Good Software and Applications for Chemistry: A Guide to Tools for Research and Analysis

Good Software and Applications for Chemistry

Chemistry professionals and students rely on a variety of specialized software and applications to assist with experiments, data analysis, illustrations, and literature management. Choosing the right tools depends largely on the branch of chemistry involved, whether it is organic synthesis, spectroscopy, computational chemistry, or data handling.

NMR Software

Nuclear Magnetic Resonance (NMR) spectroscopy requires dedicated software for analyzing spectra and interpreting data. Popular choices include:

• SpinWorks: A free NMR analysis tool compatible with Windows. It provides basic functionality necessary for spectrum interpretation without licensing costs.
• MestreNova (MNova): A comprehensive NMR processing platform widely used in academia and industry. Its advanced features assist in peak picking, integration, and structure verification. Essential when university resources do not include commercial licenses.

Both programs support a wide range of instruments and provide user-friendly interfaces for spectral examination.

Reference and Literature Management

Managing references and literature is key for research projects and publications. The main software used are:

• EndNote: Popular for reference management and paper writing collaboration. It integrates well with word processors but benefits most from uniform usage among co-authors.
• Mendeley: A reference manager and academic social network that simplifies organizing PDFs and literature lists. Offers cloud synchronization and team sharing.
• Citation Managers in general: Utilizing any citation manager reduces manual bibliography formatting errors and streamlines manuscript preparation.

Graphing and Data Analysis Tools

Data visualization and quantitative analysis require robust software. Several programs excel in this area:

• GraphPad Prism: Favored for biostatistics and graphing, Prism simplifies curve fitting and statistical tests.
• OriginLab Origin: Provides flexible graphing, analysis, and batch processing. While historically Windows-based, OriginLab Viewer supports Mac users for data viewing and extraction.
• Microsoft Excel: An essential tool to master for data organization, custom plotting, and basic computations across scientific fields.
• MATLAB: Used to generate custom figures and perform advanced mathematical modeling and simulations.
• IGOR Pro: Often utilized for data fitting and graphing, it is especially useful in synchrotron beamlines where data output formats are specialized.

Chemical Drawing and Illustration

Creating accurate chemical structures and reaction mechanisms is indispensable. Key programs include:

• ChemDraw/ChemDraw3D: Industry-standard software for drawing chemical structures, mechanisms, spectra annotation, and 3D molecule visualization. Fully integrates with Microsoft Office.
• ChemDoodle: Serves as an alternative with a modern interface and useful cross-platform compatibility.
• ChemSketch: Free for students, it offers structure drawing and basic molecular modeling capabilities.

Computational and Simulation Software

Computational chemistry encompasses quantum mechanics and molecular dynamics. Tools in this category include:

• Orca: A free quantum chemistry software focusing on Density Functional Theory (DFT) calculations used to validate experimental data and predict molecular properties.
• Chemcraft: Complements Orca by visualizing molecular orbitals, vibrational modes, and other output from electronic structure calculations.
• Quantum Espresso and VASP: Widely-used codes in solid-state physics and materials modeling for plane-wave DFT computations.
• COMSOL Multiphysics: Facilitates classical simulations involving chemical reactions, heat transfer, and fluid dynamics.
• GROMACS: High-performance molecular dynamics software often used for biomolecular simulations.
• Larch and Demeter: Specialized in X-ray absorption spectroscopy data processing, Larch is favored for scripting capability since it is Python-based.

Useful Plugins and Online Tools for Research and Writing

Efficient literature access and workflow management rely on several online tools:

• Kopernio: A browser plugin that offers one-click access to full-text papers through institutional subscriptions.
• LibKey Nomad: A Chrome extension enabling rapid discovery and download of scholarly articles.
• Chemistry Reference Resolver: A tool to directly link citations to their source papers for select journals.

Data Repositories and Databases

Access to chemical data and research materials depends on reliable repositories and databases. Noteworthy examples include:

Database	Description	Link
EBI ChEMBL	Bioactive molecule database focusing on drug-like properties.	chembl
ChemSpider	Free chemical structure database for compound search.	chemspider
NCBI Chemical Resources	Comprehensive chemical data integrated with biomedical resources.	ncbi
CCDC	Small molecule crystallographic structures repository.	ccdc
Protein Data Bank (PDB)	3D structural data of proteins and nucleic acids.	pdb
Materials Project	Material property database used in materials science.	materialsproject
DrugBank	Database providing detailed drug information and targets.	drugbank

Open access repositories that benefit data sharing include Zenodo, Figshare, and Mendeley Data. These facilitate data publication and reproducibility initiatives.

Specialized Programs and Calculators

• Molarity/Dilution Calculators: Online utilities such as GraphPad’s quickcalc assist with solution preparation calculations.
• Mercury: Program for visualizing and analyzing X-ray crystallography data.

Protocol Collections and Safety Resources

Standard operating procedure (SOP) repositories help laboratories maintain consistent protocols and safety standards.

• Chemistry SOP Collection
• Websites like ChemTips, SchlenkLine Survival Guide, and group document repositories provide practical synthetic chemistry advice.
• Protocols.io and CSH Protocols offer extensive lab procedure databases across disciplines.

Other Useful Resources

• Free Scientific Figures: Platforms like Smart Servier offer illustration assets.
• Protein Atlases: Helpful for tissue and expression analysis.
• ClinicalTrials.gov: For drug development pipeline searches.
• MSDS Search: For chemical safety sheet retrieval.
• UniProt: Comprehensive protein information database.

Programming and Writing Tools

Computational skills improve research efficiency and outputs:

• Python: Widely recommended for scripting, data analysis, and visualization. It supports many chemistry-related libraries and workflows.
• LaTeX/Overleaf: Preferred for technical writing requiring mathematical formulas and complex documents. Enhances manuscript preparation.

Preprint Servers

• ChemRxiv – chemistry preprints for rapid dissemination.
• EngRxiv – engineering sciences preprints.
• arXiv – covers physics, math, and computational chemistry.
• ChemRN – social sciences and chemistry intersection.
• bioRxiv – biology and chemical biology related preprints.

Summary of Key Takeaways

• NMR analysis often employs SpinWorks and MestreNova for spectral interpretation.
• Reference management relies heavily on EndNote and Mendeley.
• Graphing and data analysis benefit from Prism, Origin, Excel, MATLAB, and IGOR Pro.
• Chemical structure drawing is dominated by ChemDraw, ChemDoodle, and ChemSketch.
• Computational methods use Orca, Chemcraft, Quantum Espresso, and GROMACS for modeling and simulations.
• Online tools like Kopernio streamline literature access. Databases such as ChEMBL and ChemSpider support chemical information retrieval.
• Protocols and SOP collections provide reliable experimental frameworks and safety guidelines.
• Learning Python and LaTeX enhances data processing and scientific communication skills.

What free NMR software is recommended for Windows users?

Spinworks is a good free NMR program that runs on Windows. It is useful if you don’t have access to paid software like MestreNova.

Which software is best for managing chemistry references and literature?

Endnote and Mendeley are popular tools for reference management. Choose one that matches your collaborators’ preferences to streamline writing.

What programs are recommended for graphing and data analysis in chemistry?

• GraphPad Prism and Origin are widely used for graph creation.
• Excel is essential for data manipulation.
• Matlab and IGOR PRO support advanced custom figures and fitting.

Which software is preferred for drawing chemical structures and preparing figures?

ChemDraw and ChemDraw3D are highly compatible with MS Office and widely used. ChemDoodle and ChemSketch are also good alternatives, some offering free versions.

Are there free software options for computational chemistry and simulations?

Yes. Orca is a free quantum chemistry program for DFT calculations. Chemcraft supports visualization. Quantum Espresso and VASP cater to quantum simulations, while COMSOL and GROMACS handle classical and molecular dynamics simulations.