LogD - Revision history

Kirilas: /* Calculation of LogP for Microspecies */

2019-04-29T14:41:43Z

Calculation of LogP for Microspecies

← Older revision		Revision as of 14:41, 29 April 2019
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	To calculate the log''P'' of the charged microspecies, certain empirical rules were applied. Different corrections to the log''P'' values of the neutral form were applied, depending on the charge of the microspecies. For example, for zwitterionic forms we correct the log''P'' of the neutral form by –2.5 because an intensive analysis showed that this correction factor led to the best fit over a wide variety of compounds.		To calculate the log''P'' of the charged microspecies, certain empirical rules were applied. Different corrections to the log''P'' values of the neutral form were applied, depending on the charge of the microspecies. For example, for zwitterionic forms we correct the log''P'' of the neutral form by –2.5 because an intensive analysis showed that this correction factor led to the best fit over a wide variety of compounds.

	Note that the log''D'' calculation algorithm takes into account the partitioning of ion pairs. The formation of ion-pairs is referred to as physiological conditions, which presume an ionic strength of 0.15M. The ion-pairs are presumed to be transferred to organic phase like any non-charged form. The ionic strength is equal to the concentration of such monovalent ions as Na+, K+ (counter ions for organic anions) and ~~Cl–~~ and ~~Br–~~ (counter ions for organic cations).		Note that the log''D'' calculation algorithm takes into account the partitioning of ion pairs. The formation of ion-pairs is referred to as physiological conditions, which presume an ionic strength of 0.15M. The ion-pairs are presumed to be transferred to organic phase like any non-charged form. The ionic strength is equal to the concentration of such monovalent ions as Na<sup>+</sup>, K<sup>+</sup> (counter ions for organic anions) and Cl<sup>–</sup> and Br<sup>–</sup> (counter ions for organic cations).

	===Ionization Constants of Microspecies===		===Ionization Constants of Microspecies===

Kirilas: /* Calculation of LogP for Microspecies */

2019-04-29T14:40:20Z

Calculation of LogP for Microspecies

← Older revision		Revision as of 14:40, 29 April 2019
Line 90:		Line 90:

	To calculate the log''P'' of the charged microspecies, certain empirical rules were applied. Different corrections to the log''P'' values of the neutral form were applied, depending on the charge of the microspecies. For example, for zwitterionic forms we correct the log''P'' of the neutral form by –2.5 because an intensive analysis showed that this correction factor led to the best fit over a wide variety of compounds.		To calculate the log''P'' of the charged microspecies, certain empirical rules were applied. Different corrections to the log''P'' values of the neutral form were applied, depending on the charge of the microspecies. For example, for zwitterionic forms we correct the log''P'' of the neutral form by –2.5 because an intensive analysis showed that this correction factor led to the best fit over a wide variety of compounds.

			Note that the log''D'' calculation algorithm takes into account the partitioning of ion pairs. The formation of ion-pairs is referred to as physiological conditions, which presume an ionic strength of 0.15M. The ion-pairs are presumed to be transferred to organic phase like any non-charged form. The ionic strength is equal to the concentration of such monovalent ions as Na+, K+ (counter ions for organic anions) and Cl– and Br– (counter ions for organic cations).

	===Ionization Constants of Microspecies===		===Ionization Constants of Microspecies===

Kirilas at 10:02, 15 June 2017

2017-06-15T10:02:14Z

← Older revision		Revision as of 10:02, 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 12:46, 12 June 2015

2015-06-12T12:46:38Z

← Older revision		Revision as of 12:46, 12 June 2015
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	<br />		<br />

	# Displays several logD values at physiologically relevant pHs. [[File:Logd_editph.png\|right]]<br>a. Click "+/-" nodes to expand/collapse the option of new pH point's addition.<br>b. Enter desirable pH value and press "Add". The new pH point along with automatically calculated logD value will appear at the end of the list.<br>c. Hover over the pH point and press the "x" pictogram to remove it from the list.		<ol>
	# Press "Configure" button to select LogP and pKa calculation algorithms, and libraries to use for training, or set other options.<br>'''NOTE:''' Training takes place through LogP Self-training Libraries. The training procedure implemented in ACD/LogP GALAS module accepts LogD values measured at any pH and automatically recalculates these to the respective LogP of neutral species to be stored in the library. The trained LogP library may then be used in both LogP and LogD calculations.		<li>Displays several logD values at physiologically relevant pHs.[[File:Logd_editph.png\|right]]<br><br>a. Click "+/-" nodes to expand/collapse the option of new pH point's addition.<br>b. Enter desirable pH value and press "Add". The new pH point along with automatically calculated logD value will appear at the end of the list.<br>c. Hover over the pH point and press the "x" pictogram to remove it from the list.</li><br>
	# Click and drag the slider to see calculated logD at precise pH value displayed on the right.		<li>Press "Configure" button to select LogP and pKa calculation algorithms, and libraries to use for training, or set other options.<br><br>'''NOTE:''' Training takes place through LogP Self-training Libraries. The training procedure implemented in ACD/LogP GALAS module accepts LogD values measured at any pH and automatically recalculates these to the respective LogP of neutral species to be stored in the library. The trained LogP library may then be used in both LogP and LogD calculations.</li><br>
			<li>Click and drag the slider to see calculated logD at precise pH value displayed on the right.</li>
			</ol>
	<br>		<br>

Kirilas: /* Calculation of LogP for Microspecies */

2013-03-07T13:21:20Z

Calculation of LogP for Microspecies

← Older revision		Revision as of 13:21, 7 March 2013
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	===Calculation of Log''P'' for Microspecies===		===Calculation of Log''P'' for Microspecies===

	To calculate the log''P'' of the neutral form of a given chemical structure, one of the different available ACD/LogP models (Classic, GALAS, or Consensus), that is set as a '''Default LogP model''' is used. Further details of these algorithms may be found in the [[LogP#~~Technical Information~~\|ACD/LogP Technical ~~Information~~]] section.		To calculate the log''P'' of the neutral form of a given chemical structure, one of the different available ACD/LogP models (Classic, GALAS, or Consensus), that is set as a '''Default LogP model''' is used. Further details of these algorithms may be found in the [[LogP#Technical_information\|ACD/LogP Technical information]] section.

	To calculate the log''P'' of the charged microspecies, certain empirical rules were applied. Different corrections to the log''P'' values of the neutral form were applied, depending on the charge of the microspecies. For example, for zwitterionic forms we correct the log''P'' of the neutral form by –2.5 because an intensive analysis showed that this correction factor led to the best fit over a wide variety of compounds.		To calculate the log''P'' of the charged microspecies, certain empirical rules were applied. Different corrections to the log''P'' values of the neutral form were applied, depending on the charge of the microspecies. For example, for zwitterionic forms we correct the log''P'' of the neutral form by –2.5 because an intensive analysis showed that this correction factor led to the best fit over a wide variety of compounds.

Kirilas: /* Ionization Constants of Microspecies */

2013-03-07T13:20:33Z

Ionization Constants of Microspecies

← Older revision		Revision as of 13:20, 7 March 2013
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	To calculate the ionization constants of microspecies, the program creates a full scheme for the dissociation of a compound, and then all microconstants are calculated using one of the two available pKa prediction algorithms (Classic or GALAS) that is set as a '''Default pKa model''' in '''ACD/Percepta''' settings.		To calculate the ionization constants of microspecies, the program creates a full scheme for the dissociation of a compound, and then all microconstants are calculated using one of the two available pKa prediction algorithms (Classic or GALAS) that is set as a '''Default pKa model''' in '''ACD/Percepta''' settings.

	Further details of the prediction algorithm for the ionization constants of microspecies may be found in the [[pKa#~~Technical_Information~~\|ACD/pKa Technical ~~Information~~]] section.		Further details of the prediction algorithm for the ionization constants of microspecies may be found in the [[pKa#Technical_information\|ACD/pKa Technical information]] section.

	===References===		===References===

Kirilas at 13:16, 7 March 2013

2013-03-07T13:16:46Z

← Older revision		Revision as of 13:16, 7 March 2013
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	# Press "Configure" button to select LogP and pKa calculation algorithms, and libraries to use for training, or set other options.<br>'''NOTE:''' Training takes place through LogP Self-training Libraries. The training procedure implemented in ACD/LogP GALAS module accepts LogD values measured at any pH and automatically recalculates these to the respective LogP of neutral species to be stored in the library. The trained LogP library may then be used in both LogP and LogD calculations.		# Press "Configure" button to select LogP and pKa calculation algorithms, and libraries to use for training, or set other options.<br>'''NOTE:''' Training takes place through LogP Self-training Libraries. The training procedure implemented in ACD/LogP GALAS module accepts LogD values measured at any pH and automatically recalculates these to the respective LogP of neutral species to be stored in the library. The trained LogP library may then be used in both LogP and LogD calculations.
	# Click and drag the slider to see calculated logD at precise pH value displayed on the right.		# Click and drag the slider to see calculated logD at precise pH value displayed on the right.
			<br>

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

	==Technical information==		==Technical information==
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	# Warren J. Lyman, et al. ''Handbook of Chemical Property Estimation Methods''. ACS, Washington, DC, 1990.		# Warren J. Lyman, et al. ''Handbook of Chemical Property Estimation Methods''. ACS, Washington, DC, 1990.

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

Kirilas at 13:09, 7 March 2013

2013-03-07T13:09:39Z

@@ Line 15: / Line 15: @@
 # Press "Configure" button to select LogP and pKa calculation algorithms, and libraries to use for training, or set other options.<br>'''NOTE:''' Training takes place through LogP Self-training Libraries. The training procedure implemented in ACD/LogP GALAS module accepts LogD values measured at any pH and automatically recalculates these to the respective LogP of neutral species to be stored in the library. The trained LogP library may then be used in both LogP and LogD calculations.
 # Click and drag the slider to see calculated logD at precise pH value displayed on the right.
 <br />

Kirilas: /* Interface */

2013-01-21T13:55:32Z

Interface

← Older revision		Revision as of 13:55, 21 January 2013
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	# Displays several logD values at physiologically relevant pHs. [[File:Logd_editph.png\|right]]<br>a. Click "+/-" nodes to expand/collapse the option of new pH point's addition.<br>b. Enter desirable pH value and press "Add". The new pH point along with automatically calculated logD value will appear at the end of the list.<br>c. Hover over the pH point and press the "x" pictogram to remove it from the list.		# Displays several logD values at physiologically relevant pHs. [[File:Logd_editph.png\|right]]<br>a. Click "+/-" nodes to expand/collapse the option of new pH point's addition.<br>b. Enter desirable pH value and press "Add". The new pH point along with automatically calculated logD value will appear at the end of the list.<br>c. Hover over the pH point and press the "x" pictogram to remove it from the list.
	# Press "Configure" button to select LogP and pKa calculation algorithms, and libraries to use for training, or set other options.		# Press "Configure" button to select LogP and pKa calculation algorithms, and libraries to use for training, or set other options.<br>'''NOTE:''' Training takes place through LogP Self-training Libraries. The training procedure implemented in ACD/LogP GALAS module accepts LogD values measured at any pH and automatically recalculates these to the respective LogP of neutral species to be stored in the library. The trained LogP library may then be used in both LogP and LogD calculations.
	# Click and drag the slider to see calculated logD at precise pH value displayed on the right.		# Click and drag the slider to see calculated logD at precise pH value displayed on the right.
	<br />		<br />

Kristina: /* Interface */

2012-05-29T13:33:20Z

Interface

← Older revision		Revision as of 13:33, 29 May 2012
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	<br />		<br />

	[[Image:~~logd~~.png\|center]]		[[Image:Logd.png\|center]]
	<br />		<br />

	# Displays several logD values at physiologically relevant pHs. [[File:~~logd_editph~~.png\|right]]<br>a. Click "+/-" nodes to expand/collapse the option of new pH point's addition.<br>b. Enter desirable pH value and press "Add". The new pH point along with automatically calculated logD value will appear at the end of the list.<br>c. Hover over the pH point and press the "x" pictogram to remove it from the list.		# Displays several logD values at physiologically relevant pHs. [[File:Logd_editph.png\|right]]<br>a. Click "+/-" nodes to expand/collapse the option of new pH point's addition.<br>b. Enter desirable pH value and press "Add". The new pH point along with automatically calculated logD value will appear at the end of the list.<br>c. Hover over the pH point and press the "x" pictogram to remove it from the list.
	# Press "Configure" button to select LogP and pKa calculation algorithms, and libraries to use for training, or set other options.		# Press "Configure" button to select LogP and pKa calculation algorithms, and libraries to use for training, or set other options.
	# Click and drag the slider to see calculated logD at precise pH value displayed on the right.		# Click and drag the slider to see calculated logD at precise pH value displayed on the right.
	<br />		<br />