Particle Shape Calculator for CCDC/Mercury - Revision history

Mtsukanov: /* VisualHabit */

2023-05-23T21:25:02Z

VisualHabit

Mtsukanov: /* BFDH */

2023-05-23T21:22:56Z

BFDH

Mtsukanov: /* BFDH */

2023-05-23T21:21:34Z

BFDH

Mtsukanov: /* VisualHabit */

2023-05-23T21:20:46Z

VisualHabit

← Older revision		Revision as of 21:20, 23 May 2023
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	1. Launch Mercury by clicking its icon. In the Structure Navigator toolbar,		1. Launch Mercury by clicking its icon. In the Structure Navigator toolbar,
	type UREAXX to bring up the structure for urea.		type UREAXX to bring up the structure for urea.

	2. Click on the CSD-Particle menu, select Morphology, then select VisualHabit…		2. Click on the CSD-Particle menu, select Morphology, then select VisualHabit…
	3. In the VisualHabit dialogue box, you will see several options. On the left, you		3. In the VisualHabit dialogue box, you will see several options. On the left, you
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	the synthons in Å. These short, strong types of hydrogen bonds in the crystal		the synthons in Å. These short, strong types of hydrogen bonds in the crystal
	structure of urea are key to understanding its growth and the shape of its		structure of urea are key to understanding its growth and the shape of its
	crystals.		crystals.

	==Conclusion==		==Conclusion==

Mtsukanov: Created page with "This tutorial will introduce you to the morphology calculation features included with Mercury under the CSD-Particle toolset, namely BFDH Morphology and VisualHabit. BFDH crystal morphology is an approximation based on crystallographic geometrical considerations. For a given structure, the BFDH algorithm will predict the habit or shape of a crystal using the corresponding unit cell and symmetry operator information. The VisualHabit tool calculates a morphology for your m..."

2023-05-23T21:20:18Z

Created page with "This tutorial will introduce you to the morphology calculation features included with Mercury under the CSD-Particle toolset, namely BFDH Morphology and VisualHabit. BFDH crystal morphology is an approximation based on crystallographic geometrical considerations. For a given structure, the BFDH algorithm will predict the habit or shape of a crystal using the corresponding unit cell and symmetry operator information. The VisualHabit tool calculates a morphology for your m..."

New page

This tutorial will introduce you to the morphology calculation features included
with Mercury under the CSD-Particle toolset, namely BFDH Morphology and
VisualHabit.
BFDH crystal morphology is an approximation based on crystallographic
geometrical considerations. For a given structure, the BFDH algorithm will predict
the habit or shape of a crystal using the corresponding unit cell and symmetry
operator information.
The VisualHabit tool calculates a morphology for your material based on its
crystal structure. Using a range of forcefields, we can calculate the intermolecular
interactions, or synthons, in a crystal structure; the sum of these gives the lattice
energy for that system. From these lattice energies, we can calculate slice energies
and, consequently, the attachment energy for each slice. Crystal growth rates
assumed to be proportional to these attachment energies and can be used to
predict crystal shapes. The VisualHabit tool is used to calculate and analyze these
energies and to visualize the resulting morphologies, an instrumental step in
enabling solid form and particle design for small molecule crystal structures

==BFDH==
1. Open Mercury by double-clicking the Mercury icon on the desktop.
2. In the Structure Navigator toolbar type the refcode KAXXAI10.
3. We want to identify facets of interest in this morphology. We will first create
the morphology using the BFDH morphology feature.
4. From the top-level menu select CSD-Particle > Morphology > BFDH… to
generate the morphology. BFDH morphology uses the unit cell to create the
morphology you see, therefore it does not account for the chemistry of the
structure.
5. Rotate the structure to view the various facets that have been generated. If
you wish, explore options in the Morphology window.
6. In the following exercises you may decide to calculate the BFDH morphology
to compare the results.
7. The morphology can be modified, for example, if you want to represent a
crystal observed from growth experiments. In the Morphology window, click
Save… and place the .cif file in a folder where you have permission.
8. Using a text editor of your choice open the morphology .cif file. You will see
the data that corresponds to the HKLs and perpendicular distances. You can
modify these values to change the morphology. For the sake of example, we will
simply switch the values of some of the perpendicular distances. Note that
these changes are not based on experimental observation
9. Back in Mercury, In the Morphology window click Open… and select your
modified .cif file to visualize your new morphology

==VisualHabit==

The shape of a crystal results from the relative growth rates in different
directions. Strong intermolecular interactions, or synthons, in one direction, can
result in elongated crystal shapes like needles forming. Needle-shaped crystals
are common in pharmaceuticals and are undesirable due to their poor processing
characteristics. Being able to predict needle formation from a crystal structure is
helpful to understand potential manufacturing challenges.

1. Launch Mercury by clicking its icon. In the Structure Navigator toolbar,
type UREAXX to bring up the structure for urea.
2. Click on the CSD-Particle menu, select Morphology, then select VisualHabit…
3. In the VisualHabit dialogue box, you will see several options. On the left, you
will find options to change the calculation settings, such as which forcefield
is used and the limiting radius for the calculation. You can also choose
whether to add an electrostatic correction or not. On the right you will see
where the lattice energy results will appear once the calculation is complete.
For the purposes of this tutorial, we will keep the default options. These
typically work well for most situations, but if you know you are looking at
specific chemistry or a charged system, you may want to change these
settings.
4. Click the Calculate button to start.
5. The dialogue box will now update to show the results of the VisualHabit
calculation. The lattice energy results are shown in the section on the right in
kJ mol-1
. From here, you can see the total lattice energy as well as the
contributions from the electrostatic, van der Waals, and hydrogen bonding
energy terms. It’s clear from these results that the lattice energy for urea is
dominated by the hydrogen bonding energy in the crystal structure.
6. The convergence chart shows how the lattice energy changes over the course
of the calculation out to the limiting radius and gives an indication of whether
the calculation has converged successfully (indicated by the green tick at the
bottom of the chart). This chart tells us that the lattice energy comes close to
its final value in a small distance for this structure. Urea is a small molecule,
so this is what we would expect to see.
7. If we look at the Mercury visualizer, we will see that the calculated
morphology for urea is now shown. VisualHabit calculates an elongated
morphology for urea where the long axis is aligned to the polar axis of the
urea molecule.
8. We will now explore the reasons for this elongated shape by examining the
nature of the intermolecular interactions, or synthons, in more detail. Click
on the Synthons tab in the VisualHabit dialogue to change the information
that is shown.
9. The synthons that contribute to the lattice energy, along with the centroid-centroid
distance and component energy terms, are now shown. Click on the
Interaction Energy header (you may need to scroll along to see it) to sort this
column from the strongest interaction to the weakest. Once again, you will
see that the lattice energy for urea is dominated by a small number of strong
hydrogen bonding interactions.
10. Now let’s look at the two most important interactions. Click on one of the
rows in the table to highlight that interaction and show the synthon in the
Mercury visualizer. You can select multiple rows by holding down Ctrl and
clicking on the rows of interest. Holding down Shift and clicking will let you select
multiple rows at once. Select the top two interactions for UREAXX
(synthons 8 and 9).
11. You will see in the Mercury visualizer that two other urea molecules have
appeared above and below the central molecule. The red dashed lines
between the molecules highlight the synthon, and the value beside the line
shows the interaction energy. You can clearly see that the strongest
interaction in urea aligns with the fastest growth direction.
12. Click the Visualiser tab in the VisualHabit dialogue. From this tab you can
change the way that the morphology is displayed in Mercury, such as
changing the colour of the faces and the edges. You can also change how
synthons are displayed.
13. Click the radio dial in the Synthons section to display Distance rather than
Energy.
14. The Mercury visualizer will update to show the centroid-centroid distance of
the synthons in Å. These short, strong types of hydrogen bonds in the crystal
structure of urea are key to understanding its growth and the shape of its
crystals.

==Conclusion==
Crystal shape is governed by the relative growth rates in different directions.
Strong intermolecular interactions, or synthons, in one direction can result in
elongated morphologies. The crystal structure of urea is dominated by strong
hydrogen bonding interactions that occur in tapes that propagate along the
crystallographic c-axis. This results in an elongated morphology for urea.

You should now know how to calculate a morphology using VisualHabit for a
CSD structure in Mercury and how to visualize and explore the key interactions
in that structure relative to the calculated crystal shape.

← Older revision		Revision as of 21:25, 23 May 2023
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	2. Click on the CSD-Particle menu, select Morphology, then select VisualHabit…		2. Click on the CSD-Particle menu, select Morphology, then select VisualHabit…

	3. In the VisualHabit dialogue box, you will see several options. On the left, you		3. In the VisualHabit dialogue box, you will see several options. On the left, you
	will find options to change the calculation settings, such as which forcefield		will find options to change the calculation settings, such as which forcefield
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	specific chemistry or a charged system, you may want to change these		specific chemistry or a charged system, you may want to change these
	settings.		settings.

	4. Click the Calculate button to start.		4. Click the Calculate button to start.

	5. The dialogue box will now update to show the results of the VisualHabit		5. The dialogue box will now update to show the results of the VisualHabit
	calculation. The lattice energy results are shown in the section on the right in		calculation. The lattice energy results are shown in the section on the right in
	kJ mol-1		kJ mol-1. From here, you can see the total lattice energy as well as the
	. From here, you can see the total lattice energy as well as the
	contributions from the electrostatic, van der Waals, and hydrogen bonding		contributions from the electrostatic, van der Waals, and hydrogen bonding
	energy terms. It’s clear from these results that the lattice energy for urea is		energy terms. It’s clear from these results that the lattice energy for urea is
	dominated by the hydrogen bonding energy in the crystal structure.		dominated by the hydrogen bonding energy in the crystal structure.

	6. The convergence chart shows how the lattice energy changes over the course		6. The convergence chart shows how the lattice energy changes over the course
	of the calculation out to the limiting radius and gives an indication of whether		of the calculation out to the limiting radius and gives an indication of whether
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	its final value in a small distance for this structure. Urea is a small molecule,		its final value in a small distance for this structure. Urea is a small molecule,
	so this is what we would expect to see.		so this is what we would expect to see.

	7. If we look at the Mercury visualizer, we will see that the calculated		7. If we look at the Mercury visualizer, we will see that the calculated
	morphology for urea is now shown. VisualHabit calculates an elongated		morphology for urea is now shown. VisualHabit calculates an elongated
	morphology for urea where the long axis is aligned to the polar axis of the		morphology for urea where the long axis is aligned to the polar axis of the
	urea molecule.		urea molecule.

	8. We will now explore the reasons for this elongated shape by examining the		8. We will now explore the reasons for this elongated shape by examining the
	nature of the intermolecular interactions, or synthons, in more detail. Click		nature of the intermolecular interactions, or synthons, in more detail. Click
	on the Synthons tab in the VisualHabit dialogue to change the information		on the Synthons tab in the VisualHabit dialogue to change the information
	that is shown.		that is shown.

	9. The synthons that contribute to the lattice energy, along with the centroid-centroid		9. The synthons that contribute to the lattice energy, along with the centroid-centroid
	distance and component energy terms, are now shown. Click on the		distance and component energy terms, are now shown. Click on the
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	see that the lattice energy for urea is dominated by a small number of strong		see that the lattice energy for urea is dominated by a small number of strong
	hydrogen bonding interactions.		hydrogen bonding interactions.

	10. Now let’s look at the two most important interactions. Click on one of the		10. Now let’s look at the two most important interactions. Click on one of the
	rows in the table to highlight that interaction and show the synthon in the		rows in the table to highlight that interaction and show the synthon in the
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	multiple rows at once. Select the top two interactions for UREAXX		multiple rows at once. Select the top two interactions for UREAXX
	(synthons 8 and 9).		(synthons 8 and 9).

	11. You will see in the Mercury visualizer that two other urea molecules have		11. You will see in the Mercury visualizer that two other urea molecules have
	appeared above and below the central molecule. The red dashed lines		appeared above and below the central molecule. The red dashed lines
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	shows the interaction energy. You can clearly see that the strongest		shows the interaction energy. You can clearly see that the strongest
	interaction in urea aligns with the fastest growth direction.		interaction in urea aligns with the fastest growth direction.

	12. Click the Visualiser tab in the VisualHabit dialogue. From this tab you can		12. Click the Visualiser tab in the VisualHabit dialogue. From this tab you can
	change the way that the morphology is displayed in Mercury, such as		change the way that the morphology is displayed in Mercury, such as
	changing the colour of the faces and the edges. You can also change how		changing the colour of the faces and the edges. You can also change how
	synthons are displayed.		synthons are displayed.

	13. Click the radio dial in the Synthons section to display Distance rather than		13. Click the radio dial in the Synthons section to display Distance rather than
	Energy.		Energy.

	14. The Mercury visualizer will update to show the centroid-centroid distance of		14. The Mercury visualizer will update to show the centroid-centroid distance of
	the synthons in Å. These short, strong types of hydrogen bonds in the crystal		the synthons in Å. These short, strong types of hydrogen bonds in the crystal

← Older revision		Revision as of 21:22, 23 May 2023
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	you wish, explore options in the Morphology window.		you wish, explore options in the Morphology window.

	6~~. In the following exercises you may decide to calculate the BFDH morphology~~		6. The morphology can be modified, for example, if you want to represent a
	~~to compare the results.~~

	7. The morphology can be modified, for example, if you want to represent a
	crystal observed from growth experiments. In the Morphology window, click		crystal observed from growth experiments. In the Morphology window, click
	Save… and place the .cif file in a folder where you have permission.		Save… and place the .cif file in a folder where you have permission.

	8. Using a text editor of your choice open the morphology .cif file. You will see		7. Using a text editor of your choice open the morphology .cif file. You will see
	the data that corresponds to the HKLs and perpendicular distances. You can		the data that corresponds to the HKLs and perpendicular distances. You can
	modify these values to change the morphology. For the sake of example, we will		modify these values to change the morphology. For the sake of example, we will
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	these changes are not based on experimental observation		these changes are not based on experimental observation

	9. Back in Mercury, In the Morphology window click Open… and select your		8. Back in Mercury, In the Morphology window click Open… and select your
	modified .cif file to visualize your new morphology		modified .cif file to visualize your new morphology

← Older revision		Revision as of 21:21, 23 May 2023
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	==BFDH==		==BFDH==
	1. Open Mercury by double-clicking the Mercury icon on the desktop.		1. Open Mercury by double-clicking the Mercury icon on the desktop.

	2. In the Structure Navigator toolbar type the refcode KAXXAI10.		2. In the Structure Navigator toolbar type the refcode KAXXAI10.

	3. We want to identify facets of interest in this morphology. We will first create		3. We want to identify facets of interest in this morphology. We will first create
	the morphology using the BFDH morphology feature.		the morphology using the BFDH morphology feature.

	4. From the top-level menu select CSD-Particle > Morphology > BFDH… to		4. From the top-level menu select CSD-Particle > Morphology > BFDH… to
	generate the morphology. BFDH morphology uses the unit cell to create the		generate the morphology. BFDH morphology uses the unit cell to create the
	morphology you see, therefore it does not account for the chemistry of the		morphology you see, therefore it does not account for the chemistry of the
	structure.		structure.

	5. Rotate the structure to view the various facets that have been generated. If		5. Rotate the structure to view the various facets that have been generated. If
	you wish, explore options in the Morphology window.		you wish, explore options in the Morphology window.

	6. In the following exercises you may decide to calculate the BFDH morphology		6. In the following exercises you may decide to calculate the BFDH morphology
	to compare the results.		to compare the results.

	7. The morphology can be modified, for example, if you want to represent a		7. The morphology can be modified, for example, if you want to represent a
	crystal observed from growth experiments. In the Morphology window, click		crystal observed from growth experiments. In the Morphology window, click
	Save… and place the .cif file in a folder where you have permission.		Save… and place the .cif file in a folder where you have permission.

	8. Using a text editor of your choice open the morphology .cif file. You will see		8. Using a text editor of your choice open the morphology .cif file. You will see
	the data that corresponds to the HKLs and perpendicular distances. You can		the data that corresponds to the HKLs and perpendicular distances. You can
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	simply switch the values of some of the perpendicular distances. Note that		simply switch the values of some of the perpendicular distances. Note that
	these changes are not based on experimental observation		these changes are not based on experimental observation

	9. Back in Mercury, In the Morphology window click Open… and select your		9. Back in Mercury, In the Morphology window click Open… and select your
	modified .cif file to visualize your new morphology		modified .cif file to visualize your new morphology