Teaching with Schrödinger

Updated: 1-23-22

Substitution Nucleophilic (SN2) Reactions
Created with: Release 2021-3
Prerequisites: working knowledge of Maestro
Files Supplied: SN2_reactions_worksheet
Categories:
organic chemistry

About this Lesson
In this lesson plan, students will examine bimolecular substitution nucleophilic (SN2)reactions. Transition state theory will be introduced to analyze the concerted
mechanism of how a nucleophile attacks an electrophile to form a given product.
Reaction energy diagrams will be investigated to determine whether a reaction isexergonic or endergonic.
Using Maestro, students will use Jaguar’s AutoTS panel to perform geometry
optimization calculations of the reactants and products of an SN2 reaction, determine
which bonds are breaking and forming, establish correspondence between atoms in
the reactants and the products, and generate a transition state structure. Then, they
will render a potential energy surface diagram to show the activation energy barrier.

Learning Objectives
Identify transition state structures of SN2 reaction mechanisms● Plot reaction energy diagrams with activation energy barriers to determine theirchemical reactivity characteristics (i.e. endergonic, exergonic, etc.)●

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○●

Substitution mechanisms (Conceptual Topics)
Organic Chemistry – Reaction Mechanisms (3.C)

AAMC MCAT○

Structure, function, and reactivity of biologically-relevant molecules (5D)

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 of chemical reactivity
Visual assessment of student-generated transition state structures and reaction energy
diagrams of SN2 reactions

Warm-Up Questions: To be done on their own or at the beginning of class
Read the Khan Academy article on endothermic vs. exothermic reactions. Then, consider thefollowing four reaction energy diagrams.

1) Which energy diagram(s) correspond with a two-step mechanism?
2) Which energy diagram(s) correspond with a one-step mechanism?
3) Compare energy diagrams A and C. Which has a relatively larger activation energy (Ea)barrier?
4) Compare energy diagrams A and D. Which has a positive Δ G?
5) Compare energy diagrams A and C. Which has a negative Δ G?
6) Compare all four energy diagrams. Which has the largest activation energy (Ea) barrier?
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.
2.
3.
4.
5.

What you will need for this lesson - p. 3
Introduction to SN2 Reactions - p. 5
Locating Transition States with AutoTS - p. 6
Individual Exercises - p. 14
Summary, Additional Resources, and References - p. 16

1. What you will need for this lesson
1. Go to the ‘Data’ folder and open yourClass Folder found on the virtual
cluster’s desktop.
2. Right-click on the folder called“SN2_Reactions” 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

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 “SN2_Reactions” folder thatyou duplicated to your Desktop, andclick Choose

Figure 1-1. Change Working Directory option.

6. Next, go to File > Save Project As
7. Type “SN2_tutorial” and click Savea. The project will be titled
SN2_tutorial.prj

Figure 1-2. Save Project panel.

Figure 1-3. 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 mousewith a scroll wheel, meaning the scroll
wheel is a button as well as a wheel. If
you do not have a mouse, choose
Trackpad.

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.

2.

Introduction to SN2 Reactions

Substitution reactions are common reactions in organic chemistry. Its importancecan be attributed to the fact that it can be used to introduce many functional groups fromalkyl halide precursors. For example, substitution reactions are vital in the synthesis ofalcohols, ethers, thiols, sulfides, nitriles, azides, halides, esters, and acetylenes.
There are two types of substitution reactions: SN1 and SN2 reactions. For thislesson, we will be focusing on the characteristics and mechanism of SN2 reactions. SN2
reactions are based on a concerted (one-step) mechanism where a nucleophile
substitutes the place of a leaving group in an electrophile. See the figure below for thedifferent components of an SN2 reaction.

Figure 2.1. The components of a general SN2 reaction.
Nucleophiles are chemical species that are electron donors while electrophiles
are electron acceptors. See the lesson on Nucleophiles (link this) for a deeper dive on
their chemical properties. In an SN2 mechanism, the nucleophile attacks the α-carbon,
which is the carbon atom that the leaving group is attached to. Simultaneously, thecarbon-leaving group bond breaks. An SN2 reaction progresses by going from reactants
to transition state structure to products, but we will touch more on transition states in
section 4 of this lesson. See the figure below for a general arrow-pushing mechanism ofan SN2 reaction.

Figure 2.2. Arrow-pushing mechanism of an SN2 reaction.
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.

Example #1. Predict the product and arrow-pushing mechanism of the following SN2reaction3.

Locating Transition States with AutoTS

In this lesson, we are going to analyze the SN2 reaction between chloroethane
and a bromide ion by determining the energetics of the reactants, transition state
structure, and products. To do this, we will be using Maestro, Schrödinger’s molecularmodeling software.

Figure 3.1. General potential energy surface.
Used with permission. Created by Professor H. Bernhard Schlegel, Wayne State
University, Detroit, MI.
Locating a transition state is essential for computing the activation energy of areaction, and thereby the reaction rate. As a result, finding transition states is useful inmany applications: predicting reactivity, understanding reaction mechanisms, catalyst
design and optimization, predicting outcomes of various competing reactions and more.
Besides, locating a transition state is unique to computation -- meaning the transition
state cannot be ‘found’ in the lab. Read more about Schrödinger’s work in the space ofCatalysis and Chemical Reactivity.
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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.

Searching for a transition state is typically a relatively difficult task in molecularmodeling. Unlike an optimization to a minimum (see: Introduction to Geometry
Optimizations, Functionals and Basis Sets), the search for a transition state highly
depends on the quality of the initial guess, the initial Hessian and the search direction.
Search for transition states is sometimes described as an ‘art’. Experience and practice
are key, as well as maintaining a thorough understanding of the available tools.
There are several alternative approaches to searching for a transition state with
Jaguar (Schrödinger’s Quantum Mechanics Engine). For this lesson, we will be using
the AutoTS panel which is an automated workflow in which reactants and products are
input and interpolation is used to search for the transition state with minimal userintervention. AutoTS is an automated way of finding transition states, particularly forelementary reactions. Its workflow requires only the structures of the reactants and the
products as input, and then automates the rest of the process: it optimizes reactants
and products, determines which bonds are breaking and forming, establishes
correspondence between atoms in the reactants and the products, generates atransition state guess (either from a template or using an interpolated reaction path),launches a transition state search with the DFT engine Jaguar, verifies if the locatedtransition state is trustworthy, runs frequency calculations, connects the transition statewith the reactants and the products using an intrinsic reaction coordinate (IRC)
algorithm and finally prints the potential energy surface diagram showing the transition
state barrier. AutoTS works best on reactions that have only one transition state
between the reactants and the products, such as the SN2 reaction.
We will be using the AutoTS panel for the SN2 reaction between bromoethane
and a chloride ion. Before we get started, answer the following question:
Example #2. Predict the product and arrow-pushing mechanism of the following SN2reaction. Include the transition state structure of the reaction.

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.

Computational Exercise #1: Generating a Transition State, Geometriesof Reactants and Products, and an Energy Diagram using AutoTS
Let’s employ the AutoTS panel for the SN2 reaction between bromoethane and achloride ion. When an AutoTS job is submitted, it produces the following results:
1) Optimized geometries of the reactants and products
2) A transition state structure with an animation to show bonds breaking andforming3) A potential energy surface diagram that includes a transition state barrier

We will first perform an AutoTS
calculation on a simple SN2 reaction
between chloroethane and a bromide ion
to learn the mechanics of the panel.
Figure 3-1. Opening the AutoTS panel.

Figure 3-2. Sketching the EtBr reactant in
the AutoTS panel.

1. Go to Tasks and type AutoTS.
Click
AutoTS…
Other
Applications (under the AutoTS
category)○ The
AutoTS:
Perform
Calculations panel opens
2. Change the Reaction Name toSN2_bromoethane_Cl
3. Under Reactants, click Sketch anddraw bromoethane. In the 2D
Sketcher, select the carbon single
bond, then click and drag to form
a C–C single bond. Then click Br
to place a bromine at the end ofthe
2-carbonchain.
Under
Molecular Properties, ensure the
Total Charge is 0, Spin Multiplicity
is 1, and the box to Add
Hydrogens is checked. Click Save.

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.

Figure 3-3. Sketching the Cl – reactant in
the AutoTS panel.

4. Under Reactants, click Sketch anddraw a chloride ion. Select Cl
and place one atom in theworkspace. Notice that HCl wasplaced rather than a single Cl
atom. Click the lightning bolt
minus symbol. This will decrease
the charge to Cl– so you are left
with a chloride ion. Under
Molecular Properties, ensure the
Total Charge is -1 since this is ananion, Spin Multiplicity is 1, andthe box to Add Hydrogens ischecked. Click Save.
5. Under Products, repeat theprocess and draw the products of
the SN2 reaction.
○ Your inputs should matchthe Figure 3-4.

Figure 3-4. Sketching the products in the
AutoTS panel.

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.

6. Go to the Advanced Settings tab○ We will keep the settings asdefault in this case
○ Level of theory:i. Method: B3LYP-D3
ii. Basis Set: 6-31G**
7. Change the Job name toSN2_bromoethane_Cl_AutoTS

Figure 3-5. Advanced settings andnaming the job.

Figure 3-6. Adjusting job settings fromthe gear icon and running the job.

8. Adjust the job settings () asneeded○ Change host from local hostto CPU host.
○ Change the Maximum # ofProcessors to 12. The job
can be completed in about
5 minutes on a 12 CPU host
9. If you would like to run the job
yourself, click Run. Otherwise, we
can import pre-generated outputs
in the analysis stages
10. Close the AutoTS panel
Note: The Preview Reaction Complex tab
can be used to generate reactant andproduct complexes (merged structures)and to see a guess at the reaction path.
Adjustments can be made as needed

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.

When the job is complete, we can viewthe results in the AutoTS: View Results
panel. The AutoTS calculation assesses
various paths without any additional user
input

Figure 3-7. Importing the results of the
AutoTS calculation.

11. Go to File > Import Structures
12. SelecttheSN2_bromoethane_Cl_AutoTS_
full_path.mae file and clickOpen○ If you did not perform thecalculation yourself and
wish
to
open
the
pre-generated
results,
selectthe
Ethyl_Br_SN2_full_pat
h.mae file and click Open○ An entry group including thereactant, transition stateand product structures is
added to the entry list
13. Use the Workflow Action Menu
(WAM) button (Results panel) to access theAlternatively, go to Tasks and type
AutoTS
Results
and
load
the
full_path.mae file via the Import button

11
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.

The AutoTS: View Results panel contains
the energy diagram associated with thereaction. If you are interested in viewing
the vibration associated with thetransition state, use the vibration viewer () in the entry list and animate in theworkspace
Figure 3-8. AutoTS results.
Example #3. Using the AutoTS results, let’s analyze the SN2 reaction further. Answer
the following questions:a) Take screenshots of the optimized geometries for the reactants, transition state
structure, and products.
b) List the bond distances of each molecule using the Measure button in units ofångstroms.
Reactants

Transition State Structure

Products

Screenshot:

Screenshot:

Screenshot:

C–C bond distance:

C–C bond distance:

C–C bond distance:

C–Br bond distance:

C–Br bond distance:

C–Cl bond distance:

C–Cl bond distance:

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.

c) Now let’s analyze the transition state structure. Look at the animation of its vibration.
What is the geometry of the central carbon atom at the transition state? How does thisdiffer from the electrophile’s starting geometry as a reactant?

d) Take a screenshot of the reaction energy diagram. Is the reaction exergonic orendergonic? What is the activation energy barrier in units of kcal/mol? Would thereaction speed up or slow down if the nucleophile was iodide instead? Why?

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.

4.

Individual Exercise
Answer the following questions based on the following SN2 reaction:a) Predict the product and arrow-pushing mechanism of the SN2 reaction. Include thetransition state structure of the reaction. Take note of any stereochemical inversions aswell.

b) Look at the AutoTS results of this reaction. Go to Tasks and type AutoTS Results. Then
import SN2_1-Chloro-2-Methylcyclohexane_full_path.mae.Recall that
cyclohexane is not planar but is in a chair conformation. Redraw your SN2 mechanism inchair conformation and take note of the substituent positions – are they in axial or
equatorial positions? (Note: The carbon with chloride is C1 and the carbon with methyl is
C2; the numbering of the ring is going clockwise).

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.

c) Take screenshots of the optimized geometries for the reactants, transition state
structure, and products. Try your best to capture the chair conformations by rotating themolecule. Also, list the bond distances of each molecule using the Measure button inunits of ångstroms.
Reactants

Transition State Structure

Products

Screenshot:

Screenshot:

Screenshot:

C–Cl bond distance:C(chair)–C(alkyne) bondC(chair)–C(alkyne) bonddistance:

distance:

C–Cl bond distance:d) Take a screenshot of the reaction energy diagram. Is the reaction exergonic orendergonic? What is the activation energy barrier in units of kcal/mol?

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.

5.

Summary, Additional Resources, and References

Using Maestro, students learned how to use Jaguar’s AutoTS panel to perform geometry
optimization calculations of the reactants and products of an SN2 reaction, determine whichbonds are breaking and forming, establish correspondence between atoms in the reactants andthe products, and generate a transition state structure. Lastly, they learned how to render apotential energy surface diagram to show the activation energy barrier.
For further learning:

For some related practice, proceed to explore other relevant tutorials:●

Introduction to Geometry Optimizations, Functionals, and Basis Sets●

Locating Transition States

For further reading:
●
●
●
●
●

Exploring potential energy surface for chemical reactions: An overview of some
practical methods. DOI:10.1002/jcc.10231
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

Glossary of Terms:

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 apanel, displayed below the Browse row. (Right-click to delete.)

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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.

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"the selection" or "the atom selection". Workspace operations are performed on theselected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row
for the entry is highlighted. 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 inindividual boxes rather than being overlaid in the same space17
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.