pKa - Revision history

Kirilas: Updated for 2023 release

2023-07-26T09:29:08Z

Updated for 2023 release

← Older revision		Revision as of 09:29, 26 July 2023
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	<br />		<br />
	# Ionizable groups are highlighted using color shading (red for acid, blue for base, purple for amphoteric ionization centers). More intensive shading denotes strongest acid and base groups		# Ionizable groups are highlighted using color shading (red for acid, blue for base, purple for amphoteric ionization centers). More intensive shading denotes strongest acid and base groups
			# Select which type of pKa values to predict:
			#* Apparent pKa: simulates the actual ionization of the compound in aqueous solution, accounting for the protonation states of other ionizable groups at relevant pH
			#* Single pKa: estimates theoretical pKa that would be observed if the considered ionization center would be the only ionizable group in the molecule, so that the remainder of the molecule would always stay electrically neutral
	# Strongest acid and base pK<sub>a</sub> values including reliability range in ±log units		# Strongest acid and base pK<sub>a</sub> values including reliability range in ±log units
	# List of pK<sub>a</sub> constants for all stages of ionization		# List of pK<sub>a</sub> constants for all stages of ionization

Kirilas: /* Limitations */

2021-03-01T13:22:21Z

Limitations

← Older revision		Revision as of 13:22, 1 March 2021
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	* Contain atoms other than C, H, O, S, P, N, F, Cl, Br, I, Se, Si, Ge, Pb, Sn, As, and B		* Contain atoms other than C, H, O, S, P, N, F, Cl, Br, I, Se, Si, Ge, Pb, Sn, As, and B
	* Contain two or more fragments		* Contain two or more fragments
	* Contain more than 20 ionizable centers		* Contain more than 30 ionizable centers
	* Contain d-block or f-block metal atoms		* Contain d-block or f-block metal atoms
	* Contain textual abbreviations which cannot be transformed to structural fragments.		* Contain textual abbreviations which cannot be transformed to structural fragments.

	'''Note:''' There certainly exist some structures that formally meet the aforementioned limitations, but cannot be calculated with the current algorithm.		'''Note:''' There certainly exist some structures that formally meet the aforementioned limitations, but cannot be calculated with the current algorithm.

Kirilas at 08:54, 8 August 2018

2018-08-08T08:54:30Z

← Older revision		Revision as of 08:54, 8 August 2018
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	ACD/pKa does not explicitly flag cases of vinylology, although a message about tautomeric forms may appear.		ACD/pKa does not explicitly flag cases of vinylology, although a message about tautomeric forms may appear.

			====Limitations====

			ACD/pKa Classic algorithm will refuse to predict the pKa for structures that:
			* Contain more than 255 atoms (note that the program refuses to predict pKa for some cyclic compounds having less than 255 atoms due to the fact that the program uses a cycle-breaking algorithm that increases the number of atoms)
			* Do not contain an ionization center
			* Contain atoms of non-typical valence
			* Contain atoms other than C, H, O, S, P, N, F, Cl, Br, I, Se, Si, Ge, Pb, Sn, As, and B
			* Contain two or more fragments
			* Contain more than 20 ionizable centers
			* Contain d-block or f-block metal atoms
			* Contain textual abbreviations which cannot be transformed to structural fragments.

			'''Note:''' There certainly exist some structures that formally meet the aforementioned limitations, but cannot be calculated with the current algorithm.

Kirilas at 10:08, 15 June 2017

2017-06-15T10:08:32Z

← Older revision		Revision as of 10:08, 15 June 2017
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	</ol>		</ol>

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

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

Kirilas: /* Database of Electronic Substituent Constants (σ) */

2013-03-21T11:45:08Z

Database of Electronic Substituent Constants (σ)

← Older revision		Revision as of 11:45, 21 March 2013
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	\| σ<sub>R</sub> \|\| 453		\| σ<sub>R</sub> \|\| 453
	\|-		\|-
	\| σ<sub>R</sub><sup>-</sup> \|\| 157		\| σ<sub>R</sub><sup>–</sup> \|\| 157
	\|-		\|-
	\| σ<sub>R</sub><sup>+</sup> \|\| 143		\| σ<sub>R</sub><sup>+</sup> \|\| 143
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	\| σ<sub>Meta</sub> \|\| 431		\| σ<sub>Meta</sub> \|\| 431
	\|-		\|-
	\| σ<sub>Para</sub> \|\| 142		\| σ<sub>Para</sub><sup>–</sup> \|\| 142
	\|-		\|-
	\| σ<sub>Para</sub><sup>+</sup> \|\| 135		\| σ<sub>Para</sub><sup>+</sup> \|\| 135

Kirilas: /* Description of ACD/pKa GALAS Algorithm */

2013-03-08T11:21:56Z

Description of ACD/pKa GALAS Algorithm

← Older revision		Revision as of 11:21, 8 March 2013
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	<span style="font-size:8pt">		<span style="font-size:8pt">
	<sup>1</sup>Experimental ~~pKa~~ values obtained from ''The Merck Index'' (see full citation below).		<sup>1</sup>Experimental pK<sub>a</sub> values obtained from ''The Merck Index'' (see full citation below).
	</span>		</span>

Kirilas: /* Description of ACD/pKa GALAS Algorithm */

2013-03-08T11:21:21Z

Description of ACD/pKa GALAS Algorithm

← Older revision		Revision as of 11:21, 8 March 2013
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	===Description of ACD/pKa GALAS Algorithm===		===Description of ACD/pKa GALAS Algorithm===

	Estimation of ionization constants using this algorithm is a multi-step procedure involving estimation of pK<sub>a</sub> microconstants for all possible ionization centers in a hypothetical state of an uncharged molecule ("fundamental microconstants"), numerous corrections of these initial pK<sub>a</sub> values according to the surrounding of the reaction center and calculation of charge influences of ionized groups to the neighbouring ionization centers. Calculation routine utilizes a database of 4,600 ionization centers, a set of ''ca.'' 500 various interaction constants and four interaction calculation methods for different types of interactions, producing a full range of microconstants from which pK<sub>a</sub> macroconstants are obtained. This allows for a simulation of complete distribution plot of all protonation states of the molecule at different pH conditions. For example, the complete simulated ionization profile for cysteine molecule is illustrated in the figure ~~below~~:		Estimation of ionization constants using this algorithm is a multi-step procedure involving estimation of pK<sub>a</sub> microconstants for all possible ionization centers in a hypothetical state of an uncharged molecule ("fundamental microconstants"), numerous corrections of these initial pK<sub>a</sub> values according to the surrounding of the reaction center and calculation of charge influences of ionized groups to the neighbouring ionization centers. Calculation routine utilizes a database of 4,600 ionization centers, a set of ''ca.'' 500 various interaction constants and four interaction calculation methods for different types of interactions, producing a full range of microconstants from which pK<sub>a</sub> macroconstants are obtained. This allows for a simulation of complete distribution plot of all protonation states of the molecule at different pH conditions. For example, the complete simulated ionization profile for cysteine molecule is illustrated in the following figure:

	[[File:Cysteine_Ionization_Profile.png\|center]]		[[File:Cysteine_Ionization_Profile.png\|center]]

Kirilas: /* Description of ACD/pKa GALAS Algorithm */

2013-03-08T11:20:42Z

Description of ACD/pKa GALAS Algorithm

← Older revision		Revision as of 11:20, 8 March 2013
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	[[File:Cysteine_Ionization_Profile.png\|center]]		[[File:Cysteine_Ionization_Profile.png\|center]]

			<span style="font-size:8pt">
			<sup>1</sup>Experimental pKa values obtained from ''The Merck Index'' (see full citation below).
			</span>

	ACD/pKa GALAS algorithm is based on a training set containing 17,593 compounds (>20,000 ionization centers) obtained from various articles in peer-reviewed scientific journals and well-known reference books:		ACD/pKa GALAS algorithm is based on a training set containing 17,593 compounds (>20,000 ionization centers) obtained from various articles in peer-reviewed scientific journals and well-known reference books:

Kirilas: /* Description of ACD/pKa GALAS Algorithm */

2013-03-08T11:17:46Z

Description of ACD/pKa GALAS Algorithm

← Older revision		Revision as of 11:17, 8 March 2013
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	Estimation of ionization constants using this algorithm is a multi-step procedure involving estimation of pK<sub>a</sub> microconstants for all possible ionization centers in a hypothetical state of an uncharged molecule ("fundamental microconstants"), numerous corrections of these initial pK<sub>a</sub> values according to the surrounding of the reaction center and calculation of charge influences of ionized groups to the neighbouring ionization centers. Calculation routine utilizes a database of 4,600 ionization centers, a set of ''ca.'' 500 various interaction constants and four interaction calculation methods for different types of interactions, producing a full range of microconstants from which pK<sub>a</sub> macroconstants are obtained. This allows for a simulation of complete distribution plot of all protonation states of the molecule at different pH conditions. For example, the complete simulated ionization profile for cysteine molecule is illustrated in the figure below:		Estimation of ionization constants using this algorithm is a multi-step procedure involving estimation of pK<sub>a</sub> microconstants for all possible ionization centers in a hypothetical state of an uncharged molecule ("fundamental microconstants"), numerous corrections of these initial pK<sub>a</sub> values according to the surrounding of the reaction center and calculation of charge influences of ionized groups to the neighbouring ionization centers. Calculation routine utilizes a database of 4,600 ionization centers, a set of ''ca.'' 500 various interaction constants and four interaction calculation methods for different types of interactions, producing a full range of microconstants from which pK<sub>a</sub> macroconstants are obtained. This allows for a simulation of complete distribution plot of all protonation states of the molecule at different pH conditions. For example, the complete simulated ionization profile for cysteine molecule is illustrated in the figure below:

	[[File:Cysteine_Ionization_Profile.~~gif~~\|center]]		[[File:Cysteine_Ionization_Profile.png\|center]]

	ACD/pKa GALAS algorithm is based on a training set containing 17,593 compounds (>20,000 ionization centers) obtained from various articles in peer-reviewed scientific journals and well-known reference books:		ACD/pKa GALAS algorithm is based on a training set containing 17,593 compounds (>20,000 ionization centers) obtained from various articles in peer-reviewed scientific journals and well-known reference books:

Kirilas at 11:14, 8 March 2013

2013-03-08T11:14:33Z

← Older revision		Revision as of 11:14, 8 March 2013
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	ACD/pKa does not explicitly flag cases of vinylology, although a message about tautomeric forms may appear.		ACD/pKa does not explicitly flag cases of vinylology, although a message about tautomeric forms may appear.

	~~</div>~~
	~~</div>~~