Starting as a new student

When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done. There are a few things you will have to take care of yourself, preferably before starting the internship:

• Obtaining a Radboud campus card with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).
• A science account, which you can get from C&Cz as a student or they are applied for by Marieke to C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at here.
  

See also Presentation for new SOC members.

The mandatory stuff

Registration & Access to the wings

In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary Marieke Egbertzen (marieke.egbertzen@ru.nl). She will ask you to read & sign the following documents:

• The registration new employees, which you can fill in yourself and send to Marieke.
• The registration in wings Cluster Orgchem.docx for which you will need a signature from your supervisor.
• A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is Declaration Guest researchers 2023.docx
• The checklist for new members of the Molecular Chemistry Cluster. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.

After signing the forms, Marieke Egbertzen (marieke.egbertzen@ru.nl) will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.

Going into the lab

In order to go into the lab you need to take care of the following things:

• Complete the safety test. Prior to taking the test you need to acquaint yourself with the safety manual (found here) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.
• Obtain the relevant safety equipment such as a lab coat and safety goggles. These can be obtained from Hernando Tuñon (hernando.tunon@ru.nl) for working in Mercator and Samuel Bosma (samuel.bosma@ru.nl) for working in Huygens.
• Obtain a physical lab journal (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from Hernando Tuñon (hernando.tunon@ru.nl) in M3.
• Gain access to the electronic lab notebook (ELN) for which we currently use Chemotion. Chemotion can be accessed here. Daniel Blanco-Ania is the person responsible for this and can give you access. Hence, send an email to him or pass by his office. Important: as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found here. The minimal requirements according to the Boltje lab of ELN recording are found here.

Lab equipment access

Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at the booking portal, where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below.
See Booking Platform for Scientific Devices for more information.

Ensure you make a backup of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.

NMR access

NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue you are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.

NMR in Huygens

There are two NMRs in wing 4, floor 3 of the Huygens building: a 400 MHz and a 500 MHz. The 400 is always in automation mode, which means you add your sample to a queue, and it will measure your sample automatically. To minimize the waiting time during the day your experiments cannot be longer than 10 minutes. If they are, you will have to measure them during the night, either on the 400 or 500.
The 500 is not in automation mode during the day and typically not available for students.
Please ask for training before using.
Training: Nuwanthika Kumarage.

MS access

There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. The ISQ in Huygens (HG03.411) is a MS for pure samples only, while the ISQ in Mercator is a LC-MS, for analyzing mixtures. A guide on how to operate the ISQs can be found here, which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.
The current mass tutors are Daan Hamstra and Robin Schenker for the ISQ in Huygens, and Robin Schenker and Enebie Ramos Caceres for the ISQ in Mercator 3.

HRMS

High resolution mass spectrometry (HRMS) is used to obtain high quality mass spectra. This is not necessary for every sample, but only for important compounds and when lower resolution measurements are unclear.
Jan Zelenka is in charge of measuring HRMS. These measurements typically take place once a month. Before each measurement, Jan will send round an email asking people to submit samples.

Other equipment

Below are some other devices which are available. Not all of these are necessary for working here, but you may find some of them useful.

Purification equipment

Preparative HPLC

There are several preparative HPLCs available for purifying synthesized compounds:
Wing 1 in the Huygens building has two standard reverse phase prep HPLCs, and a larger one (for runs of 10-150 mg of sample) with a mass detector. All have autosamplers and automatic collectors.
Instructional video
Please ask for training before using.
Training: Frank Veldhuizen, intern supervisor or other user.

Biotage Isolera

We have several automatic flash chromatographs with column cartridges for quick purification after synthesis.
Most supervisors want their interns to learn by running several glass columns manually before being allowed to use the Biotage.
Quick guide
Training: Intern supervisor or other user.

Analysis equipment

IR

HG03.222
Infrared spectrums are usually not essential, but they are needed for full characterization of a compound. IR can also be useful for identifying functional groups that are otherwise difficult to characterize. For example, azide groups are hard to detect using NMR, but are easily found with IR spectroscopy. Samples can be pure solid, liquid, or dissolved in a volatile solvent.
Training: Frank Veldhuizen.

Analytical HPLC

HG03.130
Used to determine the purity of a sample.
Training: Frank Veldhuizen, intern supervisor or other user.

Chiral HPLC

HG03.130
Used to determine the racemization of a sample.
Training: Frank Veldhuizen, intern supervisor or other user.

LC-MS

HG03.411
The LC-MS (“The Fleet”) can be used to analyse samples and determine the mass of compounds.
Training: Robin Schenker, Helene Amatdjais-Groenen, Frank Veldhuizen.

SFC

HG03.120
SFC (supercritical fluid chromatography, also known as convergence chromatography or CC) is a chromatography method using supercritical CO2 as solvent. It is faster and more efficient than HPLC. Several columns (including chiral) are available. This instrument has a UV-Vis detector and a mass detector.
Instructional video
Please ask for training before using.
Training: Frank Veldhuizen.

TLC-MS

HG03.115
This instrument can quickly make a mass spectrum of a spot on a TLC plate. Aluminium TLC plates are preferred for this device.
Instructional video
Please ask for training before using.
Training: Frank Veldhuizen.

Synthesis equipment

Synthesis microwave

Can be used to initiate reactions at high temperature.
Training: Frank Veldhuizen?

Autoclave

HG03.115 H9
For high pressure reactions up to 60 bar.
An extensive manual is available here.
Training: ?

High pressure machine

HG03.442
For high pressure reactions up to 15 kbar.
Manual
Training: Frank Veldhuizen

Working from home, vacation or being sick

When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.

Regular lab events

Regular lab events are generally lab specific and are found at Regular lab events.

Synthesizing a new compound

Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a novel compound (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to keep an aliquot (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.

Full characterization of a NCE

TLC, NMR, and HRMS are mandatory for new compounds.
An infrared spectrum can be made if the structure is unclear from NMR and HRMS, and is necessary for publication.

How to behave in the lab

In order to have a productive and healthy working environment, please adhere at least to these rules:

• If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.
• If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.
• Keep the general working area and benches clean and tidy.
• Replace liquid waste containers before they are full but rather at 80% capacity. See Waste disposal.
• Replace solid waste containers. See Waste disposal.
• Most labs have a weekly cleaning moment. Please be present for these moments.

General (analysis) software

Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC

Chemdraw

Chemdraw is a molecular drawing software which allows us to draw compounds and reactions. The Chemdraw installation guide is detailed here by CnCz. Within SOC we adhere to the 'ACS Document 1996' drawing style which is activated with 'File | Apply Document Settings From | ACS Document 1996'.

MestreNova

MestreNova is a licensed software with which we can analyze recorded NMR-spectra. MestreNova can be obtained from the install network drive of CnCz, where also an install guide is found.

When leaving the lab

When finished with your internship, it is important to leave the lab in a good state, and the data of your experiments should be stored properly. Use the checklist below to make sure you do not miss anything.
Leaving the lab Checklist

Other useful but non-mandatory things

Molecular modelling software

At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at Molecular software.

Shared drives & back-ups: Surf-drive

Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.

Knowledge transfer

NMR

As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:

• The basics
• The more advanced