properties include e.g. molecular structures (usually local minima and transition states), energies, spectroscopic parameters/properties, dipole moments, polarizabilities and non-observables such as atomic charges and topological analysis
- properties can be calculated prior to conducting experimental measurements to guide synthesis (computational screening) or a posteriori to help interpret experimental results atomistically
- the application range depends on the level of theory used. Correlated wave function methods are commonly applied to systems with less than 100 atoms, density functional theory (DFT) up to 500 atoms, semiempirical methods can be routinely applied in the range of thousands
What kind of data is generated?
- data formats depend strongly on the program that is used for the QM calculations, e.g. Gaussian, ORCA, Molpro, TURBOMOLE or Jaguar, but generally formatted text files are used as input and log files. Compressed data formats are used to store wavefunction, density information and operators. Molecular structures are provided in human-readable format
- data analysis is carried out using custom scripts. A few programs provide their own scripts for common tasks (such as plotting of molecular orbitals) and dedicated GUIs
How to do it FAIR?
- documentation of all research data and metadata is carried out digitally using a suitable repository (e.g. NOMAD, ioChem-BD or a general-purpose repository) to store the input files, main log and structures files (if not included in the log)
- reproducibility of calculations to within numerical accuracy can be ensured by storing the input files and adding the program and its version (ideally even the compiler version and any compiler flags) as metadata. Numerical thresholds are well defined but reproducibility of calculations across different programs and versions is not guaranteed. This warrants the safekeeping of version specific source files for the same time period as the stored data
- data analysis scripts should be uploaded to the repository in open file formats, attached directly to the corresponding data entry and accompanied with appropriate documentation
- if possible, analysis and evaluation of calculations should be conducted with open, non-proprietary software tools
- simultaneously with publication as a research article in a scientific journal, the data in the repository is linked to the article (incl. semantically richly annotated raw and processed data, if possible in open data formats for reuse)
- a unique persistent identifier (e.g. DOI) is generated for the dataset as well as for the journal publication
- XML and CML (Chemical Markup Language) is used by a few software packages but this is not common practice