Teaching with Schrödinger

Updated: 1-23-22

Introduction to Infrared Spectroscopy
Created with: Release 2021-3
Prerequisites: working knowledge of Maestro
Files Supplied: IR_worksheet
Categories:
organic chemistry

About this Lesson
In this lesson, students will learn the fundamentals of infrared (IR) spectroscopy and themany different kinds of vibrational excitation, including stretching and bending. IR
spectroscopy can be used to identify which functional groups are present in acompound.
Using Maestro, students will perform frequency calculations and visualize various
vibrational modes of small molecules. Students will then generate IR spectra, identify
various regions that correspond to particular functional groups, and determine which IR
spectrum matches to a given organic compound.

Learning Objectives
Visualize vibrational modes of small molecules by performing frequency
calculations● Correspond a given IR spectrum to an organic compound through functionalgroup identification●

1
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Standards●

ACS Guidelines○●

ETS Chemistry GRE○●

Deducing structures by interpretation of modern spectroscopic and computational
data (Practical Topics)
Structure, Bonding and Nomenclature – IR Spectroscopy (3.A)

AAMC MCAT○

Molecular Structure and Absorption Spectra (4D)

Assessments
The following types of formative assessments are embedded in this lesson:●●

Assessment of student understanding through discussion of warm-up questions andfilling in any knowledge gaps about functional group identification
Visual assessment of student-generated IR spectra and correct molecule matching

Warm-Up Questions: To be done on their own or at the beginning of class
Watch the Khan Academy videos on IR spectroscopy.

All of the molecules shown above absorb IR radiation in the range between 1600 and 1850
cm–1. In each molecule:1) Label the functional groups that are present.

2) Identify the specific bond(s) responsible for the absorption(s) and predict theapproximate wavenumber of absorption for each of these bonds.

2
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Lesson Outline
1. What you will need for this lesson - p. 3
2. Introduction to Infrared Spectroscopy - p. 5
3. Fundamental Vibrational Modes of Water - p. 6
4. IR Active versus IR-inactive - p. 9
5. Functional Groups and Trends - p. 10
6. Resonance Effects - p. 12
7. Mass Effects - p. 14
8. Individual Exercises - p. 15
9. Conclusion and References - p. 17
10. Glossary of Terms - p. 17

1. What you will need for this lesson
Before you begin, it is important to note that as you run through each computation, you may findthe exact output numbers/CPU time may not be identical to those proposed here. For some
types of calculations, the exact numbers are dependent on the starting geometry and operating
system and, while the qualitative conclusions are the same, the exact numbers may differ
slightly.
1. Go to the ‘Data’ folder and open yourClass Folder found on the virtual
cluster’s desktop.
2. Right-click on the folder called“IR_spectroscopy” and copy folder to
Desktop● Here, you will find the lesson
plan, worksheet, and any
additional resources
3. Open Maestro
a. See Starting Maestro if you
need help
Figure 1-1. Open Maestro.

3
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

4. Go to File > Change Working
Directory
5. Find your “IR_spectroscopy” folderthat you duplicated to your Desktop,
and click Choose

Figure 1-2. Change Working Directory option.

6. Next, go to File > Save Project As
7. Type “IR_tutorial” and click Savea. The project will be titledIR_tutorial.prj

Figure 1-3. Save Project panel.

Figure 1-4. Choose the best mouse option foryour set up.

8. Finally, check your Mouse Actions
a. PC : Edit > Customize Mouse
Actionsb. Mac : Workspace >Customize Mouse Actions
9. Make sure you have the best option
chosen for your set up. This lesson
was written with a three-button mouse

4
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

with a scroll wheel, meaning the scroll
wheel is a button as well as a wheel. If
you do not have a mouse, choose
Trackpad.

2. Introduction to Infrared Spectroscopy
Each form of spectroscopy uses a different region of the electromagnetic spectrum
and involves a different kind of excitation. The interaction between molecules and infrared (IR)radiation promotes vibrational excitations of the bonds in a molecule. Each type of bond in amolecule will absorb a characteristic frequency, allowing us to determine which types of bonds
are present in a molecule. Chemists irradiate an unknown compound with all frequencies of IR
radiation and then detect which frequencies were absorbed. A plot is then constructed showing
which frequencies were absorbed by a sample. In this way, IR spectroscopy can be used to
identify the presence of functional groups in a molecule. IR spectroscopy is commonly used byorganic chemists to verify the structures of compounds that are made in a laboratory.
An IR spectrometer measures the percent transmittance as a function of frequency. A
plot called an absorption spectrum is generated where each signal, called an absorption band,
points downwards on an IR spectrum. The position where a signal lies corresponds to afrequency-related unit called a wavenumber in units of inverse centimeters (cm–1) where thevalues can range from 400 to 4000 cm–1. It’s important to note that wavenumber is proportional
to frequency; therefore, a larger wavenumber represents higher energy. Signals that appear on
the left side of an IR spectrum correspond with higher energy radiation, whereas signals on theright side of an IR spectrum correspond with lower energy radiation.
There are three characteristics in every signal that appears in an IR spectrum:
wavenumber, intensity, and shape. The wavenumber of a signal is determined by bond strengthand the masses of the atoms sharing the bond. The intensity of a signal is dependent on the
dipole moment of the bond giving rise to the signal. The shape of a signal can either be broador sharp. Each type of functional group lies within a certain region of an absorption spectrum.
Use the IR spectroscopy functional group stretching frequency chart that your instructor has
provided you.

5
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

3. Fundamental Vibrational Modes of Water
IR radiation causes vibrational excitation of the bonds in a molecule. There are different
kinds of vibrational excitation since bonds store vibrational energy in a number of ways. Bonds
can stretch, similar to how a spring stretches, and bonds can also bend in various directions.
Even though there are several types of bending vibrations, we will mostly be focusing on various
stretching vibrations.
In this section, we will learn the steps for performing a standard frequency calculation.
We will also analyze the vibrational modes of a water molecule and view the predicted
spectrum.

1. Go to Edit > 2D Sketcher○ The 2D Sketcher
opens
2. Draw the structure of H2O

panel

The 2D sketcher functions like many
standard 2D molecular drawing tools. For
a complete overview of using the sketcher
panel, see the 2D Sketcher Paneldocumentation.
3. Click on Save as New and for
Input Entry Title write H2O. ClickOK.

Figure 3-1. Sketching and saving H2O.

6
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

4. Close the 2D Sketcher panel○ The H2O molecule isselected in the entry list andincluded in the workspace
5. Change the representation toball-and-stick by clicking on the
Style menu and choosing Applyball-and-stick representation
Figure 3-2. Viewing and stylizing H2O.
Now let us optimize the molecule at thequantum mechanical level and request afrequency calculation.
6. With the H2O entry selected andincluded, go to Tasks > Jaguar >Optimization○ The Jaguar - Optimization
panel opens
7. Maintain the defaults on the Inputtab
8. On the Properties tab, check
Calculatefor
Vibrationalfrequencies
9. Run the job

Figure 3-3. Setting the Optimization
panel.

7
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

When the job completes, an output groupis incorporated into the entry list

Figure 3-4. Animating the vibrations.

10. Select and include the output entry
11. Click the vibration viewer button ()
Three frequencies are shown as well as
the symmetry and intensity
12. Check Animate and visualize all
three modes (bending, symmetricstretchingandantisymmetricstretching)○ Take screenshots of each
vibrational mode for the IR
worksheet.
You can plot the spectrum.
13. With the output entry selected andincluded, go to Tasks > Jaguar >Plot Spectra○ The Spectrum Plot panel
opens
14. Click Load

Figure 3-5. Plotting the IR spectrum.

The predicted gas phase IR spectrum isshown. Take a screenshot of the IR
spectrum for the IR worksheet.

8
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

4. IR-active versus IR-inactive
In this section, we will study the frequency output for acetylene to visualize thedifference between IR-active and IR-inactive modes.

1. Repeat the above steps performedfor H2O for an acetylene molecule(C2H2)○ Sketch, save, visualize andperform QM calculation
2. Select and include the output entry
3. Click the vibration viewer button ()
Figure 4-1. Animating the vibrations for
C2H2.

Seven frequencies are shown as well as
the symmetry and intensity
4. Check Animate and visualize allseven modes○ Take screenshots of each
vibrational mode for the IR
worksheet.
Vibrations of bonds with dipole moments
generally result in IR absorptions that are‘active,’ whereas modes in which thevibration produces no change in the
dipole moment are typically ‘inactive.’

Figure 4-2. Animating the vibrations for
C2H2.

9
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

5. Plot the IR spectrum following thesame steps from Section 2, take ascreenshot, and put it in the IR
worksheet. Notice that only two
peaks appear.
○ Take screenshots of each
vibrational mode for the IR
worksheet.
Figure 4-3. Predicted acetylene IR
spectrum.

5. Functional Groups and Trends
In this section, we will study the frequency output for several organic molecules tofamiliarize ourselves with the typical shifts associated with different functional groups.

1. Repeat the above steps performedfor H2O for the organic molecules
shown in Figure 3-1○ Sketch, save, visualize andperform QM calculation

Figure 5-1. Structures to draw.

Note: Recall that these jobs can besubmitted and run simultaneously by
selecting all of the entries before opening
the Jaguar - Optimization panel

10
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 5-2. Outputs for five organic
molecules.

Proceed to analyze the vibrations for thevarious organic molecules. Can you
identify the diagnostic aldehyde C-H
stretch, the carbonyl stretch, the CN triple
bond? What are the key differences
between the butane and 1-butene
spectra?
○ Fill in the Table withdiagnostic frequencies in
the IR worksheet
To answer the latter question, let’s overlay
the spectra from butane and 1-butene in
the spectra viewer.

Figure 5-3. Outputs for five organic
molecules.

2. Select both the output from butane
and butene
3. Go to Tasks > Jaguar > Plot
Spectra○ The Spectrum Plot panel
opens
4. Click Load
5. Normalize the spectra
6. View in either Stacked mode orOverlaid
There are two noticeable characteristics
that differentiate the butane and 1-butene
spectra11
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6. Resonance Effects
In this section, we will compare the IR frequency output for cyclohexanone and2-cyclohexen-1-one to demonstrate the effect of resonance on diagnostic modes.

1. Repeat the above steps performedfor 2-cyclohexen-1-one○ Sketch, save, visualize andperform QM calculation

Figure 6-1. 2-cyclohexen-1-one in theworkspace.

Figure 6-2. Structures.

Compare the key carbonyl vibrations forthe two compounds. Which stretchingfrequency is lower? Can you explain why
based on a simple Lewis structure
approach? Answer these questions in the
IR worksheet.

12
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

13
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

7. Mass Effects
In this section, we will compare the IR frequency output for acetylene and acetylene-d2
to demonstrate the effect of mass on diagnostic modes.

1. Repeat the above steps foracetylene-d2○ Sketch, save, visualize andperform QM calculation
Note: In the 2D sketcher, hover over ahydrogen with your mouse and type ‘d’ on
your keyboard to change the hydrogen toa deuterium atom. Alternatively, right-click
the hydrogens in the workspace andadjust the isotope.

Figure 7-1. Adding deuterium to theacetylene model.
Compare the IR spectra of acetylene andacetylene-d2.

Figure 7-2. Vibrations for the acetylene-d2
structure.

What do you notice about the spectrum of
thenon-deuterated
moleculeascompared to the deuterated molecule?
Why do you think this difference isobserved? How can this be useful for asynthetic chemist?

14
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

8. Individual Exercises
Two infrared spectra are shown, corresponding to two of the following compounds.
Match the corresponding structure to each IR spectrum by:
1) Identifying how the major peaks (above 1500 cm–1) in each spectrum correspondto the structure you have chosen
2) Using molecular modeling to perform a vibrational analysis with Maestro to
confirm your answers

IR Spectrum A:

15
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

IR Spectrum B:

16
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

9. Conclusion and References
For further learning:
For introductory content, focused on navigating the Schrödinger Materials Scienceinterface, an Introduction to Maestro for Materials Science tutorial is available.
For some related practice, proceed to explore other relevant tutorials:
●
●
●
●
●
●
●

Introduction to Multistage Quantum Mechanical Workflows
Locating Transition States
Optoelectronics
Band ShapepKa Predictions with Jaguar pKa
Computing Atomic Charges with Jaguar
Reaction Workflow with Polyethylene Insertion

For further reading:●●●●Introduction to Computational Chemistry, 3rd Edition
Essentials of Computational Chemistry: Theories and Models, 2nd Edition
Molecular Modelling: Principles and Applications, 2nd Edition
See the Jaguar help documentation

10. Glossary
Entry List - a simplified view of the Project Table that allows you to perform basic operations
such as selection and inclusion
Included - the entry is represented in the Workspace, the circle in the In column is blue
Project Table - displays the contents of a project and is also an interface for performing
operations on selected entries, viewing properties, and organizing structures and data
Recent actions - This is a list of your recent actions, which you can use to reopen a panel,
displayed below the Browse row. (Right-click to delete.)
Scratch Project - a temporary project in which work is not saved. Closing a scratch project
removes all current work and begins a new scratch project
Selected - (1) the atoms are chosen in the Workspace. These atoms are referred to as "theselection" or "the atom selection". Workspace operations are performed on the selected atoms.
17
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

(2) The entry is chosen in the Entry List (and Project Table) and the row for the entry ishighlighted. Project operations are performed on all selected entries
Working Directory - the location that files are saved
Workspace - the 3D display area in the center of the main window, where molecular structures
are displayed
2D Workspace - the 2D panel that opens from the “edit” dropdown that allows for theconstruction of molecules using a 2D sketcher
Tile - if multiple entries are included, included entries are displayed side by side in individual
boxes rather than being overlaid in the same space18
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.