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ACD/LogP DB

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Calculation Procedures for Molecular Lipophilicity: A Comparative Study
Comparison with SciLogP (PDF, 140 KB)
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Other Comparisons

ACD/LogP has been tested against the following calculation methods:

ALOGP - the atomic constant approach of Viswanadhan,
BLOGP - the molecular orbital approach of Bodor,
CLOGP - the fragmental constant approach of Leo, and
KLOGP - the extended group contribution approach of Klopman.

Comparisons (Calculations are made using ACD/LogP DB version 5.0)

Table 1: Compare the experimental logP values (LogP_Exp) of 47 nucleosides and nucleoside bases to those calculated by different methods.
Table 2: Compare the results of correlations between the experimental and calculated logP values for the different methods from the Table 1.
Table 3: Compare ACD/LogP to LOGK developed by Klopman et al. for the selected compounds:
Table 4: Compares the results of correlations for all of 71 structures which have proven difficult to calculate using the LOGK method.

Table 1:

The following table compares the experimental logP values (LogP_Exp) of 47 nucleosides and nucleoside bases to those calculated by different methods:

No.	Name	LogP_Exp	ACD/LogP	KLOGP	ALOGP	CLOGP	BLOGP
1	Ado	-1.23	-1.26± 0.46	-2.13	-1.240	-2.941	0.182
2	dAdo	-0.54	-0.53± 0.58	-1.29	-0.630	-2.531	0.356
3	ddAdo	-0.21	-0.49± 0.45	-0.46	-0.190	-1.116	0.406
4	ddeAdo	-0.35	-0.56± 0.48	-0.42	0.040	-1.600	0.379
5	FddAdo	0.08	-0.49± 0.54	-0.23	-0.020	-1.273	0.522
6	Guo	-1.89	-1.89± 0.52	-3.09	-1.630	-3.923	-0.210
7	dGuo	-1.30	-1.28± 0.62	-2.26	-1.010	-3.338	-0.013
8	ddGuo	-1.00	-0.73± 0.52	-1.43	-0.580	-1.923	0.177
9	ddeGuo	-1.21	-0.80± 0.54	-1.39	-0.350	-2.407	0.115
10	dDAPR	-0.52	-0.55± 0.58	-1.38	-0.910	-2.592	-0.101
11	ddDAPR	-0.46	-0.52± 0.46	-0.55	-0.470	0.067	0.067
12	FddDAPR	0.05	-0.52± 0.54	-0.32	-0.300	-1.333	0.249
13	Urd	-1.71	-1.78± 0.39	-2.28	-1.590	-2.560	0.085
14	dUrd	-1.50	-1.47± 0.49	-1.44	-0.980	-2.090	0.456
15	ddUrd	-0.88	-1.18± 0.39	-0.61	-0.540	-0.675	0.667
16	ddeUrd	-1.07	-1.26± 0.40	-0.57	-0.320	-1.159	0.645
17	FddUrd	-0.48	-1.15± 0.45	-0.38	-0.370	-0.832	0.912
18	dThd	-1.17	-1.18± 0.50	-1.03	-0.820	-1.591	0.817
19	ddThd	-0.63	-0.82± 0.39	-0.20	-0.390	-0.176	1.042
20	ddeThd	-0.81	-0.90± 0.40	-0.16	-0.160	-0.660	0.999
21	FddThd	-0.27	-0.82± 0.46	0.03	-0.220	-0.333	1.269
22	Cyd	-2.51	-2.10± 0.39	-2.86	-1.420	-3.111	0.113
23	dCyd	-1.77	-1.79± 0.49	-2.03	-0.810	-2.549	0.478
24	ddCyd	-1.30	-1.50± 0.39	-1.20	-0.370	-1.133	0.619
25	ddeCyd	-1.42	-1.59± 0.40	-1.16	-0.140	-1.617	0.571
26	FddCyd	-0.91	-1.51± 0.46	-0.97	-0.200	-1.290	0.775
27	F6ddP	0.00	-0.20± 0.45	0.28	0.490	-0.906	0.247
28	F62AddP	-0.05	-0.25± 0.45	-0.11	0.210	-0.970	0.375
29	Br6ddP	0.35	0.15± 0.45	0.81	1.080	-0.356	0.798
30	Br62AddP	0.33	0.14± 0.45	0.42	0.800	-0.420	0.765
31	Cl6ddP	0.23	0.04± 0.40	0.50	0.780	-0.386	0.489
32	Cl62AddP	0.21	0.01± 0.40	0.11	0.500	-0.450	0.545
33	I6ddP	0.52	0.33± 0.45	1.00	1.080	0.074	1.011
34	I62AddP	0.52	0.32± 0.45	0.61	0.800	0.010	0.996
35	ddI	-1.24	-1.33± 0.50	-1.55	-0.950	-1.755	-0.335
36	uracil	-1.07	-0.71± 0.29	-0.86	-0.720	-1.060	-0.585
37	adenine, 8Aza	-0.96	-0.94± 0.40	-0.11	-0.670	-0.063	-0.034
38	guanine, 8Aza	-0.71	-0.71± 0.47	-1.14	-1.060	-1.004	-0.836
39	cytocine	-1.73	-1.71± 0.37	-1.45	-0.550	-1.846	-0.769
40	adenine	-0.09	-0.09± 0.39	0.23	-0.360	-0.426	0.036
41	thioguanine	-0.07	-0.08± 0.42	-0.37	-0.020	-1.824	0.308
42	adenine, 9Ppl	0.74	0.73± 0.38	0.50	0.690	0.437	1.327
43	uracil, 6Aza	-0.59	-1.95± 0.63	-0.91	-0.490	-0.593	-1.013
44	guanine	-0.91	-0.90± 0.38	-1.17	-0.750	-1.264	-0.891
45	thymine	-0.62	-0.12± 0.29	-0.45	-0.560	-0.557	-0.130
46	hypoxanthine	-1.11	-1.11± 0.39	-0.89	-0.880	-1.260	-0.873
47	purine	-0.37	-0.37± 0.24	0.53	-0.280	-0.290	-0.139

In this table the experimental data and results of calculations by KLOGP, ALOGP CLOGP and BLOGP have been taken from the following references:

Viswanadhan, V. N.; et al, J. Comput. Chem. 1993, 14, 1019

Klopman, G.; J. Chem. Inf. Comput. Sci. 1994, 34, 752.

Note that only the ACD/LogP method provides calculated values with uncertainty limits. Also note that nucleosides always exist in several tautomeric forms and in most cases are ionized. Among all of the tested programs only ACD/LogP automatically generates different tautomeric forms and provides them with typical pK_a ranges.

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Table 2:

The following table compares the results of correlations between the experimental and calculated logP values for the different methods from the table above:

Method	Intercept	Slope	No of data points	Correlation Coefficient	Standard Deviation
ACD/LogP	0.092±0.074	0.960±0.067	47	0.9050	0.311
KLOGP	-0.187±0.063	0.675±0.052	47	0.8853	0.340
ALOGP	-0.348±0.066	0.927±0.088	47	0.8415	0.395
CLOGP	-0.023±0.122	0.512±0.075	47	0.7105	0.515
BLOGP	-0.810±0.109	0.499±0.171	47	0.3987	0.671

Note that a good calculation method must give not only a high correlation coefficient and a low standard deviation, but also intercept close to zero and slope close to unit.

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Table 3:

The following table compares ACD/LogP to LOGK developed by Klopman et al. for the selected compounds:

No	Name	LogP_Exp	ACD/LogP	LOGPK
1	9-fluorenone	3.58	3.58±0.26	2.66
2	cyclohexylamine	1.49	1.40±0.19	0.44
3	Ado	-1.23	-1.26±0.46	-2.13
4	Guo	-1.89	-1.89±0.52	-3.09
5	dGuo	-1.30	-1.28±0.62	-2.26
6	dDAPR	-0.52	-0.55±0.58	-1.38
7	purine	-0.37	-0.37±0.24	0.53
8	acetaldoxime	-0.12	-0.13±0.27	0.82
9	2,4,5-tribromoimidazole	1.96	2.00±0.49	2.79
10	thiazole	0.44	0.44±0.29	1.25
11	pyrazine	-0.22	-0.28±0.21	0.82
12	2,3,4,5,6-pentachloropyridine	3.53	3.61±0.36	4.47
13	pyridine 1-oxide	-1.30	-1.69±0.25	-0.23
14	2-methylpyrazine	0.23	0.18±0.21	1.23
15	g-pyridylmethylamine	-0.38	-0.40±0.22	0.47
16	4,6-dimethylpyrimidine	0.62	0.59±0.18	1.64
17	m-aminobenzenesulfonamide	-1.20	-1.20±0.22	-0.10
18	trifluoromethoxyhenzene	3.17	3.17±0.59	2.28
19	phenyl-trifluoromethyl sulfone	2.68	2.71±0.69	1.86
20	o-phenylenethiourca	1.66	1.66±0.26	0.71
21	p-(fluorosulfonyl)toluene	2.74	2.74±0.28	1.40
22	2-(g-pyridyl)ethy1amine	-0.01	-0.03±0.20	0.88
23	p-trifluoroacetamide bromobenzene	3.34	3.42±0.66	2.51
24	p-(fluorosulfonyl)phenoxyacetic acid	1.84	1.82±0.39	0.90
25	p-aminophenylacetate	-0.16	-0.16±0.22	0.92
26	N-phenylglycine	0.62	0.62±0.24	-0.35
27	8-sulfonamidoquinoline	0.36	0.36±0.22	1.19
28	8-trifluoromethylquinoline	2.50	2.50±0.26	3.32
29	N-methyl-4-quinolone	0.44	0.44±0.26	1.28
30	p-hydroxybenzoic acid butyl ester	3.57	3.46±0.22	2.70
31	4,7-phenanthroline	2.05	2.05±0.22	2.85
32	carbazol	3.72	3.72±0.25	2.69
33	(4-isothiocyanophenyl) phenyl sulfoxide	4.40	4.40±0.37	3.53
34	1-(3,4-dichlorophenyl)-3-phenylurea	4.70	4.76±0.35	3.67
35	3,6-diaminoacridine	1.10	1.10±0.35	1.92
36	4,4'-diisothiocyanatebiphenyl	5.50	5.42±0.28	6.35
37	benzil	3.38	3.38±0.30	2.37
38	N-(3-(trifluoromethyl)phenyl)anthranilic acid	5.62	5.62±0.48	4.69
39	4-cyclohexylphenoxyacetic acid	3.79	3.86±0.25	2.99
40	atenolol	0.16	0.10±0.25	1.04
41	bisphenol	3.32	3.43±0.23	4.34
42	diazepam	2.66	2.96±0.46	3.59
43	labetalol	2.51	2.87±0.40	3.42

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Table 4:

In this table the experimental data and results of calculations by KLOGP have been taken from Klopman, G.; J. Chem. Inf. Comput. Sci. 1994, 34, 752. This reference lists 71 structures which have proven difficult to calculate using the LOGK method. The following table compares the results of correlations for all of these structures:

Method	Intercept	Slope	No of data points	Correlation Coefficient	Standard Deviation
ACD/LogP	0.104±0.053	0.927±0.019	71	0.9849	0.350
KLOGP	-0.038±0.150	0.898±0.054	71	0.8923	0.913

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This page was last updated 07 November 2007