Links
I also have a Learn organic chemistry online page, with problem sets, total synthesis databases, group meeting slides, resource collections, and more.
Research Tools
Chemistry Reference Resolver
Chemistry Reference Resolver
Alex Zhurakovskyi's unmissable tool allows fast access to papers simply by typing in the reference or DOI. Also supports MSDS and Sigma-Aldrich reagent search.
Image: books by Abdo from the Noun Project
Zotero
Zotero is a highly versatile reference manager. Store, organize, and easily cite as many papers as you need. It's so easy to search and use tags, and is full of clever features. I switched from a different reference manager in 2022, and I haven't looked back.
Chemical Vendor Search
Chemical Vendor Search
I made this tool to save me time searching multiple vendor sites for chemicals. Works best by typing in the CAS number. Powered by Google, so check any missing vendors' websites in case the products are non‑indexed. There's also a US version.
Image by Mfomich, CC0
Ring Replacement Recommender
A data-driven tool from Novartis, for exploring bioisosteric ring replacements in medicinal chemistry. Select your ring scaffold, and the tool shows which potential bioisosteres you might be able to replace it with for enhanced bioactivity. Peter Ertl hosts his other chemoinformatic web tools on his website Molecular.
Image by Fredrik Edfors at the Noun Project
ESI Common Background Ions
A Waters guide to common adducts and background ions in ESI mass spectrometry.
nmrpeaks.com
nmrpeaks.com
If you can't identify an unwanted peak in your NMR, type in its frequency (and multiplicity if desired). This handy web and iOS tool (web API available) will give you a list of suspected impurities. Works with many common solvents, for 1H and 13C NMR.
The Schlenk line survival guide
The Schlenk line survival guide
The Schlenk line survival guide, created by Andryj Borys, is for everything you could ever want to know about Schlenk lines, and more.
Chemistry Tips & Tricks
Chemistry Tips & Tricks
Titled Med Chem Tips and Tricks, this page from the ACS contains useful tricks for any kind of synthetic organic chemist, particularly those based in industry. There's probably something on there you didn't know already!
101 Ways to design an experiment
Intro to DoE: 101 Ways to design an experiment
An article from way back when in 1975, written by an OG DoE practitioner on getting started with the wonder that is Design of Experiments methodology!
Not Voodoo X.4
Not Voodoo X
Recently updated to be easier to use! Clever tricks for new researchers, and some that might be news to an old hand too. The workup section is not to be missed.
Image: Kettle by Jennifer Maestas from the Noun Project
Boiling Point Calculator
A simple tool to approximate a boiling point at a given pressure, given a reference boiling point (and pressure). Created by Witek Mozga.
Writing and Presentation Tools
Communication in Organic Synthesis
Communication in Organic Synthesis
A video guide to organic synthesis communication both for writing and for presentations. This is part of the Synthesis Workshop video series – they're all brilliant!
Character Map
Character Map
A handy set of special scientific characters to copy & paste. Possibly better than memorizing all their alt codes.
Totally Synthetic ChemDraw stylesheet by Paul Docherty
ChemDraw Stylesheets
The cult favourite ChemDraw stylesheet by Paul Docherty, originally posted on his site Totally Synthetic (no longer updated). Download from the links below, and save the file in your ChemDraw Items folder.
Standard mode: Totally Synthetic.cds
Dark mode: Totally Dark and Synthetic.cds
(dark mode is not fully supported by ChemDraw)
Chemdraw Tips
ChemDraw Tips and Shortcuts
I wrote up some ChemDraw tips for PerkinElmer. I hope they're useful for beginners and anyone who's not so familiar with time-saving shortcut keys!
SED Arial font
SED Arial font
My grad school advisor liked us to use ChemDraw with serifs only on the 'I' character, to differentiate them from straight-line bonds. This font does it for you, and is hence named after him. Click here to download, and then install the font file. You can then set it as a default for atom labels in ChemDraw.
Chem-Station templates/span>
ChemDraw structure templates
Easy toolbar-access ChemDraw templates for hard-to-draw structures, including common metal catalysts, organocatalysts, and photoredox catalysts.
Chemistry Dictionary
Chemistry Dictionary
Sick of red, wavy lines under everything you write? Adam Azman's 104,000‑word Chemistry Dictionary for MS Word will put an end to that. Autocorrect will start doing your bidding instead of recasting aminal as animal for the hundredth time.
Automatic Compound Numbering
Automatic Compound Numbering
How to update numbered chemical compounds automatically in MS Word. Old method still works well! Devised by Margaret Scheuermann (Western Washington University), an absolute lifesaver for long writes like theses or book chapters.
SCRE
SCRE (System for Characterizing and Reporting Easily)
A useful Excel-based tool to centralize all characterization information for your compounds and generate a standardized SI- or thesis-ready report. Made by researchers at ICIQ.
zbib.org
zbib.org
This site lets you quickly create a bibliography in any major citation style - even if you don't have all your references stored properly in your reference manager. As with every other tool, I still recommend manually checking afterwards, but it's a huge time-saver!
University of Manchester Academic Phrasebank
Academic Phrasebank
Looking for a scholarly-sounding phrase to boost your confidence while writing? From highlighting previous studies' inadequacies to describing your own trends, the Academic Phrasebank has you covered.
Constructing an Abstract
How to Construct an Abstract
Stu Cantrill of Nature Chemistry has put together a must‑see recipe for how to write an abstract for any kind of scientific paper.
Free Paper Grader
Paper Rater
More than a spellchecker: this free tool analyses vocabulary, grammar, and sentence length, without falling into the usual MS Word traps.
Seminar on Seminars
Seminar on Seminars
Ken Suslick (University of Illinois at Urbana-Champaign)'s popular presentation on how to make effective presentation slides.
HTE
High-throughput experimentation (HTE) is an enabling technology for pharma and other, diverse fields (polymers, battery technology, materials chemistry, biotechnology). The most important difference from bench chemistry is being prepared to adopt an HTE mindset, but HTE can be used for a variety of purposes including reaction optimization, parallel synthesis, crystallization, formulation, and physicochemical measurements. People often ask about recommended papers for how to get into HTE, particularly for small-molecule and reaction optimization purposes, so here is a non-exhaustive list of some great ones. Note: I'm not endorsing any companies involved with the publications.
Luigi da Via (GSK) and I also curate a Peeriodicals overlay journal, where you can read or subscribe for updates of new, relevant, small-molecule HTE papers. You can subscribe by email above, or just follow the RSS feed.
You can view a list of upcoming automation conferences at this link, or a list of upcoming conferences on all chemistry topics here.
The ACS eBook The Power of High-Throughput Experimentation goes across all the following categories, and is an amazing resource written by HTE experts from around the world! I put in a chapter on Data Visualization in High-Throughput Experimentation.
Volume 1: General Topics and Enabling Technologies for Synthesis and Catalysis
Volume 2: Case Studies from Drug Discovery, Drug Development, and Catalyst Discovery
Myths of high-throughput experimentation and automation in chemistry
Chem 2021, 7, 2259–2260
10.1016/j.chempr.2021.08.012
The Evolution of High-Throughput Experimentation in Pharmaceutical Development and Perspectives on the Future
Org. Process Res. Dev. 2019, 23, 1213–1242
10.1021/acs.oprd.9b00140
The power and accessibility of high-throughput methods for catalysis research
Nature Catal. 2019, 2, 2–4
10.1038/s41929-018-0220-4
Rise of the Robots
Chem. Eur. J. 2020, 26, 3194–3196
10.1002/chem.202000656
High throughput analysis enables high throughput experimentation in pharmaceutical process research
React. Chem. Eng. 2019, 4, 1895–1911
10.1039/c9re00234k
Reaction screening in multiwell plates: high-throughput optimization of a Buchwald–Hartwig amination
Nat. Protoc. 2021, 16, 1152–1169
10.1038/s41596-020-00452-7
Practical High-Throughput Experimentation for Chemists
ACS Med. Chem. Lett. 2017, 8, 601–607
10.1021/acsmedchemlett.7b00165
A Perspective on the Analytical Challenges Encountered in High-Throughput Experimentation
Org. Process Res. Dev. 2021, 25, 354–364
10.1021/acs.oprd.0c00463
Autonomous platforms for data-driven organic synthesis
Nat. Commun. 2022, 1075
10.1038/s41467-022-28736-4
The Power of High-Throughput Experimentation in Homogeneous Catalysis Research for Fine Chemicals
Eur. J. Org. Chem. 2003, 799–811
10.1002/ejoc.200390122
Autonomous Discovery in the Chemical Sciences Part I: Progress
Angew. Chem. Int. Ed. 2020, 59, 22858–22893
10.1002/anie.201909987
Autonomous Discovery in the Chemical Sciences Part II: Outlook
Angew. Chem. Int. Ed. 2020, 59, 23414–23436
10.1002/anie.201909989
High-Throughput Experimentation as an Accessible Technology for Academic Organic Chemists in Europe and Beyond
Chem. Methods 2023, e202200059
10.1002/cmtd.202200059
Automation and computer-assisted planning for chemical synthesis: A primer
Nat. Rev. Methods Primers 2021, 1, 23
10.1038/s43586-021-00022-5
Engineering Chemistry Innovation
ACS Med. Chem. Lett. 2019, 10, 703–707
10.1021/acsmedchemlett.9b00096
Nanomole-scale high-throughput chemistry for the synthesis of complex molecules
Science 2015, 347, 49–53
10.1126/science.1259203
High Throughput Strategies for the Discovery and Optimization of Catalytic Reactions
Angew. Chem. Int. Ed. 2019, 58, 7180–7191
10.1002/anie.201812534
High-Throughput Automation in Chemical Process Development
Annu. Rev. Chem. Biomol. Eng. 2017, 8, 525–547
10.1146/annurev-chembioeng-060816-101411
Recent Advances in High-Throughput Automated Powder Dispensing Platforms for Pharmaceutical Applications
Org. Process Res. Dev. 2020, 24, 2752–2761
10.1021/acs.oprd.0c00411
Recent Advances in High-Throughput Automated Powder Dispensing Platforms for Pharmaceutical Applications
Org. Process Res. Dev. 2018, 22, 1500–1508
10.1021/acs.oprd.8b00259
Automated High-Throughput Partition Coefficient Determination with Image Analysis for Rapid Reaction Workup Process Development and Modeling
Org. Process Res. Dev. 2021, 25, 2738–2746
10.1021/acs.oprd.1c00343
A Validated “Pool and Split” Approach to Screening and Optimization of Copper-Catalyzed C–N Cross-Coupling Reactions
J. Org. Chem. 2021, 86, 1528–1539
10.1021/acs.joc.0c02392
A “Pool and Split” Approach to the Optimization of Challenging Pd-Catalyzed C–N Cross-Coupling Reactions
J. Org. Chem. 2022, Articles ASAP
10.1021/acs.joc.2c00104
Chemistry informer libraries: a chemoinformatics enabled approach to evaluate and advance synthetic methods
Chem. Sci. 2016, 7, 2604–2613
10.1039/C5SC04751J
MISER chromatography (multiple injections in a single experimental run): the chromatogram is the graph
Tetrahedron Asymmetry 2010, 21, 1674–1681
10.1016/j.tetasy.2010.05.029
High-Throughput Reaction Screening with Nanomoles of Solid Reagents Coated on Glass Beads
Angew. Chem. Int. Ed. 2019, 58, 7987–7991
10.1002/anie.201900536
Versatile Methods to Dispense Submilligram Quantities of Solids Using Chemical-Coated Beads for High-Throughput Experimentation
Org. Process Res. Dev. 2019, 23, 1900–1907
10.1021/acs.oprd.9b00213
High-Throughput Electrochemistry: State of the Art, Challenges, and Perspective
Org. Process Res. Dev. 2021, 25, 2587–2600
10.1021/acs.oprd.1c00167
High-Throughput Analysis for High-Throughput Experimentation in Organic Chemistry
Ed. Paul Knochel, Ch. 9.02 in Comprehensive Organic Synthesis II (Second Edition), Elsevier, 2014. pp. 28–53
10.1016/B978-0-08-097742-3.00921-6
A platform for automated nanomole-scale reaction screening and micromole-scale synthesis in flow
Science 2018, 359, 429–434
10.1126/science.aap9112
Nanoscale synthesis and affinity ranking
Nature 2018, 557, 228–232
10.1038/s41586-018-0056-8
Reagent Design and Ligand Evolution for the Development of a Mild Copper-Catalyzed Hydroxylation Reaction
Org. Lett. 2017, 19, 3033–3036
10.1021/acs.orglett.7b01403
Enabling synthesis in fragment-based drug discovery by reactivity mapping: photoredox-mediated cross-dehydrogenative heteroarylation of cyclic amines
Chem. Sci. 2019, 10, 2264–2271
10.1039/C8SC04789H
Predicting Performance of Photochemical Transformations for Scaling Up in Different Platforms by Combining High-Throughput Experimentation with Computational Modeling
Org. Process Res. Dev. 2020, 24, 2128–2138
10.1021/acs.oprd.0c00182
Microtiter Plate (MTP) Reaction Screening and Optimization of Surfactant Chemistry: Examples of Suzuki–Miyaura and Buchwald–Hartwig Cross-Couplings in Water
Org. Process Res. Dev. 2018, 22, 1453–1457
10.1021/acs.oprd.8b00200
The Open Reaction Database
J. Am. Chem. Soc. 2021, 143, 18820–18826
10.1021/jacs.1c09820
Predicting Reaction Yields via Supervised Learning
Acc. Chem. Res. 2021, 54, 1856–1865
10.1021/acs.accounts.0c00770
Bayesian reaction optimization as a tool for chemical synthesis
Nature 2021, 590, 89–96
10.1038/s41586-021-03213-y
Ultrahigh-Throughput Experimentation for Information-Rich Chemical Synthesis
Acc. Chem. Res. 2021, 54, 2337–2346
10.1021/acs.accounts.1c00119
Changing the HTS Paradigm: AI-Driven Iterative Screening for Hit Finding
SLAS Discov. 2021, 26, 257–262
10.1177/2472555220949495
Next-Generation Experimentation with Self-Driving Laboratories
Trends Chem. 2019, 1, 282–291
10.1016/j.trechm.2019.02.007
Laboratory automation & accelerated synthesis: Empowering tomorrow's chemist
US National Academies (3.5 + 2.5 h)
Accessible high-throughput experimentation: From startup to scale
Cell Press (51 min)
Accelerating research via high throughput workflows
Unchained Labs YouTube Channel (36 min)
Making high-throughput experimentation more accessible and efficient
Unchained Labs YouTube Channel (33 min)
Bayesian optimization for chemical synthesis
Unchained Labs YouTube Channel (58 min)
Hybrid mechanistic & machine learning models,
Data management for high-throughput chemistry
VISTA conference (63 min)
Artificial intelligence-driven autonomous lab by IBM & ChemSpeed
Chemspeed Technologies (50 min)
Driving digital transformation in the lab with structured and accessible research data
Lab of the Future Digital Dialogues (63 min)
Data science-driven autonomous reaction optimization by UBC, Merck Co Ltd & ChemSpeed
Chemspeed Technologies (46 min)
Feeding the beast: Sample supply for future closed-loop make-test-design platforms
Chemspeed Technologies (73 min)
Combining AI and automation towards the prediction of crystal structure landscapes
Chemspeed Technologies (48 min)
Bayesian reaction optimization: Part I, Part II
Center for Computer-Assisted Synthesis (8 + 15 min)
Labroots Laboratory Automation conferences:
Laboratory Automation 2021
Laboratory Automation & Informatics 2020
Laboratory Testing & Automation 2019
Laboratory Automation 2018
Laboratory Automation 2017
20/15 Visioneers Conference Recordings
Recordings of multiple conferences
LRIG (Laboratory Research & Innovation Group) YouTube Channel
YouTube channel
Coding
Women Who Code
Women Who Code is an amazing global organization supporting women in technology. They provide a lot of free resources, including beginner resources. There are also plenty of local WWC networks that host both virtual and in-person training and events.
Data Science Hangout
An informal weekly chat run by Posit. It's very cross-industrial and international, and we usually end up talking about careers and daily life in data science.
FreeCodeCamp
People often ask me how I got started as a total beginner to basic coding. A while ago (for this website!), I learned about html and CSS on FreeCodeCamp. They do much more, including Python, data science and Git, and although I haven't tried those tutorials, I've heard good things too.
R for Data Science
The guy who taught me R (mikeksmith) has been working with it for over a decade. He swears by this book, and it's all available for free online, thanks to author Hadley Wickham – Chief Scientist at Posit. This is a general introduction for newbies to R (some basic programming skills may be useful), on how to use it for data science.
Harvard CS50 Introduction to Computer Science
The famous Harvard CS50 'Introduction to Computer Science' course, which is free or payable for a certificate, on edX. It's self-paced and online, and doesn't require any prior comp sci or coding knowledge.
MolSSI Coding Workshops
The Molecular Sciences Software Institute (MolSSI) creates brilliant introductory and intermediate coding workshops of all kinds for molecular scientists. They also run online workshops, and in-person courses in the US.
pythoninchemistry
pythoninchemistry is an open source teaching initiative from Bath University. I hear great things about it for total newbies to Python. They plan on continually adding new resources.
Practical Cheminformatics with Open Source Software
A collection of Jupyter notebooks for learning chemoinformatics, written by Patrick Walters.
PySimpleGUI
PySimpleGUI is exactly that – simple. It's a way to develop all kinds of GUI's in Python. I use this with PyInstaller to create familiar-looking Windows programs for people who don't have Python installed. There's even a comprehensive course to learn PySimpleGUI on Udemy!
PyInstaller
PyInstaller turns Python files into executable files for all popular operating systems. I use it in conjunction with PySimpleGUI to create familiar .exe programs for users who don't have Python installed.
DeepChem
Machine learning for chemistry, with extensive tutorials.
Regex101
A simple and easy regex tester for all flavours of regular expressions! I use this every time I have a regex. There's the web version, and also an API.
Write better Python code today
A long and valuable list of pertinent tips on how to make your Python code more readable for future developers.
Awesome Python Chemistry
A list of Python frameworks, libraries, software, and resources for chemists.
Interesting
Highlightable periodic table
Highlightable periodic table
I made an offline script back in 2019 (before I knew coding really!), so you can create your own highlighted periodic table in MS Excel. I've been using it as a checklist of all the elements I've ever used in the lab!
Bristol University Molecule of the Month
Bristol University Molecule of the Month
Reportedly one of the longest-running chemistry webpages, this features a new and interesting molecule every month to learn a little about. Contributions are sourced from the public, including a few from high school groups!
The Periodic Bagel podcast
The Periodic Bagel podcast
Podcast of fun chemist interviews and epic bantz, created by Chemjobber and Alex Goldberg.
IBM RXN logo
IBM RXN
IBM RXN is an AI-driven reaction prediction tool. Input your reactants, and if you wish, reagents (eg: Pd) to see the AI-predicted products, with a confidence percentage.
OUSS logo
Oxford University Scientific Society
OUSS is the world's oldest, student-run scientific society. You don't have to be a student or academic to be a part of it. Check out their popular Facebook page full of interesting science content.