PhysChem Profiler - Revision history

Kirilas: Updated for 2023 release

2023-07-26T10:28:01Z

Updated for 2023 release

← Older revision		Revision as of 10:28, 26 July 2023
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	<li>'''Structure Pane'''<br>The '''Structure Pane''' displays a 2-D representation of the chemical structure used for calculation. A compound name is displayed only for those structures which are found in the '''Dictionary'''.<br>[[Image:Paste.png]] '''(Ctrl+V)''': Pastes an input structure from the clipboard to the '''Structure Pane'''. Also, if you are pasting a SMILES string from the clipboard, you can save a step by clicking directly on this button to display the 2-D structure. The calculation will be performed automatically for the input structure.<br>[[Image:Copy_pictogram.png]] '''(Ctrl+C)''': Copies the active structure in the '''Structure Pane''' to the clipboard.<br>[[Image:Opendictionary.png]] '''(Ctrl+D)''': Opens the '''Dictionary''' with >117,000 available names to find the corresponding structure and display it. When a compound is selected from the list and the selection confirmed by clicking '''OK''', calculations for the chosen compound will be performed automatically.<br>[[Image:SMILES_pictogram.png]] '''(Ctrl+S)''': Type or paste SMILES notation string in this field. The string will automatically be converted to 2-D structure. Calculation will be performed automatically for the input structure.<br> [[Image:Open_pictogram.png]] '''(Ctrl+O)''': Opens a file containing a molecular structure. '''ACD/Percepta''' supports all versions of MDL .mol files, ACD/ChemSketch .sk2, as well as ISIS Draw .skc, and ChemDraw .cdx formats.<br>[[Image:Edit_pictogram.png]] '''(Ctrl+E)''': Allows to edit the active molecule. </li><br>		<li>'''Structure Pane'''<br>The '''Structure Pane''' displays a 2-D representation of the chemical structure used for calculation. A compound name is displayed only for those structures which are found in the '''Dictionary'''.<br>[[Image:Paste.png]] '''(Ctrl+V)''': Pastes an input structure from the clipboard to the '''Structure Pane'''. Also, if you are pasting a SMILES string from the clipboard, you can save a step by clicking directly on this button to display the 2-D structure. The calculation will be performed automatically for the input structure.<br>[[Image:Copy_pictogram.png]] '''(Ctrl+C)''': Copies the active structure in the '''Structure Pane''' to the clipboard.<br>[[Image:Opendictionary.png]] '''(Ctrl+D)''': Opens the '''Dictionary''' with >117,000 available names to find the corresponding structure and display it. When a compound is selected from the list and the selection confirmed by clicking '''OK''', calculations for the chosen compound will be performed automatically.<br>[[Image:SMILES_pictogram.png]] '''(Ctrl+S)''': Type or paste SMILES notation string in this field. The string will automatically be converted to 2-D structure. Calculation will be performed automatically for the input structure.<br> [[Image:Open_pictogram.png]] '''(Ctrl+O)''': Opens a file containing a molecular structure. '''ACD/Percepta''' supports all versions of MDL .mol files, ACD/ChemSketch .sk2, as well as ISIS Draw .skc, and ChemDraw .cdx formats.<br>[[Image:Edit_pictogram.png]] '''(Ctrl+E)''': Allows to edit the active molecule. </li><br>

	<li>[[Image:Create_pdf_pictogram.png]] Creates a PDF report with the displayed results.<br>[[Image:Copy_results_pictogram.png]] Copies the displayed results to the clipboard.</li><br>		<li>[[Image:Batch_pdf_pictogram.png]] Saves a PDF report for each compound in the active project in the directory of your choice.<br>[[Image:Create_pdf_pictogram.png]] Creates a PDF report with the displayed results.<br>[[Image:Copy_results_pictogram.png]] Copies the displayed results to the clipboard.</li><br>

	<li>The '''pKa results''' pane displays the output of pK<sub>a</sub> predictions: strongest acid and base pK<sub>a</sub> values including reliability range in ±log units, a list of pK<sub>a</sub> constants for all stages of ionization, as well as a list of partial ionization reactions (microstages) responsible for each ionization stage. Contribution of each microstage to the final pK<sub>a</sub> value is given in percent. The results may slightly differ depending on the designated preferences of the Expert View. ''For more information see [[General\|How to set the default algorithms for logP, pKa and LogS calculation?]] and [[pKa]]''</li><br>		<li>The '''pKa results''' pane displays the output of pK<sub>a</sub> predictions: strongest acid and base pK<sub>a</sub> values including reliability range in ±log units, a list of pK<sub>a</sub> constants for all stages of ionization, as well as a list of partial ionization reactions (microstages) responsible for each ionization stage. Contribution of each microstage to the final pK<sub>a</sub> value is given in percent. The results may slightly differ depending on the designated preferences of the Expert View. ''For more information see [[General\|How to set the default algorithms for logP, pKa and LogS calculation?]] and [[pKa]]''</li><br>

Kirilas: Updated for 2021.1 release

2021-07-28T08:45:05Z

Updated for 2021.1 release

← Older revision		Revision as of 08:45, 28 July 2021
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	<li>[[File:physchem_profiler_phdependent_pane.png\|right]]The '''pH dependent results''' pane presents predicted values of ionization-dependent properties, such as octanol-water distribution (LogD) and solubility in buffer (LogS) in both graphical and tabular form.<br><br>		<li>[[File:physchem_profiler_phdependent_pane.png\|right]]The '''pH dependent results''' pane presents predicted values of ionization-dependent properties, such as octanol-water distribution (LogD) and solubility in buffer (LogS) in both graphical and tabular form.<br><br>
	<ol style="list-style-type:lower-latin">		<ol style="list-style-type:lower-latin">
			<li>View the calculated isoelectric point - the pH value at which the molecule has zero net charge. When isoelectric point cannot be calculated, the value is replaced by the appropriate comment:
			<ul>
			<li>'''Not ionizable''': the compound does not have any ionizable groups and therefore, remains electrically neutral throughout the entire pH scale</li>
			<li>'''Not available''': isoelectric point does not exist, because the compound has no acid or no base groups, or if it is never electrically neutral</li>
			</ul>
			</li>
	<li>Click the tab of interest to view the plot of pH dependency of LogD, LogS, or Net Charge.</li>		<li>Click the tab of interest to view the plot of pH dependency of LogD, LogS, or Net Charge.</li>
	<li>Click and drag the slider to see the calculated ~~logD~~ values at precise pH value.</li>		<li>Click and drag the slider to see the calculated LogD values at precise pH value.</li>
	<li>The two tabs in the bottom part of this pane enable switching between ''Default'' and ''Custom'' views of the results table. The ''Default'' table is read-only and list calculated LogD, LogS, and fractions of the compound having different net charges throughout the entire pH scale (0-14) at 0.1 intervals. ''Custom'' table is editable and allows adding and deleting user-defined pH points.</li></ol><br>		<li>The two tabs in the bottom part of this pane enable switching between ''Default'' and ''Custom'' views of the results table. The ''Default'' table is read-only and list calculated LogD, LogS, and fractions of the compound having different net charges throughout the entire pH scale (0-14) at 0.1 intervals. ''Custom'' table is editable and allows adding and deleting user-defined pH points.</li></ol><br>
	</li><br>		</li><br>

Kirilas: /* Dielectric Constant, ε (Permittivity) */

2020-10-06T11:58:43Z

Dielectric Constant, ε (Permittivity)

← Older revision		Revision as of 11:58, 6 October 2020
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	'''ACD/Percepta '''calculates the dielectric constant from calculated ''MV'' (see above) and a proprietary empirical additive function.		'''ACD/Percepta '''calculates the dielectric constant from calculated ''MV'' (see above) and a proprietary empirical additive function.

			'''Note:''' Dielectric constant is derived only for hydrocarbons.

	====Polarizability====		====Polarizability====

Kirilas at 09:54, 15 June 2017

2017-06-15T09:54:09Z

← Older revision		Revision as of 09:54, 15 June 2017
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	<br>		<br>

	<div class="mw-collapsible ~~mw-collapsed~~">		<div class="mw-collapsible">

	==Technical information==		==Technical information==

Kristina at 15:38, 18 February 2015

2015-02-18T15:38:31Z

← Older revision		Revision as of 15:38, 18 February 2015
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	</li>		</li>
	</ol>		</ol>
			<br>

	<div class="mw-collapsible mw-collapsed">		<div class="mw-collapsible mw-collapsed">

Kristina at 13:42, 18 February 2015

2015-02-18T13:42:19Z

← Older revision		Revision as of 13:42, 18 February 2015
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	<li>[[Image:Create_pdf_pictogram.png]] Creates a PDF report with the displayed results.<br>[[Image:Copy_results_pictogram.png]] Copies the displayed results to the clipboard.</li><br>		<li>[[Image:Create_pdf_pictogram.png]] Creates a PDF report with the displayed results.<br>[[Image:Copy_results_pictogram.png]] Copies the displayed results to the clipboard.</li><br>

	<li>The '''pKa results''' ~~roll-down~~ pane displays the output of pK<sub>a</sub> predictions: strongest acid and base pK<sub>a</sub> values including reliability range in ±log units, a list of pK<sub>a</sub> constants for all stages of ionization, as well as a list of partial ionization reactions (microstages) responsible for each ionization stage. Contribution of each microstage to the final pK<sub>a</sub> value is given in percent. The results may slightly differ depending on the designated preferences of the Expert View. ''For more information see [[General\|How to set the default algorithms for logP, pKa and LogS calculation?]] and [[pKa]]''</li><br>		<li>The '''pKa results''' pane displays the output of pK<sub>a</sub> predictions: strongest acid and base pK<sub>a</sub> values including reliability range in ±log units, a list of pK<sub>a</sub> constants for all stages of ionization, as well as a list of partial ionization reactions (microstages) responsible for each ionization stage. Contribution of each microstage to the final pK<sub>a</sub> value is given in percent. The results may slightly differ depending on the designated preferences of the Expert View. ''For more information see [[General\|How to set the default algorithms for logP, pKa and LogS calculation?]] and [[pKa]]''</li><br>

	<li>Ionizable groups are highlighted using color shading (red for acid, blue for base, purple for amphoteric). More intensive shading denotes strongest acid and base groups</li><br>		<li>Ionizable groups are highlighted using color shading (red for acid, blue for base, purple for amphoteric). More intensive shading denotes strongest acid and base groups</li><br>

	<li>[[File:physchem_profiler_phdependent_pane.png\|right]]The '''pH dependent results''' ~~roll-down~~ pane presents predicted values of ionization-dependent properties, such as octanol-water distribution (LogD) and solubility in buffer (LogS) in both graphical and tabular form.<br><br>		<li>[[File:physchem_profiler_phdependent_pane.png\|right]]The '''pH dependent results''' pane presents predicted values of ionization-dependent properties, such as octanol-water distribution (LogD) and solubility in buffer (LogS) in both graphical and tabular form.<br><br>
	<ol style="list-style-type:lower-latin">		<ol style="list-style-type:lower-latin">
	<li>Click the tab of interest to view the plot of pH dependency of LogD, LogS, or Net Charge.</li>		<li>Click the tab of interest to view the plot of pH dependency of LogD, LogS, or Net Charge.</li>
	<li>Click and drag the slider to see the calculated logD values at precise pH value.</li>		<li>Click and drag the slider to see the calculated logD values at precise pH value.</li>
	<li>The two tabs in the bottom part of this pane enable switching between ''Default'' and ''Custom'' views of the results table. The ''Default'' table is read-only and list calculated LogD, LogS, and fractions of the compound having different net charges throughout the entire pH scale (0-14) at 0.1 intervals. ''Custom'' table is editable and allows adding and deleting user-defined pH points.</li></ol><br>		<li>The two tabs in the bottom part of this pane enable switching between ''Default'' and ''Custom'' views of the results table. The ''Default'' table is read-only and list calculated LogD, LogS, and fractions of the compound having different net charges throughout the entire pH scale (0-14) at 0.1 intervals. ''Custom'' table is editable and allows adding and deleting user-defined pH points.</li></ol><br>
	~~'''Note:''' Roll-down menus can be viewed simultaneously by dragging them partway up or down the pane.~~</li><br>		</li><br>

	<li>A list of basic physicochemical and molecular properties:		<li>A list of basic physicochemical and molecular properties:

Kirilas at 11:06, 20 March 2013

2013-03-20T11:06:00Z

← Older revision		Revision as of 11:06, 20 March 2013
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			==Overview==

	'''PhysChem Profiler''' is a special workspace that integrates the output of all physicochemical property predictors included in '''ACD/Percepta''' and presents it a single straihgtforward interface.<br>		'''PhysChem Profiler''' is a special workspace that integrates the output of all physicochemical property predictors included in '''ACD/Percepta''' and presents it a single straihgtforward interface.<br>
	<br>		<br>

Kirilas at 09:50, 20 March 2013

2013-03-20T09:50:41Z

← Older revision		Revision as of 09:50, 20 March 2013
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	~~==Interface==~~

	'''PhysChem Profiler''' is a special workspace that integrates the output of all physicochemical property predictors included in '''ACD/Percepta''' and presents it a single straihgtforward interface.<br>		'''PhysChem Profiler''' is a special workspace that integrates the output of all physicochemical property predictors included in '''ACD/Percepta''' and presents it a single straihgtforward interface.<br>
	<br>		<br>
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	</ul>		</ul>
	-->		-->

			==Interface==

	[[File:physchem_profiler.png\|center]]<br>		[[File:physchem_profiler.png\|center]]<br>

Kirilas at 09:45, 20 March 2013

2013-03-20T09:45:15Z

← Older revision		Revision as of 09:45, 20 March 2013
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			==Interface==

	'''PhysChem Profiler''' is a special workspace that integrates the output of all physicochemical property predictors included in '''ACD/Percepta''' and presents it a single straihgtforward interface.<br>		'''PhysChem Profiler''' is a special workspace that integrates the output of all physicochemical property predictors included in '''ACD/Percepta''' and presents it a single straihgtforward interface.<br>
	<br>		<br>

Kirilas at 09:44, 20 March 2013

2013-03-20T09:44:22Z

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