You can upload mol and sd files from MNova via the "Upload" facility below the structure editor (sd files only work in MNova 11 or higher). The structure and custom numbering, if in the file, will be read. From the sd file the shift lists will also be read. If there is more than one spectrum in the files you can choose which one you want to submit in the next step ("Set spectrum type"). If you want to submit more than one spectrum you can repeat the upload after submitting a spectrum.
Set spectrum type: Here you enter the type of the spectrum (13C, 1H etc.) you want to submit.
Add shifts: Here you enter the signals of your spectrum. For 1D spectra you need to give one signal per line, shift and intensity separated by ;. Example:
The intensities are optional. They will be scaled to be in a range from 0 to 1, if they are not. After you input the spectrum, click the "Submit signals". You can add additional signals later by the same steps. You can also upload a jcamp file by hitting "Browse..." and choosing the file. If the file contains a peak table, this will be used, if not, a peak picking is performed. If the spectrum type (nucleus) is in the file, it will be used, else you also need to choose the spectrum type. If the spectrum type is 1H, you need to perform a partly manual peak picking. You will be presented with an applet containing all individual peaks. Most likely, these will contain multiplets, noise etc. You need to left click on the field and go over some peaks and release the mouse. Then the average of all peaks in this range will be calculated and added to the peak list on the right. If you submit, this peak list will replace the automatic peak list.
For 2D spectra the format is slight different:
The first two figures are the values on the two axis. The third gives the coupling constant and is optional. These peaks will not be processed in any way, but saved as given.
Do assignment (for standard 1D spectra only): Here you have got one line per atom, showing a drop-down box for the shifts and the expected range for the shift. These predictions are calculated based on HOSE codes, as in the prediction function. Additionally there is a range for the signal given. In some rare cases the predicted value will be identical with one of the limits of the range. Blue figures indicate that your value is inside this range, red means outside. Choose a shift for every atom. In the "Atom identifier" column you can enter identifiers for the atoms (any character allowed) which will be used instead of the standard numbers. You should make sure identifiers are unique. If there is no identifier for an atom the number from the "Atom number" column will be used. You can also use this to renumber the atoms by using numbers as identifiers. Again the numbers should be unique. If you enter a spectrum for an existing structure you can chose an existing set of identifiers below the structure diagram. "Standard" means the numbers as they appear in the structure drawing. You can also edit an existing set by changing some identifiers. Shifts not assigned can be deleted in a later step or kept as unasssigned - this is also a way to get rid of mistyped shifts. After you assigned all signals, press the "Submit assignments" button. If you forgot to submit a signal, finish this step and go to "Add shifts" and then "Do assignments" again. If you have entered only one shift, it gets assigned to all atoms automatically and you may skip this step. You can also enter multiplicities for atoms (except for proton spectra, the default is calculated by the proton count of an atom) and coupling constants for every atom-atom combination. If you have not entered the shifts before this step, you can them enter here directly.
Add miscallenous data: Please choose first if the spectrum is measured or calculated. Then enter the chemical names, any links to web-literature about the molecule and the CASNumber and autonom name of the molecule, if known (you do not need to do that if the molecule is already in the database). From time to time IUPAC and index names for molecules in nmrshiftdb2 will be auto-created, so you do not need to enter them. You can also enter literature and web pages about the spectrum. Further more, you can give keywords for the molecule and categories for the spectrum - either existing ones or new ones. Molecule keywords should be compund-specific, e. g. alcaloids. The spectrum categories, on the other hand, should refer to the spectrum, e. g. a certain institution they have been measured at.
You also need to enter the conditions for the spectrum (required). Which conditions are needed depends on if the spectrum is experimental or calculated, which can bothe be stored in nmrshiftdb2. The experimental spectra are acquired by dissolving a small amount of a real world compound in a solvent. The solution is inserted into a strong magnet of a given field strength at a given temperature (typically around room temperature) and irradiated with strong electromagnetic pulses in the radio band. The electromagnetic response given by the molecule yields the NMR spectrum, which can - for the 1-dimensional case - be characterized as a collection of signals at a particular radio frequency, one for each atom of the chemical element type for which the experiment has been performed.
While physicists use the SI unit "Tesla" as the correct unit for magnet strength, NMR spectroscopists traditionally use the resonance frequency of protons, which depends on the magnet strength, to denominate the strength of an NMR magnet. In magnets with a magnetic field strength of 11.75 Tesla, for example, protons resonate at 500 MHz.
The parameters used by nmrshiftdb2 to characterize the experimental conditions under which a spectrum has been recorded are:
Temperature [K] (example value: 298)
Spectrometer Frequency for 1H [MHz] (example value: 500). Note that the frequency of the spectrometer is required, irrespective of the nucleus. This will be tranformed automatically. E. g. if you measure on a 500 MHz machine and the spectrum type is 13C, you enter 500 and 125 MHz will be displayed as "Field Strength [MHz]" in the database.
Solvent (example value: CDCl3)
Assignment method (example value: longrange Hetcor). If you are a labgroup user (not relevant for public servers), you will be presented with a list of possible experiments in your lab. The experiments which you click will be concatenated to form the assignment method. Alternatively, you can enter a text.
The calculation conditions focus on describing the quantum chemical computer program, which has been used to perform the calculation as well as the theoretical methods involved. There are a number of different ways to calculate an optimal molecular geometry and its associated NMR spectrum. It is important to list the terms commonly used for these methods together with the calculated spectrum in order to give users the opportunity to judge the quality of the calculated data.
Since the qualitiy of a calculated nmr spectrum depends on the quality of the underlying molecular geometry, both the calculation method for the geometry as well as the method for calculating the chemical shifts have to be listed.
At the time of this writing we restrict the type of calculated spectra which are allowed in nmrshiftdb2 to those calculated by so called ab initio methods, as opposed to semi-empirical and other methods, like HOSE code based or neural network based methods.
The parameters used by nmrshiftdb2 to characterize the calculation parameters by which spectrum and molecular geometry have been calculated are:
Program (example value: Gaussian98)
Means "Quantum Chemical Program". The computer program by which the calculation has been performed (e. g. Gaussian 98)
NMRMethod (example value: GIAO)
A methods described in the literature by which the Magnetic shielding tensors are calculated (e.g. GIAO for Gauge Independent Atomic Orbitals or CSGT for Continuous Set of Gauge Transformations)
GeomModel (example value: B3LYP)
The model chemistry used for the geometry optimization, like RHF for Restricted Hartree Fock or B3LYP for Becke's frequentyl used DFT parameter functional.
GeomBasisSet (example value: 6-31G(d))
The basis set used for the geometry optimization, like 6-31G(d)
NMRModel (example value: B3LYP)
The model chemistry used for the shielding tensor calculation (possible values like in GeomModel)
NMRBasisSet (example value: 6-31G(d))
The basis set used for the shielding tensor calculation (possible values like in GeomBasisSet)
NMRStandard (example value: TMS)
Ab Initio calculations of magnetic properties yield shielding tensors, which are absolute physical quantities, whereas experimental spectra yield so called NMR chemical shifts which are given relative to the resonance frequencies of a given standard compound (usually Tetramethylsilane, TMS). Isotropic shielding values obtained by an ab initio calculation thus need to be subtracted from the isotropic shielding values obtained for a reference compound (usually also TMS). The calculation for the reference compound needs to be performed under exactly the same calculation conditions that have been used for the actualy compound in question.
Add literature items (optional): Here you may enter literature references for your data. Press "Submit literatures" once you have entered the literature items.
Attach files: Here you can attach a JCAMP-DX, PDF, raw data or image file to your data. The file will be saved and displayed with the data and be available for download. Note that this file is saved independently from the peak list. If you used a JCAMP-DX file for creating the peak list, the file uploaded for the peak list will also be saved. You can remove the file using this function if you do not like your file to be included. The image file is mandatory for 2D and 1D spectra other then the standard ones.
Final submit: Once you have entered all the data (the timeline is completely green) you finally submit your data here. You can choose to submit the data as private data (see Private Submissions ) and you can decide to submit a further spectrum for this molecule. If you choose this option, you will be taken to the start of the timeline with molecule-related data taken from your last submit. Click the "Write to database" button to finish your submit.
Your data will not be available immediately, but after they have been confirmed by a reviewer (you will get an email telling you who is your reviewer). To check the status of your contributions, use the "Show all my contributions" link on the Search pane. If for some reasons your submit is interrupted, you can continue that when you log in next time. You will see a blue box on top of the submit page where you can choose to continue or to discard the broken submit.
If you are logged in, you can edit molecules you have entered. In the details portlet, you will see a button "Edit this spectrum". If you click this, you can follow the submit procedure and change anything you like. The changes need to be approved by the reviewer of the original spectrum.
You can keep data you submit private and publish them later. This can be done by checking the checkbox "I want to keep this submission private" on the final submit page. This means that the data will not be visible to anybody except you. For you, they will be found by the normal searches and can be viewed via the link "Show all my contributions" on the search page or via your personal page (tab "My private submissions"). If you view the data, you will find the export facilities in the normal place and a button "Submit for review" under your spectrum. If you press this button, the dataset will be submitted for review and will be treated like any other submit. In the details view, you can also download your data in the same formats as other data. You can also edit your data and keep them in private status. In this way, you can enter your data while working on them and only publish them once you have the final data. When you view your private data there is a "Copy link for reviewer" option, where you can copy a link which enables access to this spectrum for a third party. The link contains a secret key and only works for this spectrum. Everybody who gets the link can view the specrum. Only you have access to the link and can decide to give it to others.
A word on data protection here: Whilst we take any reasonable effort to secure our servers agains intruders, we cannot guarantee that there is no succesfull hacker attack. So we cannot take responsibility for loss or damage incured by your private data becoming known to third parties in any way.
Reviews can only be done by registered reviewers. If you are one, you get notification by email about reviews assigned to you. In this email you find a direct link to the review page. You may also enter the id given in the email in the text field on the review page.
In every case you get a graphical representation of the molecule and the spectrum. You will also find the signals assigned to an atom and the predicted signals and range, as during a submit. Decide if the data seems correct and click one of buttons at the bottom of the page. "Accept" means that data will be available for searches from now, "Reject" means spectra will be deleted from the databse, "Edit and accept" gives you the chance to change things before data becomes available, with "Abort" nothing happens and with "Send" you can send an email to the reviewer. With the "Ask the contributor to edit the contribution ?"-checkbox you can decide if the user should be asked to change something in the data. Nothing happens to the data, so you will need to review them later (you will be notified if the submitter has edited the data). After a review it may take up to an hour till data actually become available for spectrum and structure searches (other searches work immediatelly).
Via the "Personal Page" link on top of the page, you can go to a list of all reviews assigned to you and not yet done. Here you can choose an unreviewed spectrum and go directly to the review page.
As a logged-in reviewer, you can edit all data by clicking the "Edit this spectrum" button in the details portlet. You can follow the input procedure and change anything. A review is not necessary.
nmrshiftdb2 can do an automatic assignment if you have a spectrum and a structure. This can help you in preparing data e. g. for a publication. To do so, you need to enter your molecule (about entering molecules see Submitting Spectra) and your spectrum as a list of shifts (ppm values) and to submit both. Your structures are collected in the structures history. The assignment is done by doing a prediction and assigning your shifts so that the similarity between the prediction and your spectrum is maximized. Therefore, the quality of the assignment depends on the quality of the prediction and the same limitations apply (see Prediction). You are then presented with the assignment in a table and a picture. If you hover over the table, an atom and its shift are marked. The table also gives the prediction for each atom and the difference of the prediction and your shift.
Once the assignment is done, you actually have an almost complete nmrshiftdb2 dataset. You are therefore encouraged to submit your data by hitting the "submit your data" link above the table. During the submit, you can also correct assignment manually and add a literature reference. Submitted data can also be exported for publication.
The Quick Check option offers a possibility to enter a 13C and a 1H spectrum as easily as possible and produce a quality measure for the spectra at a mouseclick. If satisfied the spectra can be submitted. A tutorial on the Quick Check is available.
You can upload mol and sd files from MNova directly (sd files only work in MNova 11 or higher). The structure and custom numbering, if in the file, will be read. From the sd file the 13C and a 1H spectra are read.
nmrshiftdb2 offers you the possibility to predict spectra of all type. The quality of the prediction depends on the database content, so for types with only a few spectra it is unlikely you get a good prediction. To do so, you need to enter your molecule (about entering molecules see Submitting Spectra) and to submit it. Your structures are collected in the structures history. You can also choose (via "Use measured and/or calulated spectra") to use only measured or calculated spectra (checking none of both options has the same effect as checking both). There might be errors in the calculated spectra sometimes, so measured only is the default choice. You are then presented with the predicted spectrum in a table and a picture. If you hover over the table, an atom and its shift are marked.
For spectrum types other than 1H the predictions are based on HOSE codes. These basically describe the neighbourhood of an atom in concentric rings ("spheres"). If two molecules have a similar neighbourhood, they will have the same HOSE code for a certain number of spheres. The number of spheres used is also given. The more spheres used, the better the prediction. Up to 6 spheres may be used; if less are actually used this means that there are no atoms with a higher number of identical spheres in the database. Since the predictions are won of similar atoms in the molecules in nmrshiftdb2, there can be multiple values for one molecule. What you get in the shift column of the table is actually the average of these. The statistics column gives also the minimum, the maximum, the median and the standard deviation of all values.
The checkbox "Use 3D hose codes" is checked by default. If this is used, a stereochemically extended HOSE code is used. This will lead to stereochemistry aware predictions with respect to double bond configurations and chiral centres. Figure 1 and Figure 2 give examples for this. Also certain diastereotopic carbons are respected (see Figure 3). Note that two requirements must be fulfilled for a stereochemistry aware prediction: you must specify the input with wedge bonds (3d coordinates, "perspective drawings" etc. will not be considered) and a matching neighbourhood must exist in the database. If this is not the case, prediction falls back to normal HOSE codes.
Figure 1. A tetrahedral centre with different predictions for atoms 24 and 31, which would be considered equal in normal HOSE codes.
Figure 2. A double bond configuration with different predictions for atoms 22 and 24, which would be considered equal in normal HOSE codes.
Figure 3. The diastereotopic atoms 8 and 9, which would be considered equal in normal HOSE codes, have different shifts.
For proton prediction apart from HOSE code, a prediction based on 3D descriptors and Support Vector Machines ("SVMs") is offered. This can give better results than HOSE codes, but should be treated with care. See this paper for details.
In order to enable quality control by users, we have a rating system working. Every spectrum has a rating from 1 to 10, default is 10. Every registered user can "vote" on a spectrum. The rating of a spectrum is the average of all ratings, including the default rating. There are two important thresholds: If the rating is less than 5, it is no longer used for predictions, is not included in the spectrum search and does not count for the current usage statistics. If the rating is below 3, it needs an extra click to view it. Spectra never get deleted because of ratings. If the rating of a spectrum falls below the threshold, the administrators are notified and can check the spectrum.
nmrshiftdb2 automatically collects the last 20 structures you painted in search by structure, predict or submit. You can load one of these structeres at any time by clicking the "Import from structures history" button next to a sketcher. You get a window where you can choose a structure. Clicking "Import" imports this and closes the import window.
The collection of stcructures is session-based, which means that structures are lost if you log in, log out or close the browser window. This is not true for registered and logged in users - they will find their old structures history if they log in again.
nmrshiftdb2 can work as a user and order administration system for NMR labs. Note that the lab system is an additional feature which must be installed in-house. The standard nmrshiftdb2 servers do not offer it. The concept of the lab system is centered around two roles, operator and user, and the concept of an order.
Users can assign themself membership of a labgroup, either as operator or user. They need to be approved by the group leader. Once this is done, a user can submit orders and a operator can work on them.
A user, when logged in, has an additional tab "NMR lab administration". Here, he has a form which he needs to fill out to submit an order. There are three possible ways to handle an order:
an operator: This means a lab operator will handle the order. After the submission, it will show up in the list of open orders. If a operator has dealt with this, it goes to the fullfilled orders list. The user can click on a fullfilled order and can download the raw data files then. He can also start an assignment of peaks here, which is done via the normal NRMShiftDB input.
By the user himself: Here the user needs to do the measurement. When he clicks on the order on the open orders list, he can browse through the data files and attach them to the order. Once this is done, the procedure is the same as above.
By the user via a sample changer: Here the user needs to put his probe into the sample changer and it will be measured during the next night. The data files get attached automatically and the order goes to the fullfilled orders list.
The user can delete (=cancel) orders which have not yet been processed. Once an order is processed (i. e. has files assigned to it) it can not be deleted, because it is needed for statistcs. It stays in the "done orders" till a peak assignment is done. If the user does not want to do a peak assignment, he can view the order by clicking it and choose "I do not want to assign the spectra", having checked "confirm" before, which will take the order from the list as well. If the user wants to see the the orders which either have a peak assignment or where the user decided not to do it, he can choose "Also show orders already assigned" and press "Change dates/show alreayd assigned". With "I want to measure this sample again" the order is marked as not to be assigned and the user gets the submit order form, with the data of the order filled in. There is also a direct link to the Faces Scheduling System on the page, which only works, if user name and password are the same in Faces as in nmrshiftdb2
An operator, when logged in, also has the "NMR lab administration" tab. He sees a list of open orders. When clicking on one, he can assign raw data files to it and declare the order to be finished. The operator can also delete "operator"-orders. It will then disappear from the list. The worker can also view orders, which have been done by users or sample changer for a certain period. These orders can be made an "operator"-order by the operator. This is helpful in case the automatic assignment does not work (e. g. misspelled ID), it can then be processed manually. Furthermore, operators can generate statistics in pdf format.
One operator is designated as group leader; he can admit users to the group and administer the spectrometers and experiments.
In order to create a new labgroup on a machine (which must be under the administration of the group. which wants to use the feature), an entry into the labgroup table must be done manually.