Teaching with Schrödinger

Updated: 1-17-23

Chemical Bonding

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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" WITHOUT WARRANTY OF
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Chemical Bonding
About this Lesson:
In this lesson, students will examine the relationship between the electronic structure of
atoms and the ionic and covalent chemical bonds they form. Students will learn aboutbond polarity and electronegativity by looking at electron distributions of various small
molecules.
Using Maestro, students will create a map of electrostatic potential (ESP) of various small
molecules with Jaguar and examine the electrostatic potential on the molecular surface.
These renderings will help with visualizing electronegativity trends and gauging thepolarity of chemical bonds.
Learning Objectives:●

Explain the relationship between the type of bonding and the properties of theelements participating in the bond.

●Use electronegativity differences to identify nonpolar covalent, polar covalent, andionic bonds.

●

Identify a chemical bond type by mapping electrostatic potential surfaces ontomolecules.

Lesson Contents:
1. Setting Up the Maestro Session
2. Lewis Electron-Dots
3. Ionic Bonding
4. Covalent Bonding
5. Bond Polarity and Electronegativity
6. Individual Exercises
7. Summary, Additional Resources, and References
8. Glossary of Terms

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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" WITHOUT WARRANTY 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.

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Standards Alignment:
●

●

●

●

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Connections to AP○ Molecular and Ionic Compound Structure
and Properties (SAP 6)
IB Diploma Programme:○ Chemical Bonding and Structure (CoreTopic 4)ACS Guidelines○ Understand molecular structure andbonding (Section 5.2)
ETS Chemistry GRE○ Inorganic Chemistry – General Chemistryon Molecular Substances (2.A)
AAMC MCAT○ Nature of molecules and intermolecularinteractions (5B)

Assessments for Understanding:
The following types of formative
assessments are embedded in thislesson:●Assessment of student
understanding throughdiscussion of warm-up
questions and filling in any
knowledge gaps aboutchemical bond types●

Visual assessment ofstudent-generated
electrostatic potential maps

Associated Documentation Pages: Jaguar Geometry Optimization: The Basics, QM
Multistage Workflow
Warm-Up Questions:
Watch the Khan Academy videos on molecular and ionic compound structure andproperties.
1. Using Lewis symbols, diagram the reaction between magnesium and oxygen atoms
to give the ionic substance MgO.
2. How many electrons are transferred?
3. Which atom loses electrons in the reaction?

Need help? Contact us at teaching@schrodinger.com

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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" WITHOUT WARRANTY 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.

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1. Setting Up the Maestro Session
At the start of the Maestro session, it is essential to 1) check your mouse actions, 2) change
the file path to the Working Directory for this lesson, and 3) save your project file. The
working directory indicated in this section contains the files necessary to complete thislesson. If you do not set the appropriate working directory, you will be unable to run any
calculations.
1. Launch the Virtual Cluster

Figure 1-1. Virtual workstation login page.
2. Double-click the course-data folder
on the desktop

Figure 1-2. Course-data folder on the desktop.

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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" WITHOUT WARRANTY 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.

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3. Right-click the chemical_bonding
folder and select Copy to > Desktop

Figure 1-3. Copy the lesson folder to the
Desktop.
4. Double-click the Maestro icon on
the desktop

5. Check your mouse actions.
○

Go to Workspace >Customize Mouse Actions○

Note: This lesson was madewith a three-button mouse

Figure 1-4. Change the mouse actions.

with a scroll wheel, but a
trackpad can still be used○

Trackpad keys:■

Up/Down trackpad =Zoom In/Out■

Option = Rotate■

Control = Translate

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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" WITHOUT WARRANTY 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.

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6. Go to File > Change Working
Directory

Figure 1-5. Change Working Directory option.
7. Navigate to Desktop >chemical_bonding folder and click
ChoosePre-generated input and results files areincluded for running jobs or examining
outputFigure 1-6. Change Working Directory panel.

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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" WITHOUT WARRANTY 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.

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8. Go to File > Save Project As

Figure 1-7. Save Project option.
9. Change the File name tochemical_bonding_lesson, click
Save○

The project is now named
chemical_bonding_lesson.prj

Figure 1-8. Save Project panel.

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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" WITHOUT WARRANTY 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.

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2. Lewis Electron DotsElectrons involved in chemical bonding are called valence electrons, which are located in
the outermost occupied shell. A simple way to show valence electrons in an atom is called a
Lewis electron-dot symbol or a Lewis symbol. A Lewis symbol for an element is made byplacing dots representing valence electrons around the symbol for a particular element.
For many common elements, the number of dots corresponds to the element’s group
number. For example, sulfur’s electron configuration is [Ne]3s23p4 and contains six valence
electrons. Therefore, the Lewis symbol for sulfur is

Figure 2-1. Sulfur’s Lewis symbol
Notice that the dots are placed around the four sides of the element symbol – top, bottom,
left, and right – and each side can hold up to two valence electrons. All four sides are equal,
which means that the placement of lone pairs of electrons vs. single electrons is arbitrary.
Generally, however, it is good practice to spread out the dots as much as possible. It isbetter to have two pairs of electrons and two single electrons, in sulfur’s case, as opposedto three pairs of electrons, one single electron, and an empty side.
Atoms typically gain, lose, or share electrons to achieve the same number of electrons as
the noble gas closest to them in the periodic table. The octet rule states that atoms tend toform compounds in ways that give them eight valence electrons, which is the electron
configuration of a noble gas. In a Lewis symbol, an octet is shown as four pairs of valence
electrons arranged around the element symbol. Although there are exceptions to the octet
rule, we won’t be covering them in this lesson plan. See this article for more information.

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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" WITHOUT WARRANTY 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.

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Example #1. Draw the electron configuration and Lewis electron dot symbol for thefollowing elements listed in the table below.
Element

Electron Configuration

Lewis Symbol

Lithium
CarbonNitrogenAluminum
Chlorine

3. Ionic Bonding
Ionic compounds are formed by the interaction of metals on the left side of the periodic
table with nonmetals on the right side, excluding noble gases in group 8A. Ioniccompounds contain several characteristic properties. For instance, they are usually
crystalline and are easy to break apart along smooth surfaces. Such characteristics result
from the electrostatic forces that maintain the ions in a rigid, well-defined,
three-dimensional arrangement. Ionic compounds are stable due to the attraction between
ions of opposite charges. This attraction draws the ions together, releasing energy andcausing the ions to form a solid lattice. Shown below is a crystal structure of sodium
chloride (NaCl):

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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" WITHOUT WARRANTY 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,
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Figure 3-1. Crystal structure of sodium chloride in bulk
The formation of Na+ from Na and Cl– from Cl2 indicates that an electron has been lost by asodium atom and gained by a chlorine atom – an electron transfer from the Na atom to
the Cl atom occurred. Recall that ionization energy indicates how easily an electron can beremoved from an atom whereas electron affinity measures how much an atom wants togain an electron. See here for more information. Electron transfer to form oppositely
charged ions occurs when one atom readily gives up an electron (low ionization energy)
and another atom readily gains an electron (high electron affinity). NaCl is a typical ioniccompound because it consists of a metal, sodium, of low ionization energy and a
non-metal, chlorine, of high electron affinity. The ionic bonding of NaCl can be represented
using Lewis electron-dot symbols shown below.

Figure 3-2. Lewis electron-dot symbols of the ionic bonding in NaCl
When oppositely charged particles, like Na+ and Cl–, attract to one another, this attractive
force is referred to as an electrostatic force. An ionic bond is the electrostatic force that
holds the ions, Na+ and Cl–, together in an ionic compound. It’s conventional to show thecation, Na+, without dots around the symbol to emphasize that the original energy levelthat contained the valence electron is now empty. The anion, Cl–, is now shown with acomplete octet of electrons.

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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" WITHOUT WARRANTY 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.

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4. Covalent Bonding
In ionic compounds, electrons are transferred between atoms of different elements toform ions. But this is not the only way that compounds can be formed. A chemical bondformed by sharing a pair of electrons is a covalent bond. Covalent bonds are formed
between two atoms when both have similar tendencies to attract electrons to themselves(i.e. when both atoms have identical or daily similar ionization energies and electron
affinities).
Compounds that contain covalent bonds exhibit different physical properties than ioniccompounds. Because the attraction between electrical neutral atoms is weaker than thatbetween electrically charged ions, covalent compounds generally have much lower melting
and boiling points than ionic compounds.
Previously you learned that the valence electrons of a single atom can be easily shown by a
Lewis electron-dot symbol. The structures of molecules that are held together by covalentbonds can be diagrammed by Lewis electron-dot structures, or Lewis structures for short.
The simplest example of a covalent bond is the hydrogen molecule, H2. Each hydrogen
atom acquires a second electron, achieving the stable, two-electron, noble-gas
configuration of helium. The two electrons in between each hydrogen atom are shared andare called a pair of bonding electrons, or a single covalent bond. A Lewis structure of H2 isshown below where the single covalent bond can be shown by either the lone pair or as adash in between the two atoms.

Figure 4-1. Lewis structure of H2

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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" WITHOUT WARRANTY 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.

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How to Draw Lewis Structures
Step #1: Add up all the valence electrons from all atoms, taking into account overall charge○

The number of valence electrons can be found from the periodic table■

Ex. Carbon is in group 4A so it has 4 valence electrons○

For an anion, add one electron to the total for each negative charge○

For a cation, subtract one electron from the total for each positive charge

Step #2: Write the symbols for the atoms, show which atoms are attached to which, andconnect them with single bonds (aka a line that represents two bonding electrons)
Step #3: Complete the octets around all the atoms bonded to the central atom○

Remember that a hydrogen atom only has a single pair of electrons around it

Step #4: Place any leftover electrons around the central atom
Step #5: If there are not enough electrons to give the central atom an octet, try multiple
bonds (double or triple bonds)
Example #2. Draw the Lewis structure for phosphorus trichloride, PCl3 and show your work
after each of the five steps.

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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" WITHOUT WARRANTY 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.

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Computational Exercise #1: Geometry Optimization using Maestro
Although the Lewis structure of PCl3 looks relatively flat and two-dimensional, now
we are going to learn how to build a three-dimensional structure of PCl3 and then optimize
its geometry using Maestro. Visualizing the molecular structure can be done in threedifferent ways:
1) Through the 2D Sketcher
2) Through the 3D Builder
3) Or, by importing pre-built molecules
We will be using the 2D Sketcher tool in Maestro.

Part 1. Build PCl3 using 2D Sketcher
Before optimizing any molecular geometry,
you will need a starting molecule in yourworkspace. Let’s draw the structure of PCl3
using the 2D sketcher.
1. Go to Edit > 2D Sketcher

Figure 4-1. Open 2D Sketcher.
The 2D sketcher functions like many standard 2D molecular drawing tools. For acomplete overview of using the sketcher panel, see the 2D Sketcher Paneldocumentation.

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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" WITHOUT WARRANTY 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.

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Here, you will draw your Lewis Structure
final answer of PCl3. You do not need to
draw in any lone pair of electrons; only
show the bonds.
2. Go to the selection bar on the left
3. Choose the phosphorus atom “P”
and click anywhere in the 2D
Workspace to place
4. Choose the chlorine atom “Cl” andclick and drag off of the “P” atom tocreate 3 P–Cl single bonds

Figure 4-2. Draw phosphorus trichloride,
PCl3.
5. Click on Save as New
6. For Input Entry Title, write PCl3.
7. Click OK.

Figure 4-3. Save the entry title for PCl3.

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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" WITHOUT WARRANTY 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.

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8. Close the 2D Sketcher panel
9. In the Entry List, ensure that the PCl3
molecule is selected and included in
the workspace
Figure 4-4. Include and select the entry.
10. Change the representation toball-and-stick by clicking on the
Style menu and choosing Applyball-and-stick representation

Figure 4-5. Viewing and styling PCl3.

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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" WITHOUT WARRANTY 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.

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Figure 4-6. Styling PCl3 as ball-and-stick.
11. To display atom labels, click Style >Apply Labels > Edit Custom
Label…

Figure 4-7. Labeling atoms.

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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" WITHOUT WARRANTY 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.

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12. The Edit Custom Label window willopen
13. Click the green plus button

Figure 4-8. Editing custom labels.
14. The Add Label Fields window willopen
15. Select Element and press OK
16. In the Edit Custom Label window,
press OK

Figure 4-9. Adding label fields.

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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" WITHOUT WARRANTY 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.

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17. Go to Style > Apply Labels > Custom
Label and now each atom in yourworkspace should be labeled○

Note: You can toggle theatom labels on and off by
clicking Annotations label
button in the Workspace
toggle on the bottom rightcornerFigure 4-10. Adding element labels.

Figure 4-11. Toggling labels on.

Figure 4-12. Toggling labels off.

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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" WITHOUT WARRANTY 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.

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This molecule is not yet optimized. The 3D
representation is simply generated fromthe 2D Sketcher as an approximate starting
point. Let’s measure the Cl–P bond distanceand the Cl–P–Cl angle to assess the starting
point:
Figure 4-13. Opening the Measure banner

18. Go to Tasks > Measure (or click
Measure in the Favorites toolbar)○

A banner appears at the topof the workspace for defining
measurements

19. With Distances selected for
Measure, select one Cl atom and
the P atom.
○

The Cl–P distance is labeled

Figure 4-14. Measuring the Cl–P distance.

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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" WITHOUT WARRANTY 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.

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20. Switch the Measure option to
Angles and select one chlorine, thenthe phosphorus, and then anotherchlorine○

The Cl–P–Cl angle is labeled

21. Feel free to measure the other two
Cl–P distances as well as the other
Cl–P–Cl angle in PCl3
22. Click OK to close the measurementbannerFigure 4-15. Measuring the Cl–P–Cl angle.
We can see that the 2D Sketcher created this 3D starting molecule with the Cl–P bondlengths equal to 2.10Å and Cl–P–Cl bond angles of 93.3º.

Part 2. Force Field Minimization
We can improve upon this starting
structure by using a force field
minimization. The molecule will still not be
optimized by quantum mechanics (QM),
but it will improve the starting geometry.
1. Select all four atoms in the
Figure 4-15. Selecting all the atoms in PCl3.

workspace (there are many
approaches to do so: Main Menu,
Select > All; or, Shift + Click + Drag)○

You will know all atoms havebeen selected when each
atom is surrounded by a light
blue cube.

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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" WITHOUT WARRANTY 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.

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2. In the Build dropdown from thetoolbar (3D Builder panel), selectMinimize selected atoms
3. The molecule is minimized, and theparameters adjust slightly

Figure 4-16. Minimizing the geometry of PCl3.
We can now see that the starting molecule has equivalent Cl–P bond lengths still equal to
2.10Å and bond angles of 94.0º. The experimental bond length is 2.07Å and a bond angleof 103º. Thus, the force field minimization improves the structure, but is still somewhat
far from being experimentally accurate.
Note: Force fields are usually good at generating structures of molecules with common
functional groups and elements. When it comes to more exotic atomic arrangements andless frequent elements (such as transition metals) or simply large molecules, force fields
can yield structures with inaccurate or even unphysical geometries, and in those cases,
quantum mechanical geometry optimizations become absolutely indispensable.

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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" WITHOUT WARRANTY 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.

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Part 3. Optimize the Geometry using
Quantum Mechanic DFT
Now let’s optimize the molecule at thequantum mechanical level.
1. Go to Tasks > Optimization using
JaguarFigure 4-15. Opening up Jaguar from theTasks bar.

○

The Jaguar Optimization
panel opens

2. Use structures from Workspace (1selected entry)

Figure 4-16. Setting the Jaguar Optimization
panel to optimization.
Note: We are optimizing one molecule, PCl3. By selecting many molecules in the entry
list, we can optimize as many molecules as we would like concurrently with the same
Quantum Mechanics (QM) settings.
Various settings can be altered dependingon the specific use case. We will only adjust
the Input tab for this example.
Figure 4-17. Setting the QM parameters for
optimization.

3. For Theory, select B3LYP-D3
4. For Basis set, select 6-31G**

22
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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" WITHOUT WARRANTY 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.

Back to Lesson Contents

A few additional comments about preparing for an optimization calculation:●

If you hover the mouse over the basis set in the table, you can see the number ofbasis functions associated with the basis set. This is useful to know since thequality of the basis set usually improves as the number of functions increases,
noting again the trade-off between quality and computational expense●

Always make sure the charge and the spin multiplicity are correct (in this case,PCl3 is a neutral, singlet, so charge = 0 and spin multiplicity = 1). Multiplicity isdefined as 2S + 1, where S is the total orbital spin of the molecule. For instance, asystem with one unpaired electron is a doublet (multiplicity = 2), since the total
orbital spin S = ½.

●

Use the Atom-Level Settings button to define per-atom basis sets●

Constraints can be defined on the Optimization tab●

Properties, such as atomic charges, vibrational frequencies, surfaces and more
can be requested on the Properties tab●

Solvent can be defined via several implicit solvation models on the Solvation tab.
Note that this example is a gas-phase geometry optimization●

Read more about geometry optimization with Jaguar here and learn more about
using the QM Multistage Workflow panel in the Introduction to Multistage
Quantum Mechanical Workflows tutorial

Figure 4-18. Naming the job.

5. Change the Job name to
PCl3_optimization

23
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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" WITHOUT WARRANTY 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.

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6. Adjust the job settings (○)

This job requires 1 CPU hostand should complete inunder 1 minute

7. Click Run

Figure 4-19. Adjusting the job settings.
Note: It is advised to also add in a Vibrational frequencies calculation (from theProperties tab). This involves a bit more computational expense, but is a useful way to be
sure that your output is a minimum (as opposed to a maximum) on the PES. For moredetail, see the Locating Transition States: Part 1 tutorial.
When the job finishes, a banner will appear
indicating that the result has been
incorporated. At this time, the moleculewith the optimized geometry is now shownin the workspace.
Figure 4-20. The output molecule of PCl3.

8. A new entry group is added to theentry list titled PCl3_optimization.01(1). Select and include the molecule
titled PCl3 in this sub-group. This is
your optimized structure
9. Repeat the measurement steps
from above, and measure the P–Cl
bond distance and Cl–P–Cl bondangle.

24
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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" WITHOUT WARRANTY 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.

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Now that we have an optimized geometry of PCl3 that we calculated on Maestro,
let’s compare our original Lewis-dot structure to the optimized geometry. Since electrons
repel one another, the lone pair of electrons on phosphorus push all three chlorine atoms
downward to form a trigonal pyramidal geometry. This is why the Cl–P–Cl bond angle wascalculated to be 101.1º as opposed to having a 90º angle which the Lewis structuresuggests.

A

simplegeometry

optimization

helps

visualizeamolecule’s

truethree-dimensional geometry that is otherwise difficult to see just on a piece of paper.
Notice that each Cl–P bond is drawn differently in the trigonal pyramidal geometry. One
Cl–P bond is drawn on an in-plane bond, another is drawn on a wedged bond which means
the Cl atom is going towards you, and another is drawn on a dashed bond which means the
Cl atom is going away from you. Drawing bonds with wedges and dashes helps picture the3-D geometry of the molecule.

Original Lewis-Dot
Structure of PCl3

Trigonal Pyramidal Geometryof PCl3

Optimized Geometry of
PCl3 using DFT

25
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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" WITHOUT WARRANTY 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.

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Example #3. Analyze the structure of dichlorodifluoromethane, or CCl2F2 by 1) drawing the
Lewis structure, 2) performing a geometry optimization using Maestro, and 3) measuring
the bond lengths and bond angles listed below. Use the same DFT method as the last
example (B3LYP-D3/6-31G**).

Lewis-Dot Structure of
CCl2F2

5.

Optimized Geometry of
CCl2F2 using DFTBond Measurements from
Optimized Geometry●

C–F length:●

C–Cl length:●

F–C–F angle:●

Cl–C–Cl angle:●

Cl–C–F angle:

Bond Polarity and Electronegativity
Bond polarity is a measure of how equally or unequally the electrons in any

covalent bond are shared. A nonpolar covalent bond is one in which the electrons areshared equally, like in Cl2, N2, or H2. In the case of Cl2, each atom starts off with sevenvalence electrons, and each Cl shares one electron with each other forming one covalentbond.

Figure 5-1. Lewis structure of Cl2
The total number of electrons around each individual atom consists of six nonbonding
electrons and two shared, bonding electrons for eight total electrons. This matches thenumber of valence electrons in the closest noble gas argon (Ar). Since the bonding atoms
are identical, Cl2 contains a nonpolar covalent bond.

26
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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" WITHOUT WARRANTY 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.

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In a polar covalent bond, there is an unequal distribution of electrons which ischaracterized by a partial positive charge on one atom and a partial negative change on theother. The atom that attracts the electrons more strongly acquires the partial negative
charge and vice versa. For example, the electrons in the H–Cl bond of a hydrogen chloride
atom spend more time near the more electronegative chlorine atom than near thehydrogen atom. Therefore, the chlorine atom carries a partial negative charge while thehydrogen atom has a partial positive charge. We can represent this charge distribution as:

Figure 5-2. Partial charges in H–Cl
The δ+ (delta plus) and δ– (delta minus) symbolize the partial positive and negative charges,
respectively. In a polar bond, these numbers are less than a full charge of the ions.
Electronegativity is the ability of an atom in a molecule to attract electrons to itself
and is used to estimate whether a given bond is nonpolar covalent, polar covalent, or ionic.
The greater an atom’s electronegativity, the greater its ability to attract electrons to itself.
American chemist Linus Pauling developed an electronegativity scale, which is based onthermochemical data shown below.

Figure 5-3. Linus Pauling’s electronegativity scale27
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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" WITHOUT WARRANTY 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.

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The absolute value of the difference in electronegativity (ΔEN) of two bonded atoms
provides a rough approximation of the polarity to be expected in the bond and, thus, thebond type. Note that electronegativity values have no units. When the difference is verysmall or zero, the bond is nonpolar covalent. When the difference is between 0.4 and 1.8,
the bond is polar covalent. When the difference is above 1.8, the bond is ionic. A tablesummarizing electronegativity differences and bond types is shown below.
Bond TypeElectronegativity Difference

Nonpolar covalent< 0.4

Polar covalent

0.4 – 1.8

Ionic

> 1.8

Table 5-1. Electronegativity differences based on bond type

Example #4. Determine the electronegativity differences and bond types of the following
fluorine-containing compounds.

F2

HF

LiF

ΔEN
Type of Bond28
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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" WITHOUT WARRANTY 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.

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Computational Exercise #2: Generating Electrostatic Potential(ESP) Maps on the Molecular Surface
Now we will calculate the electrostatic potential surfaces of F2, HF, and LiF to help us
visually identify a chemical bond type. ESP maps will show the electron-density distribution
on the surface of the molecules. This exercise involves four parts:
1) Build the molecules and minimize their geometries
2) Generate surfaces of the molecules
3) Map the electrostatic potentials to the molecular surfaces
4) Label each atom with electrostatic potential values

Part 1. Build the molecules andminimize their geometries
Before generating any surfaces, build andminimize the structures for F2, HF, and LiF
using the 2D Sketcher tool.
1. Go to Edit > 2D Sketcher. If any
existing structures are still in the 2D
Sketcher workspace, use the eraser
to delete the structure.

Figure 5-4. Open 2D Sketcher.

29
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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" WITHOUT WARRANTY 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.

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2. Draw F2○ Go to the selection bar on
the left○ Click the fluorine atom “F”
and click in the 2D
Workspace to form HF○ Click “HF” in the workspace to
add another fluorine atom

Figure 5-5. Drawing F2.
3. Click on Save as New and for Input
Entry Title write F2.
4. Click OK.

Figure 5-6. Saving F2.

30
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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" WITHOUT WARRANTY 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.

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5. Draw HF○ Reference the instructions
for F2 in steps 2-4.
○ Replicate the sketch shown in
Figure 5-7 as closely as
possible.
6. Click on Save as New and for Input
Entry Title write HF. Click OK.

Figure 5-7. Drawing and saving HF.
7. Draw LiF○ Click the periodic table andselect the Lithium atom “Li”
○ Replace the “H” atom with“Li”
8. Click on Save as New and for Input
Entry Title write LiF. Click OK.

Figure 5-8. Drawing and saving LiF.

31
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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" WITHOUT WARRANTY 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.

Back to Lesson Contents

Viewing multiple molecules at the sametime can be important for comparing andcontrasting them. We will show F2, HF, and
LiF side by side so we can easily see how
they differ.

Figure 5-9. Including all three molecules.

9. Simultaneously include (ctrl + click)
all three molecules by clicking eachof the circles to the left of each entry
name/title
10. Show workspace configuration
panel by clicking the Plus symbol at
the bottom right corner
11. Click Workspace Layout > Tile

Figure 5-10. Tiling all three molecules.

32
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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" WITHOUT WARRANTY 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.

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12. Simultaneously select (ctrl + click) all
three molecules by choosing all 3
entry names/titles

Figure 5-11. Selecting all three entries.
13. Change their representations toball-and-stick by clicking on the
Style menu and choosing Applyball-and-stick representation
14. Include atom labels if you’d like byclicking Apply Labels > Custom
Label

Figure 5-12. Applying ball-and-stick style to all
three entries.
15. To center all the molecules within
their respective areas, click Fit viewto all visible objects
Figure 5-13. Centering the views of all three
entries.

33
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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" WITHOUT WARRANTY 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.

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16. Select all three molecules in theworkspace
17. In the Build dropdown from thetoolbar (3D Builder panel), selectMinimize selected atoms○ The molecule is minimized,
and the parameters adjustslightly

Figure 5-14. Performing force field
minimization on all three entries.
Part 2. Generate surfaces for themolecules
Figure 5-15. Open the Jaguar - Single Point
Energy Panel.

18. Select all three molecules – we will
be running the next calculations inparallel (simultaneously)
19. Open the Jaguar - Single Point
Energy panel from the Task button.
To do this, click Browse > Jaguar >Single Point Energy

34
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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" WITHOUT WARRANTY 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.

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20. Go to the Properties tab
21. Select the row for Surfaces (MO,density, potential) and click thecheck box
○ The Surfaces controls are
displayed at the bottom halfof the window
22. In the Surfaces section, selectElectrostatic potential andElectron densities, and ensure thatno other surface types are selected
23. Ensure that Density only is selectedunder Electron densities
Figure 5-16. Choosing the surface controls
under the Properties tab.

24. Check the box for Atomic

electrostatic potential charges(ESP) in the Properties table
25. Ensure the Grid type is SphericalFigure 5-17. Choosing atomic electrostatic
potential charges under the Properties tab.

Figure 5-18. Running the ESP jobs in parallel.

26. Name the job ESP
27. Click Run
28. When the jobs finish (after 2

minutes or less), the structures areimported and the electron density
surfaces may be displayed. The
incorporated jobs will be shown in a
35

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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" WITHOUT WARRANTY 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.

Back to Lesson Contents

separate Entry Group in the Entry
List
Part 3. Map the electrostatic potential tothe molecular surfaces
29. Click the S button in the Entry Listfor F2 and choose Manage○ The Manage Surfaces panel
opens

Figure 5-19. Clicking the S button in the Entry
List and choosing Manage.

30. Click the In column for the electron
density surface to include it in theWorkspace
31. Click Display Options○ The Surface Display Options
panel opens
Figure 5-20. Choosing settings in the Manage
Surfaces panel.

36
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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" WITHOUT WARRANTY 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.

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32. For Color scheme, select Mappedfrom volume
33. Select F2_loner1_potential fromthe volume data list
34. From the Color ramp option menu,
choose Rainbow
35. Click OK
36. Repeat steps 29-35 for themolecules HF and LiF

Figure 5-21. Choosing settings in the Surface
Display Options panel

37. Once you have displayed all threeelectrostatic potential surfaces, Tile
the three molecules so we cancompare them
○ Feel free to play around withthem and notice any
similarities or differences
between each molecule

Figure 5-22. Tile all three electrostatic
potential surfaces.

37
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" WITHOUT WARRANTY 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.

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Part 4. Label the molecules withelectrostatic potential values
38. Select all three molecules in theworkspace
39. Click Style > Apply Labels > Edit
Custom Label○ The Edit Custom Label dialog
box opens

Figure 5-23. Edit custom labels under Style.

38
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" WITHOUT WARRANTY 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.

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40. Click Add by clicking the Plussymbol○ The Add Label Fields dialog
box opens at the Atom
Properties tab

Figure 5-23. Adding label fields.

41. Type ESP in the search bar andselect Min surface ESP and Max
surface ESP
42. Click OK
43. Select the more electronegative
atoms in each molecule:○

Both F atoms in F2○

The F atom in HF○

The F atom in LiF

44. Go to Style > Apply Label > Edit
Custom Label and only select Min
surface ESP in the list and deselectthe rest
45. Click OK○
Figure 5-24. Add surface ESP values.

All the electronegative atoms
are labeled with theirminimum ESP values on thesurface, which are negative
39

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" WITHOUT WARRANTY 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.

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46. Select the less electronegative
atoms:○The H atom in HF○

The Li atom in LiF

47. Go to Style > Apply Label > Edit
Custom Label and only select Max
surface ESP in the list and deselectthe rest
48. Click OK○

The H and Li atoms arelabeled with their maximum
ESP values on the surface,which are positive40
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" WITHOUT WARRANTY 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.

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The shift of electron density toward the more electronegative atom in a bond can beseen in each ESP surface. You can see that in F2 the electron distribution is symmetricalwhich confirms that the F–F bond is nonpolar covalent. In HF, the electron density is clearlyshifted towards fluorine where the more electron dense area is colored red, indicating thatthe H–F bond is polar covalent due to the larger difference in electronegativity. And in LiF,
this shift is even greater as characterized by the more lopsided shape of the overall surface,showing that LiF is an ionic bond.
These examples show that the greater the difference in electronegativity between
the two atoms, the more polar their bond is.

41
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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" WITHOUT WARRANTY 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.

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6.

Individual Exercises

Determine the electronegativity differences between the following hydrogen halides. Then
generate an electrostatic potential surface for each molecule and identify any differences.
For the single point calculations, use the following method:●

Theory: B3LYP-D3●

Basis Set: LACVP++**

Hydrogen Fluoride, H–F

Hydrogen Chloride, H–Cl

ΔEN =

ΔEN =

ESP Surface:

ESP Surface:42
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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" WITHOUT WARRANTY 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.

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Hydrogen Bromide, H–Br

Hydrogen Iodide, H–I

ΔEN =

ΔEN =

ESP Surface:

ESP Surface:

43
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" WITHOUT WARRANTY 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.

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Analysis:7.

Summary, Additional Resources, and References

In this lesson, you learned about chemical bonding and what properties differentiate ionic,
nonpolar covalent, and polar covalent bonding. Ionic bonds result from the electrostaticforces that exist between ions of opposite charge. In a polar covalent bond, one of theatoms exerts a greater attraction for the shared electrons than the other. And in a
nonpolar covalent bond, the electrons in the bond are shared equally by the two atoms. If
we know which atoms are connected to one another, we can draw Lewis structures formolecules and ions.
Using Maestro, a simple geometry optimization using Jaguar can be performed to not only
visualize a molecule’s structure but also analyze bond lengths and angles. Electrostatic
potential surfaces can also be generated to visualize electronegativity trends and analyze
chemical bond types.

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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" WITHOUT WARRANTY 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.

Back to Lesson Contents

For further learning:

8.

●

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 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. (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

45
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" WITHOUT WARRANTY 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.