Crystal structure search
Polymorphism phenomenon is often observed for organic molecules. CONFLEX can search possible crystal structures of an organic molecule including not only packing polymorphs but also conformational polymorphs using the original algorithm [Ishii, H., Obata, S., Niitsu, N. et al. Sci. Rep. 10, 2524 (2020).].
[Crystal structure search from a structural formula]
Cambridge Crystallographic Data Center (CCDC) carries out blind tests of crystal structure prediction (CSP) on a regular basis [P.M. Lommerse, et al, Acta Cryst. B56, 697-714, 2000]. Here, for explaining the prediction of crystal structures by CONFLEX program, we employ 5-Cyano-3-hydroxythiophene (II) (refer to the below figure) which was used in CSP blind test.
First, we create a molecular file for II by using PerkinElmer ChemDraw software. Please see a manual of ChemDraw for getting how to use that.
The molecular file of II is saved as “II.mol” using MDL-MOL file format.
II.mol file
II.mol
ChemDraw08301910352D
8 8 0 0 0 0 0 0 0 0999 V2000
0.2633 0.3011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0883 0.3011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0083 -0.4836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6758 -0.9685 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
1.3432 -0.4836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5732 0.9685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7763 -0.7385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5732 -0.9520 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 0
3 4 1 0
4 5 1 0
5 2 2 0
2 6 1 0
3 7 1 0
7 8 3 0
M END
Next, we optimize the single molecular structure of II.
[Execution by Interface]
Open the II.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed. The structure optimization of II will start.
[Execution by command line]
Store the II.mol in a folder, and execute below command. The structure optimization of II will start. When you do not prepare an ini file, CONFLEX performs the optimization of input structure in default setting.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par IIenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
Next, we perform a conformation search of II.
[Execution by Interface]
Open the II-F.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and select [Conformation Search] in the pull-down menu of [Calculation Type:] on the calculation setting dialog displayed.
Edit value of [Search Limit:] to 10.0. This parameter is used as a criteria for selecting initial structure in the conformation search. When the calculation settings are complete, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the II-F.ini file.
II-F.ini file
CONFLEX SEL=10.0
[CONFLEX] means to execute a conformation search.
[SEL=10.0] means that a search limit, which is used as a criteria for selecting initial structure in the conformation search, sets to 10.0 kcal/mol.
Store the two files of II-F.mol and II-F.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par II-Fenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
After the conformation search, we can get two conformers of II. Here, we employ the second most stable conformer for a calculation of crystal structure search.
We extract structure data of the selected conformer from “II-F.sdf” file and save as “II-c2.mol”. The II-F.sdf file is in the folder contained the II-F.mol file. When you executed the conformation search by using Interface, the file name may be II-F_conv.sdf.
II-c2.mol file
II.mol
CONFLEX 19083010373D 1 1.00000 4.54816 1
CS ,E = 4.548, G = 0.974E-10, P = 48.3970, M( 0), IFN =00000002-00000001
11 11 0 0 999 V2000
1.1214 -0.0104 0.0000 C 0 0 0 0 0
0.7822 -1.3858 0.0000 C 0 0 0 0 0
-0.0000 0.7946 -0.0000 C 0 0 0 0 0
-1.4433 -0.1296 -0.0000 S 0 0 0 0 0
-0.5732 -1.6069 0.0000 C 0 0 0 0 0
1.6924 -2.3749 0.0000 O 0 0 0 0 0
0.0137 2.2245 -0.0000 C 0 0 0 0 0
0.0454 3.3854 -0.0000 N 0 0 0 0 0
2.1374 0.3665 0.0000 H 0 0 0 0 0
-1.1076 -2.5464 0.0000 H 0 0 0 0 0
1.2623 -3.2477 0.0000 H 0 0 0 0 0
1 2 1 0 0
1 3 2 0 0
3 4 1 0 0
4 5 1 0 0
5 2 2 0 0
2 6 1 0 0
3 7 1 0 0
7 8 3 0 0
1 9 1 0 0
5 10 1 0 0
6 11 1 0 0
M END
Next, we perform a crystal structure search of II.
[Execution by Interface]
Open the II-c2.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed. A detail setting dialog will be displayed.
In order to perform the crystal structure search, in [General Settings] dialog on the detail setting dialog, select [Crystal Search] in the pull-down menu of [Calculation Type:].
Method of crystal structure optimization is [ALL] in default setting. You can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:] in [Crystal Calculation] dialog.
In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on.
Next, we set parameters for the crystal structure search by [Crystal Search] dialog.
First, to select space groups using in the search, click of [Search Space Group:].
The dialog displayed is showing top 10 space groups in the space group frequency ranking which is provided by CCDC. Check the check boxes of all space groups, and click .
[Rotation Method:] and [Position Prediction Method:] set methods to determine initial molecular orientation and position, respectively. Here, both the methods set to [Random]. If you want to search in detail, each method should set to [Grid] and [Full], respectively.
[Trial Structures:] sets the number of trial structures that are created for the search. Here, the number of trial structures sets to 10000. If you use more large number, you can perform more accuracy search but a computational cost becomes high.
When the calculation settings are complete, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the II-c2.ini file.
II-c2.ini file
CRYSTAL_SEARCH CSP_SPGP=(P21/C,P-1,C2/C,P212121,P21,PBCA,PNA21,PNMA,CC,P1) CSP_ROT_MODE=RANDOM CSP_AUS_MODE=RANDOM CSP_MAX_CRYSTAL=10000 CRYSTAL_OPTIMIZATION=ALL
[CRYSTAL_SEARCH] means to execute a crystal structure search.
Space groups using in the search are defined by [CSP_SPGP=] keyword. Here, we use P21/c, P-1, C2/c, P212121, P21, Pbca, Pna21, Pnma, Cc, and P1 that are top 10 space groups in the space group frequency ranking which is provided by CCDC.
[CSP_ROT_MODE=] and [CSP_AUS_MODE=] set methods to determine initial molecular orientation and position, respectively. Here, both the methods set to [Random]. If you want to search in detail, each method should set to [Grid] and [Full], respectively.
[CSP_MAX_CRYSTAL=] sets the number of trial structures that are created for the search. Here, the number of trial structures sets to 10000. If you use more large number, you can perform more accuracy search but a computational cost becomes high.
Method of crystal structure optimization is defined by [CRYSTAL_OPTIMIZATION=] keyword and sets to “ALL”. The “ALL” optimization relaxes molecular geometry, position, and orientation and cell dimensions of the crystal.
Store the two files of II-c2.mol and II-c2.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par II-c2enter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
Calculation results
After the calculation of crystal structure search, you can get II-C2.csp file that describes results of the search calculation in detail.
In the part of [*** PREDICTED CRYSTAL STRUCTURES:] of the II-c2.csp file, computationally suggested polymorphs of II are shown in order of crystal energy.
Structure data of the polymorphs are stored in II-c2-PCS.cif file.
*** PREDICTED CRYSTAL STRUCTURES:
IDX CID E_RNK CRYST INTRA INTER VOL DES A B C ALPHA BETA GAMMA SPGP NCALMOL NCALATM DMAX NNEV
1 571 1 -15.7921 4.6942 -20.4864 607.6657 1.3663 9.5996 8.3419 10.7545 90.0000 135.1221 90.0000 P21/C 365 4015 20.00 0
39 5295 2 -15.6634 4.7074 -20.3708 306.9963 1.3522 11.0245 7.0951 4.3469 90.0000 115.4610 90.0000 P21 371 4081 20.00 0
89 150 3 -15.6476 4.6816 -20.3292 606.6216 1.3686 7.2689 8.3106 10.7652 90.0000 111.1225 90.0000 P21/C 375 4125 20.00 0
170 3622 4 -15.6125 4.7219 -20.3344 614.2783 1.3515 4.3718 19.8181 7.0899 90.0000 90.0000 90.0000 P212121 373 4103 20.00 0
183 3677 5 -15.6089 4.6925 -20.3014 612.8164 1.3548 7.6268 9.6305 8.3433 90.0000 90.0000 90.0000 P212121 355 3905 20.00 0
204 404 6 -15.5986 4.7162 -20.3147 614.9313 1.3501 4.3234 7.1069 20.0163 90.0000 89.0064 90.0000 P21/C 371 4081 20.00 0
221 51 7 -15.4618 4.7170 -20.1789 618.7977 1.3417 4.3746 7.0720 20.4156 90.0000 78.4425 90.0000 P21/C 374 4114 20.00 0
229 2134 8 -15.3029 4.7145 -20.0173 1222.4436 1.3583 14.5999 8.3633 10.4384 90.0000 73.5604 90.0000 C2/C 357 3927 20.00 0
236 215 9 -15.2948 4.7210 -20.0158 612.9536 1.3545 4.0230 8.3785 18.2131 90.0000 86.8178 90.0000 P21/C 358 3938 20.00 0
263 28 10 -15.2940 4.7263 -20.0203 612.5302 1.3554 8.3759 18.2972 8.8552 90.0000 26.8303 90.0000 P21/C 365 4015 20.00 0
Here, comparing the experimental structure (left figure) and the 1st structure (right figure), you can see that both the structures match well.
[Crystal structure search for a multi component system]
This section explains a crystal structure search of an asymmetric unit with multi component.
Here, we employ a co-crystal of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid which was used in CSP blind test.
First, molecular files of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid are made by using PerkinElmer ChemDraw software. Please see a manual of ChemDraw for getting how to use that.
The molecular file of 2-amino-4-methylpyrimidine is saved as “AMP.mol” using MDL-MOL file format.
AMP.mol file
AMP.mol
ChemDraw09022015212D
8 8 0 0 0 0 0 0 0 0999 V2000
-0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0000 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4289 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4289 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
2 7 1 0
4 8 1 0
M END
The molecular file of 2-methylbenzoic acid is saved as “MBA.mol” using MDL-MOL file format.
MBA.mol file
MBA.mol
ChemDraw09022015232D
10 10 0 0 0 0 0 0 0 0999 V2000
-1.0717 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0717 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3572 -1.4438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3572 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3572 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3572 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0717 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3572 1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0717 1.4438 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3572 1.4438 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8 9 2 0
8 10 1 0
6 8 1 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
5 7 1 0
M STY 1 1 SUP
M SLB 1 1 1
M SAL 1 3 8 9 10
M SBL 1 1 3
M SMT 1 COOH
M SBV 1 3 0.0000 -0.8250
M END
Next, structure optimizations of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid are performed.
[Execution by Interface]
Open the AMP.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed. The structure optimization of 2-amino-4-methylpyrimidine will start.
Next, open the MBA.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed. The structure optimization of 2-methylbenzoic acid will start.
[Execution by command line]
Store the AMP.mol and MBA.mol in a folder, and execute below commands. The structure optimizations will start.
When you do not prepare ini files, CONFLEX performs the optimizations of input structures in default setting.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par AMPenterC:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par MBAenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
The 2-methylbenzoic acid molecule has some conformations. Therefore, we should perform a conformation search of 2-methylbenzoic acid.
[Execution by Interface]
Open the MBA-F.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and select [Conformation Search] in the pull-down menu of [Calculation Type:] on the calculation setting dialog displayed.
Edit value of [Search Limit:] to 10.0. This parameter is used as a criteria for selecting initial structure in the conformation search.
When the calculation settings are complete, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the MBA-F.ini file.
MBA-F.ini file
CONFLEX SEL=10.0
[CONFLEX] means to execute a conformation search.
[SEL=10.0] means that a search limit, which is used as a criteria for selecting initial structure in the conformation search, set to 10.0 kcal/mol.
Store the two files of MBA-F.mol and MBA-F.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par MBA-Fenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
After the conformation search, we can get seven conformers of 2-methylbenzoic acid.
Here, we employ the most stable conformer for a next calculation. Structure data of the selected conformer is extracted from “MBA-F.sdf” file and saved as “MBA-c1.mol”. The MBA-F.sdf file is in the folder contained the MBA-F.mol file.
MBA-c1.mol file
MBA.mol
CONFLEX 20090215293D 1 1.00000 16.90241 3
CS ,E = 16.902, G = 0.213E-06, P = 89.7913, M( 0), IFN =00000001-00000003
18 18 0 0 999 V2000
-1.3006 0.8083 0.0000 C 0 0 0 0 0
-2.4209 -0.0240 0.0000 C 0 0 0 0 0
-2.2574 -1.4041 0.0000 C 0 0 0 0 0
-0.9754 -1.9534 -0.0000 C 0 0 0 0 0
0.1671 -1.1315 -0.0000 C 0 0 0 0 0
-0.0000 0.2708 0.0000 C 0 0 0 0 0
1.5196 -1.7909 -0.0000 C 0 0 0 0 0
1.1760 1.1942 0.0000 C 0 0 0 0 0
2.3544 0.8930 0.0000 O 0 0 0 0 0
0.8165 2.4930 -0.0000 O 0 0 0 0 0
-1.4568 1.8849 0.0000 H 0 0 0 0 0
-3.4187 0.4075 0.0000 H 0 0 0 0 0
-3.1277 -2.0558 0.0000 H 0 0 0 0 0
-0.8717 -3.0372 -0.0000 H 0 0 0 0 0
2.0811 -1.5139 0.8977 H 0 0 0 0 0
1.4333 -2.8831 -0.0000 H 0 0 0 0 0
2.0811 -1.5139 -0.8977 H 0 0 0 0 0
1.6744 2.9669 -0.0000 H 0 0 0 0 0
8 9 2 0 0
8 10 1 0 0
6 8 1 0 0
1 2 2 0 0
2 3 1 0 0
3 4 2 0 0
4 5 1 0 0
5 6 2 0 0
6 1 1 0 0
5 7 1 0 0
1 11 1 0 0
2 12 1 0 0
3 13 1 0 0
4 14 1 0 0
7 15 1 0 0
7 16 1 0 0
7 17 1 0 0
10 18 1 0 0
M END
Next, by using the AMP-F.mol and MBA-c1.mol files, a structure file for a molecular complex of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid is made, and it saves as “XV.mol”.
The XV.mol file makes by adding data of atomic coordinates and bond information in the MBA-c1.mol to the AMP-F.mol file. The 4th line in the XV.mol, “33 33”, shows the number of atoms and bonds in the complex, respectively.
The bond information, “ 1 2 2 0 0”, means that the atoms 1 and 2 are bonded by a double bond. Therefore, when you add the bond information of 2-methylbenzoic acid to the AMP-F.mol file, you should change the original serial number of atoms in the bond information. For an example, change from “ 8 9 2 0 0” to “ 23 24 2 0 0”.
XV.mol file
XV.mol
33 33 0 0 999 V2000
1.2096 -1.0822 -0.0000 C 0 0 0 0 0
1.1638 0.2958 0.0000 C 0 0 0 0 0
-0.0000 0.9788 0.0000 N 0 0 0 0 0
-1.1295 0.2628 0.0000 C 0 0 0 0 0
-1.1861 -1.0719 0.0000 N 0 0 0 0 0
-0.0075 -1.7194 -0.0000 C 0 0 0 0 0
2.4311 1.0955 -0.0000 C 0 0 0 0 0
-2.3091 0.9449 -0.0000 N 0 0 0 0 0
2.1397 -1.6334 -0.0000 H 0 0 0 0 0
-0.0748 -2.8030 -0.0000 H 0 0 0 0 0
2.2152 2.1688 0.0000 H 0 0 0 0 0
3.0226 0.8673 0.8921 H 0 0 0 0 0
3.0226 0.8673 -0.8921 H 0 0 0 0 0
-3.1598 0.4121 -0.0000 H 0 0 0 0 0
-2.2706 1.9481 -0.0000 H 0 0 0 0 0
-1.3006 0.8083 0.0000 C 0 0 0 0 0
-2.4209 -0.0240 0.0000 C 0 0 0 0 0
-2.2574 -1.4041 0.0000 C 0 0 0 0 0
-0.9754 -1.9534 -0.0000 C 0 0 0 0 0
0.1671 -1.1315 -0.0000 C 0 0 0 0 0
-0.0000 0.2708 0.0000 C 0 0 0 0 0
1.5196 -1.7909 -0.0000 C 0 0 0 0 0
1.1760 1.1942 0.0000 C 0 0 0 0 0
2.3544 0.8930 0.0000 O 0 0 0 0 0
0.8165 2.4930 -0.0000 O 0 0 0 0 0
-1.4568 1.8849 0.0000 H 0 0 0 0 0
-3.4187 0.4075 0.0000 H 0 0 0 0 0
-3.1277 -2.0558 0.0000 H 0 0 0 0 0
-0.8717 -3.0372 -0.0000 H 0 0 0 0 0
2.0811 -1.5139 0.8977 H 0 0 0 0 0
1.4333 -2.8831 -0.0000 H 0 0 0 0 0
2.0811 -1.5139 -0.8977 H 0 0 0 0 0
1.6744 2.9669 -0.0000 H 0 0 0 0 0
1 2 2 0 0
2 3 1 0 0
3 4 2 0 0
4 5 1 0 0
5 6 2 0 0
6 1 1 0 0
2 7 1 0 0
4 8 1 0 0
1 9 1 0 0
6 10 1 0 0
7 11 1 0 0
7 12 1 0 0
7 13 1 0 0
8 14 1 0 0
8 15 1 0 0
23 24 2 0 0
23 25 1 0 0
21 23 1 0 0
16 17 2 0 0
17 18 1 0 0
18 19 2 0 0
19 20 1 0 0
20 21 2 0 0
21 16 1 0 0
20 22 1 0 0
16 26 1 0 0
17 27 1 0 0
18 28 1 0 0
19 29 1 0 0
22 30 1 0 0
22 31 1 0 0
22 32 1 0 0
25 33 1 0 0
M END
Next, in order to determine possible molecular positions of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid in the molecular complex, a host-ligand configuration search is performed.
[Execution by Interface]
Open the XV.mol file by CONFLEX Interface. Both the molecules are clashed at the moment, but the molecular positions change according to a search algorithm.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed. A detail setting dialog will be displayed.
In order to perform the host-ligand configuration search, in [General Settings] dialog on the detail setting dialog, select [Host Ligand Search] in the pull-down menu of [Calculation Type:].
Settings of the host-ligand configuration search calculation are made in [Host Ligand Search] dialog.
Here, in order to rotate the 2-methylbenzoic acid molecule assigned as a ligand by a step of 45 degrees, each value of “Rotational number x, y, z” sets to 8, respectively.
When you complete the settings, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the XV.ini file.
XV.ini file
HLSEARCH HLSEARCH_LIGAND_ROT=(8,8,8)
[HLSEARCH] means to execute a host-ligand configuration search calculation.
[HLSEARCH_LIGAND_ROT=(8,8,8)] is for rotating the 2-methylbenzoic acid molecule assigned as a ligand by a step of 45 degrees around x, y, and z axes.
Store the two files of XV.mol and XV.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par XVenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
After the calculation, we can get 47 structures of the complex. Here, we employ the most stable structure for a crystal structure search. Structure data of the selected structure is extracted from “XV.sdf” file and saved as “XV-c1.mol”. The XV.sdf file is in the folder contained the XV.mol file.
XV-c1.mol file
XV.mol
CONFLEX 20090215503D 1 1.00000 -86.91814 17
NONE,E = -86.918, G = 0.249E-06, P = 20.9930, M( 0), IFN =00000001-00000017
33 33 0 0 999 V2000
-4.6389 1.0672 0.0877 C 0 0 0 0 0
-3.2840 1.2059 0.3058 C 0 0 0 0 0
-2.4142 0.1779 0.1589 N 0 0 0 0 0
-2.9370 -1.0122 -0.1834 C 0 0 0 0 0
-4.2342 -1.2388 -0.4067 N 0 0 0 0 0
-5.0617 -0.1892 -0.2687 C 0 0 0 0 0
-2.7235 2.5426 0.6933 C 0 0 0 0 0
-2.0889 -2.0671 -0.3182 N 0 0 0 0 0
-5.3328 1.8902 0.1921 H 0 0 0 0 0
-6.1102 -0.3980 -0.4587 H 0 0 0 0 0
-1.6892 2.4500 1.0374 H 0 0 0 0 0
-2.7441 3.2203 -0.1656 H 0 0 0 0 0
-3.3069 2.9800 1.5099 H 0 0 0 0 0
-2.4812 -2.9552 -0.5738 H 0 0 0 0 0
-1.0952 -1.9477 -0.1563 H 0 0 0 0 0
2.8428 1.4208 -0.4637 C 0 0 0 0 0
4.1800 1.8122 -0.5390 C 0 0 0 0 0
5.1849 0.9050 -0.2233 C 0 0 0 0 0
4.8550 -0.3923 0.1698 C 0 0 0 0 0
3.5126 -0.8046 0.2572 C 0 0 0 0 0
2.4937 0.1165 -0.0682 C 0 0 0 0 0
3.2239 -2.2160 0.6905 C 0 0 0 0 0
1.0518 -0.2696 -0.0173 C 0 0 0 0 0
0.6010 -1.3998 0.0329 O 0 0 0 0 0
0.2426 0.8063 -0.0191 O 0 0 0 0 0
2.0730 2.1442 -0.7236 H 0 0 0 0 0
4.4339 2.8231 -0.8471 H 0 0 0 0 0
6.2281 1.2054 -0.2833 H 0 0 0 0 0
5.6587 -1.0857 0.4113 H 0 0 0 0 0
2.7876 -2.7870 -0.1349 H 0 0 0 0 0
4.1382 -2.7349 0.9990 H 0 0 0 0 0
2.5491 -2.2242 1.5524 H 0 0 0 0 0
-0.6842 0.4546 0.0376 H 0 0 0 0 0
1 2 2 0 0
2 3 1 0 0
3 4 2 0 0
4 5 1 0 0
5 6 2 0 0
6 1 1 0 0
2 7 1 0 0
4 8 1 0 0
1 9 1 0 0
6 10 1 0 0
7 11 1 0 0
7 12 1 0 0
7 13 1 0 0
8 14 1 0 0
8 15 1 0 0
23 24 2 0 0
23 25 1 0 0
21 23 1 0 0
16 17 2 0 0
17 18 1 0 0
18 19 2 0 0
19 20 1 0 0
20 21 2 0 0
21 16 1 0 0
20 22 1 0 0
16 26 1 0 0
17 27 1 0 0
18 28 1 0 0
19 29 1 0 0
22 30 1 0 0
22 31 1 0 0
22 32 1 0 0
25 33 1 0 0
M END
Finally, we perform the crystal structure search.
[Execution by Interface]
Open the XV-c1.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed. A detail setting dialog will be displayed.
In order to perform the crystal structure search, in [General Settings] dialog on the detail setting dialog, select [Crystal Search] in the pull-down menu of [Calculation Type:].
Method of crystal structure optimization is [ALL] in default setting. You can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:] in [Crystal Calculation] dialog.
In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on.
Next, we make settings for the crystal structure search by [Crystal Search] dialog.
In order to use space group of P21/c, edit the [Search Space Group:] from “P21/C,P212121” to “P21/C”.
When the calculation settings are complete, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the XV-c1.ini file.
XV-c1.ini file
CRYSTAL_SEARCH CSP_SPGP=(P21/C)
[CRYSTAL_SEARCH] means to execute a crystal structure search.
Space groups using in the crystal structure search are defined by “CSP_SPGP=” keyword. Here, “CSP_SPGP=(P21/C)” sets, that is, the P21/c is applied to the search.
Store the two files of XV-c1.mol and XV-c1.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par XV-c1enter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
Calculation results
After the calculation, you can get XV-c1.csp file that describes results of the search calculation in detail.
In the part of [*** PREDICTED CRYSTAL STRUCTURES:] of the XV-c1.csp file, computationally suggested polymorphs of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid co-crystal are shown in order of crystal energy.
Structure data of the polymorphs are stored in XV-c1-PCS.cif file.
*** PREDICTED CRYSTAL STRUCTURES:
IDX CID E_RNK CRYST INTRA INTER VOL DES A B C ALPHA BETA GAMMA SPGP NCALMOL NCALATM DMAX NNEV
10 166 1 -112.2561 -73.1657 -39.0905 1384.6750 1.1758 6.3597 14.7215 17.2181 90.0000 120.8001 90.0000 P21/C 426 7035 20.00 0
15 2275 2 -112.2287 -73.4042 -38.8245 1407.5982 1.1567 14.6059 11.7504 9.5465 90.0000 59.2174 90.0000 P21/C 412 6810 20.00 0
16 207 3 -112.1190 -73.0217 -39.0973 1373.5185 1.1854 12.8837 14.8932 13.7315 90.0000 148.5805 90.0000 P21/C 421 6951 20.00 0
17 1026 4 -112.0257 -72.0386 -39.9871 1368.6700 1.1895 8.9646 9.9375 15.9967 90.0000 106.1736 90.0000 P21/C 431 7128 20.00 0
24 93 5 -111.9827 -73.1843 -38.7984 1399.2561 1.1635 6.4118 15.4366 15.2107 90.0000 111.6533 90.0000 P21/C 424 6996 20.00 0
25 2294 6 -111.8335 -73.1270 -38.7065 1409.7873 1.1549 13.5655 12.0776 8.6539 90.0000 96.1068 90.0000 P21/C 421 6948 20.00 0
27 488 7 -111.7751 -73.3963 -38.3788 1415.1006 1.1505 13.0894 10.0679 11.9525 90.0000 116.0510 90.0000 P21/C 430 7092 20.00 0
29 156 8 -111.7587 -73.2931 -38.4656 1403.7919 1.1598 15.1088 11.1575 8.6903 90.0000 106.6192 90.0000 P21/C 420 6936 20.00 0
32 308 9 -111.7046 -72.2275 -39.4771 1399.2931 1.1635 7.1345 12.0828 17.0823 90.0000 71.8502 90.0000 P21/C 426 7035 20.00 0
33 2528 10 -111.5790 -72.6694 -38.9096 1366.5010 1.1914 7.8968 23.9564 8.1596 90.0000 117.7171 90.0000 P21/C 431 7125 20.00 0
Here, comparing the experimental structure (left figure) and the 3rd structure (right figure), you can see that both the structures match well.
[Crystal structure search using PXRD data]
We explain how to apply CONFLEX to a crystal structure determination from powder X-ray diffraction (PXRD) data. Here, we use the crystal structure of pamonic acid that was reported by Haynes et al [D. A. Haynes et al., Acta Cryst. 2006, E62, o1170.].
First, we create a molecular file for pamonic acid by using PerkinElmer ChemDraw software. Please see a manual of ChemDraw for getting how to use that.
The molecular file of pamonic acid is saved as “pamonic-acid.mol” using MDL-MOL file format.
pamonic-acid.mol file
pamoic-acid.mol
ChemDraw10031813162D
29 32 0 0 0 0 0 0 0 0999 V2000
-2.1471 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4326 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4326 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1471 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8616 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8616 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5761 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5761 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8616 -2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1471 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4294 -1.0931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7182 -0.4538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4326 -0.8662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1471 -0.4538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1471 0.3712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4326 0.7837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7182 0.3712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4326 1.6087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7182 2.0212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0037 1.6087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0037 0.7837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4326 -1.6912 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.8616 -0.8663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5761 -0.4538 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.8616 -1.6913 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.1471 1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8616 2.0625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.4326 2.0625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7182 0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
6 7 1 0
7 8 2 0
8 9 1 0
9 10 2 0
10 1 1 0
2 11 1 0
11 12 1 0
12 13 1 0
13 14 2 0
14 15 1 0
15 16 2 0
16 17 1 0
17 12 2 0
16 18 1 0
18 19 2 0
19 20 1 0
20 21 2 0
21 17 1 0
13 22 1 0
14 23 1 0
23 24 2 0
23 25 1 0
4 26 1 0
26 27 2 0
26 28 1 0
3 29 1 0
M END
Next, we optimize the single molecular structure of pamonic acid.
[Execution by Interface]
Open the pamonic-acid.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed. The structure optimization of II will start.
[Execution by command line]
Store the pamonic-acid.mol in a folder, and execute below command. The structure optimization of pamonic acid will start. When you do not prepare an ini file, CONFLEX performs the optimization of input structure in default setting.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par pamonic-acidenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
Next, we perform a conformation search of pamonic acid.
[Execution by Interface]
Open the pamonic-acid-F.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and select [Conformation Search] in the pull-down menu of [Calculation Type:] on the calculation setting dialog displayed.
Edit value of [Search Limit:] to 30.0. This parameter is used as a criteria for selecting initial structure in the conformation search.
When the calculation settings are complete, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the pamonic-acid-F.ini file.
pamonic-acid-F.ini file
CONFLEX SEL=30.0
[CONFLEX] means to execute a conformation search.
[SEL=30.0] means that a search limit, which is used as a criteria for selecting initial structure in the conformation search, sets to 30.0 kcal/mol.
Store the two files of pamonic-acid-F.mol and pamonic-acid-F.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par pamonic-acid-Fenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
After the conformation search, we can get 118 conformers of pamonic acid. Here, we employ the 3rd most stable conformer for a calculation of crystal structure search. Structure data of the selected conformer is extracted from “pamonic-acid-F.sdf” file and saved as “pamonic-acid-c3.mol”. The pamonic-acid-F.sdf file is in the folder contained pamonic-acid-F.mol file.
pamonic-acid-c3.mol file
pamoic-acid.mol
CONFLEX 18102311013D 1 1.00000 57.28062 16
C2 ,E = 57.281, G = 0.144E-07, P = 4.5793, M( 0), IFN =00000003-00000016
45 48 0 0 999 V2000
-1.3167 2.0796 -0.8640 C 0 0 0 0 0
-0.1166 1.2932 -0.8876 C 0 0 0 0 0
1.0079 1.7433 -0.1606 C 0 0 0 0 0
0.9563 2.9081 0.6175 C 0 0 0 0 0
-0.2214 3.6554 0.6552 C 0 0 0 0 0
-1.3466 3.2641 -0.0791 C 0 0 0 0 0
-2.5025 4.0623 -0.0282 C 0 0 0 0 0
-3.6457 3.7218 -0.7444 C 0 0 0 0 0
-3.6457 2.5743 -1.5200 C 0 0 0 0 0
-2.5025 1.7708 -1.5777 C 0 0 0 0 0
-0.0000 0.0000 -1.6979 C 0 0 0 0 0
0.1166 -1.2932 -0.8876 C 0 0 0 0 0
-1.0079 -1.7433 -0.1606 C 0 0 0 0 0
-0.9563 -2.9081 0.6175 C 0 0 0 0 0
0.2214 -3.6554 0.6552 C 0 0 0 0 0
1.3466 -3.2641 -0.0791 C 0 0 0 0 0
1.3167 -2.0796 -0.8640 C 0 0 0 0 0
2.5025 -4.0623 -0.0282 C 0 0 0 0 0
3.6457 -3.7218 -0.7444 C 0 0 0 0 0
3.6457 -2.5743 -1.5200 C 0 0 0 0 0
2.5025 -1.7708 -1.5777 C 0 0 0 0 0
-2.1663 -1.0131 -0.2688 O 0 0 0 0 0
-2.1487 -3.3401 1.3832 C 0 0 0 0 0
-3.2090 -2.7368 1.4055 O 0 0 0 0 0
-1.9746 -4.4795 2.0733 O 0 0 0 0 0
2.1487 3.3401 1.3832 C 0 0 0 0 0
3.2090 2.7368 1.4055 O 0 0 0 0 0
1.9746 4.4795 2.0733 O 0 0 0 0 0
2.1663 1.0131 -0.2688 O 0 0 0 0 0
-0.2634 4.5620 1.2557 H 0 0 0 0 0
-2.5220 4.9676 0.5759 H 0 0 0 0 0
-4.5311 4.3490 -0.6932 H 0 0 0 0 0
-4.5334 2.2918 -2.0797 H 0 0 0 0 0
-2.5709 0.8759 -2.1893 H 0 0 0 0 0
-0.8381 -0.1310 -2.3887 H 0 0 0 0 0
0.8381 0.1310 -2.3887 H 0 0 0 0 0
0.2634 -4.5620 1.2557 H 0 0 0 0 0
2.5220 -4.9676 0.5759 H 0 0 0 0 0
4.5311 -4.3490 -0.6932 H 0 0 0 0 0
4.5334 -2.2918 -2.0797 H 0 0 0 0 0
2.5709 -0.8759 -2.1893 H 0 0 0 0 0
-2.8489 -1.3798 0.3330 H 0 0 0 0 0
-2.8335 -4.6307 2.5208 H 0 0 0 0 0
2.8335 4.6307 2.5208 H 0 0 0 0 0
2.8489 1.3798 0.3330 H 0 0 0 0 0
1 2 2 0 0
2 3 1 0 0
3 4 2 0 0
4 5 1 0 0
5 6 2 0 0
6 1 1 0 0
6 7 1 0 0
7 8 2 0 0
8 9 1 0 0
9 10 2 0 0
10 1 1 0 0
2 11 1 0 0
11 12 1 0 0
12 13 1 0 0
13 14 2 0 0
14 15 1 0 0
15 16 2 0 0
16 17 1 0 0
17 12 2 0 0
16 18 1 0 0
18 19 2 0 0
19 20 1 0 0
20 21 2 0 0
21 17 1 0 0
13 22 1 0 0
14 23 1 0 0
23 24 2 0 0
23 25 1 0 0
4 26 1 0 0
26 27 2 0 0
26 28 1 0 0
3 29 1 0 0
5 30 1 0 0
7 31 1 0 0
8 32 1 0 0
9 33 1 0 0
10 34 1 0 0
11 35 1 0 0
11 36 1 0 0
15 37 1 0 0
18 38 1 0 0
19 39 1 0 0
20 40 1 0 0
21 41 1 0 0
22 42 1 0 0
25 43 1 0 0
28 44 1 0 0
29 45 1 0 0
M END
Next, we ready a diffraction data file for CONFLEX program from a raw data obtained by PXRD experiment. Haynes et al. provide the raw data of pamonic acid crystal. Here, we use “cv6632Isup2.rtv” for making a reference diffraction data, pamonic-acid-c3.xrd, shown below.
pamonic-acid-c3.xrd file
Co 8.010 79.990 0.01 7199 8.010 0.000000 8.020 0.000000 8.030 0.000000 8.040 91.252560 8.050 9.827270 8.060 0.000000 (中略) 79.970 43.877350 79.980 17.738100 79.990 42.620530
First row means a type of X-ray source, and second row shows a range and step of 2 theta and total the number of diffraction data. At the first row you can also set wave length of X-ray source, not characters of atomic name.
The diffraction data is shown on the third and subsequent rows. The intensity data at each 2-theta point are generated by subtracting “_pd_proc_intensity_bkg_calc” value from “_pd_meas_counts_total” value. If the intensity has negative value due to the subtraction, we set to “zero” as the intensity at the point.
You can find the pamonic-acid-c3.xrd in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\powder\pamonic-acid-c3.xrd).
Do not include blank lines in the xrd file, and remove back ground from the raw data for using in CONFLEX.
Finally, we perform a crystal structure search of pamonic acid
[Execution by Interface]
Open the pamonic-acid-c3.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed. A detail setting dialog will be displayed.
In order to perform the crystal structure search, in [General Settings] dialog on the detail setting dialog, select [Crystal Search] in the pull-down menu of [Calculation Type:].
Method of crystal structure optimization is [ALL] in default setting. You can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:] in [Crystal Calculation] dialog.
In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on.
Next, we set parameters for the crystal structure search by [Crystal Search] dialog.
In order to use space group of P21/c, edit the [Search Space Group:] from “P21/C,P212121” to “P21/C”.
[Rotation Method:] and [Position Prediction Method:] set methods to determine initial molecular orientation and position, respectively. Here, both the methods set to [Random].
[Trial Structures:] sets the number of trial structures that are created for the search. Here, the number of trial structures sets to 1000.
Next, we change the pull-down menu of “Crystal Search by:” from [Energy] to [Powder Pattern]. In this setting, the found crystal structures from the crystal structure search are estimated according to similarity of PXRD patterns between the found structures and experimental structure.
Finally, click of [PXRD File:], and select “pamonic-acid-c3.xrd” prepared above.
When the calculation settings are complete, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the pamonic-acid-c3.ini.
pamonic-acid-c3.ini file
CRYSTAL_SEARCH CSP_SEARCH=POWDER_PATTERN CSP_SPGP=(P21/C) CSP_AUS_MODE=RANDOM CSP_ROT_MODE=RANDOM CSP_MAX_CRYSTAL=1000 CRYSTAL_OPTIMIZATION=ALL
[CRYSTAL_SEARCH] means to execute a crystal structure search.
[CSP_SEARCH=POWDER_PATTERN] means that the found crystal structures from the crystal structure search are estimated according to similarity of PXRD patterns between the found structures and experimental structure.
[CSP_SPGP=P21/C] means to use space group of P21/c in the search.
[CSP_ROT_MODE=RANDOM] and [CSP_AUS_MODE=RANDOM] means to randomly determine initial molecular orientation and position.
[CSP_MAX_CRYSTAL=1000] means to set 1000 of the number of trial crystal structures.
[CRYSTAL_OPTIMIZATION=ALL] means to set “ALL” as a crystal structure optimization.
Store the three files of pamonic-acid-c3.mol, pamonic-acid-c3.ini, and pamonic-acid-c3.xrd in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par pamonic-acid-c3enter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
Calculation results
After the calculation, you can get pamonic-acid-c3.csp file that describes results of the search calculation in detail.
In the search using the reference diffraction data, in the part of [*** PREDICTED CRYSTAL STRUCTURES:] of the pamonic-acid.csp file, the found crystal structures from the search are arranged according to similarity of PXRD patterns between the found structures and experimental structure. The 1st structure shows the most similar diffraction pattern to the reference one. Structure data of the found crystals are stored in pamonic-acid-c3-PCS.cif file.
Gelder's method (R. de Gelder et al, J Comput Chem 22: 273–289, 2001.) is employed for the PXRD similarity calculation.
*** PREDICTED CRYSTAL STRUCTURES:
IDX CID E_RNK R_RNK PXRD_SIM CRYST INTRA INTER VOL DES A B C ALPHA BETA GAMMA SPGP NCALMOL NCALATM DMAX NNEV
1 882 1 1 0.9056 12.3774 59.3730 -46.9957 1829.5937 1.4089 20.3676 4.9453 19.2844 90.0000 109.6233 90.0000 P21/C 225 10125 20.00 0
2 662 260 2 0.8349 26.0620 65.8365 -39.7745 1834.4689 1.4052 13.7876 7.0968 28.9328 90.0000 139.6100 90.0000 P21/C 210 9450 20.00 0
4 232 76 3 0.8235 21.4836 61.1121 -39.6285 1929.2047 1.3362 12.0076 12.5142 16.0878 90.0000 52.9432 90.0000 P21/C 205 9225 20.00 0
8 6 3 4 0.8219 14.2830 58.8049 -44.5220 1897.8000 1.3583 10.1471 4.8134 39.0029 90.0000 85.0212 90.0000 P21/C 202 9090 20.00 0
9 60 383 5 0.8177 28.4589 58.0370 -29.5781 1981.9578 1.3006 4.7838 11.1176 37.2683 90.0000 90.6615 90.0000 P21/C 202 9090 20.00 0
10 38 175 6 0.8137 24.3246 58.3375 -34.0128 1917.4130 1.3444 4.9060 15.6069 25.2169 90.0000 83.2541 90.0000 P21/C 202 9090 20.00 0
19 5 45 7 0.8122 20.3188 58.3402 -38.0214 1945.9817 1.3247 4.8345 10.1697 39.5911 90.0000 88.6467 90.0000 P21/C 204 9180 20.00 0
21 56 72 8 0.8115 21.4423 59.5779 -38.1356 1926.0086 1.3384 8.7084 12.1206 18.2473 90.0000 90.2492 90.0000 P21/C 206 9270 20.00 0
22 422 404 9 0.8061 28.9872 58.8269 -29.8397 2013.9816 1.2799 8.1416 13.0775 19.6888 90.0000 73.8900 90.0000 P21/C 197 8865 20.00 0
24 541 460 10 0.8050 30.6621 59.6480 -28.9860 1940.5521 1.3284 7.5235 9.2889 27.9119 90.0000 84.1753 90.0000 P21/C 200 9000 20.00 0
Here, comparing the diffraction patterns of the 1st structure (red) and the experimental one (white), you can see that both the patterns match well. Therefore, by using the 1st structure, it is expected that a structure refinement by Rietveld analysis will be easily completed, compared with a case of that without supports of CONFLEX.
The experimental structure (left figure) and the 1st structure (right figure) are shown below. You can see that both the structures match well.
[Output files]
After the calculation of crystal structure search, below files are outputted.
| File type | Explanation |
|---|---|
| (Input file name).csp | Detail information on the crystal structure search calculation is described to this file. |
| (Input file name).cpt | Information for restarting the calculation is described to this file. |
| (Input file name).ical | Powder X-ray diffraction data of crystal structures found by the search are described to this file. The crystal structure data corresponding to the PXRD data are described in the -PCS.cif file. |
| (Input file name)-PCS.cif | Crystal structures found by the search are described to this file in order of crystal energy (or similarity of PXRD pattern). |
| (Input file name)-FCS.cif | When optimization of a trial finished in the search process, the optimized structure is outputted to this file. You can see the optimized structure before the search calculation doesn't finish. |
In the part of [*** PREDICTED CRYSTAL STRUCTURES:] of csp file, computationally suggested polymorphs are shown in order of crystal energy.
*** PREDICTED CRYSTAL STRUCTURES:
IDX CID E_RNK CRYST INTRA INTER VOL DES A B C ALPHA BETA GAMMA SPGP NCALMOL NCALATM DMAX NNEV
1 571 1 -15.7921 4.6942 -20.4864 607.6657 1.3663 9.5996 8.3419 10.7545 90.0000 135.1221 90.0000 P21/C 365 4015 20.00 0
39 5295 2 -15.6634 4.7074 -20.3708 306.9963 1.3522 11.0245 7.0951 4.3469 90.0000 115.4610 90.0000 P21 371 4081 20.00 0
89 150 3 -15.6476 4.6816 -20.3292 606.6216 1.3686 7.2689 8.3106 10.7652 90.0000 111.1225 90.0000 P21/C 375 4125 20.00 0
170 3622 4 -15.6125 4.7219 -20.3344 614.2783 1.3515 4.3718 19.8181 7.0899 90.0000 90.0000 90.0000 P212121 373 4103 20.00 0
183 3677 5 -15.6089 4.6925 -20.3014 612.8164 1.3548 7.6268 9.6305 8.3433 90.0000 90.0000 90.0000 P212121 355 3905 20.00 0
204 404 6 -15.5986 4.7162 -20.3147 614.9313 1.3501 4.3234 7.1069 20.0163 90.0000 89.0064 90.0000 P21/C 371 4081 20.00 0
221 51 7 -15.4618 4.7170 -20.1789 618.7977 1.3417 4.3746 7.0720 20.4156 90.0000 78.4425 90.0000 P21/C 374 4114 20.00 0
229 2134 8 -15.3029 4.7145 -20.0173 1222.4436 1.3583 14.5999 8.3633 10.4384 90.0000 73.5604 90.0000 C2/C 357 3927 20.00 0
236 215 9 -15.2948 4.7210 -20.0158 612.9536 1.3545 4.0230 8.3785 18.2131 90.0000 86.8178 90.0000 P21/C 358 3938 20.00 0
263 28 10 -15.2940 4.7263 -20.0203 612.5302 1.3554 8.3759 18.2972 8.8552 90.0000 26.8303 90.0000 P21/C 365 4015 20.00 0
On the other hand, when you performed the crystal structure search using a reference diffraction data, they are shown in order of PXRD pattern similarity.
*** PREDICTED CRYSTAL STRUCTURES:
IDX CID E_RNK R_RNK PXRD_SIM CRYST INTRA INTER VOL DES A B C ALPHA BETA GAMMA SPGP NCALMOL NCALATM DMAX NNEV
1 882 1 1 0.9056 12.3774 59.3730 -46.9957 1829.5937 1.4089 20.3676 4.9453 19.2844 90.0000 109.6233 90.0000 P21/C 225 10125 20.00 0
2 662 260 2 0.8349 26.0620 65.8365 -39.7745 1834.4689 1.4052 13.7876 7.0968 28.9328 90.0000 139.6100 90.0000 P21/C 210 9450 20.00 0
4 232 76 3 0.8235 21.4836 61.1121 -39.6285 1929.2047 1.3362 12.0076 12.5142 16.0878 90.0000 52.9432 90.0000 P21/C 205 9225 20.00 0
8 6 3 4 0.8219 14.2830 58.8049 -44.5220 1897.8000 1.3583 10.1471 4.8134 39.0029 90.0000 85.0212 90.0000 P21/C 202 9090 20.00 0
9 60 383 5 0.8177 28.4589 58.0370 -29.5781 1981.9578 1.3006 4.7838 11.1176 37.2683 90.0000 90.6615 90.0000 P21/C 202 9090 20.00 0
10 38 175 6 0.8137 24.3246 58.3375 -34.0128 1917.4130 1.3444 4.9060 15.6069 25.2169 90.0000 83.2541 90.0000 P21/C 202 9090 20.00 0
19 5 45 7 0.8122 20.3188 58.3402 -38.0214 1945.9817 1.3247 4.8345 10.1697 39.5911 90.0000 88.6467 90.0000 P21/C 204 9180 20.00 0
21 56 72 8 0.8115 21.4423 59.5779 -38.1356 1926.0086 1.3384 8.7084 12.1206 18.2473 90.0000 90.2492 90.0000 P21/C 206 9270 20.00 0
22 422 404 9 0.8061 28.9872 58.8269 -29.8397 2013.9816 1.2799 8.1416 13.0775 19.6888 90.0000 73.8900 90.0000 P21/C 197 8865 20.00 0
24 541 460 10 0.8050 30.6621 59.6480 -28.9860 1940.5521 1.3284 7.5235 9.2889 27.9119 90.0000 84.1753 90.0000 P21/C 200 9000 20.00 0
Meaning of the items in the part of [*** PREDICTED CRYSTAL STRUCTURES:] are shown below.
| Item | Explanation |
|---|---|
| E_RNK | Crystal energy rank |
| R_RNK | PXRD pattern similarity rank |
| CRYST | Ecrystal |
| INTRA | Eintra |
| INTER | Elattice |
| VOL | Volume of unit cell |
| DES | Density of unit cell |
| A,B,C,ALPHA,BETA,GAMMA | Lattice constants |
| SPGP | Space group |
| NCALMOL | Total the number of molecules including in the calculation |
| NCALATM | Total the number of atoms including in the calculation |
| DMAX | Cut-off distance |
| NNEV | The number of negative eigenvalues |
* On the values of “NCALMOL, NCALATM, DMAX”, when you used different cut-off distance in the calculations for vdW and coulombic interactions, these values show about the calculation of vdW interactions.
The ical file has powder X-ray diffraction data of crystal structures found by the search. The -PCS.cif file has the crystal structure data corresponding to the PXRD data. The “data_” in the -PCS.cif file and “NAME:” in the ical file match in the same structure.
------------ SIMULATED POWDER PATTERNS ------------
CID: 882
NAME: R000001E000001C000882
X-RAY: CO (KA1)
WAVE: 1.78899600
2*THETA: 8.010 - 79.990 , 0.010 STEP
H K L 2*THETA INTENSITY d
(DEGREE) (ANGSTROME)
0 0 0 8.010 1.167 0.00000
0 0 0 8.020 1.174 0.00000
0 0 0 8.030 1.182 0.00000
0 0 0 8.040 1.190 0.00000
0 0 0 8.050 1.197 0.00000
0 0 0 8.060 1.205 0.00000
0 0 0 8.070 1.213 0.00000
0 0 0 8.080 1.221 0.00000
0 0 0 8.090 1.229 0.00000
0 0 0 8.100 1.237 0.00000
0 0 0 8.110 1.246 0.00000
0 0 0 8.120 1.254 0.00000
0 0 0 8.130 1.263 0.00000
0 0 0 8.140 1.271 0.00000
* snip *
[Visualization of search results]
The polymorphs found by the search are outputted to the -PCS.cif file. Open the -PCS.cif file by CONFLEX Interface, you can see them.
Select [Spectra_Analyzer] in the menu of [Applications] with the -PCS file open, you can also see PXRD pattern of each structure.
[Restart of crystal structure search]
[Execution by Interface]
Store molecular structure, ini, and cpt files that were used in the search calculation to an one folder. If you used a reference diffraction data, the xrd file is also needed.
Open the molecular structure file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed. A detail setting dialog will be displayed.
In order to restart the search calculation, check the check box of [Restart calculation] at the bottom of [Crystal Search] dialog in the detail setting dialog.
The other settings are automatically set from the ini file. When the setting for the restart is complete, click .
If you executed the search calculation by and manually added keywords, you should click and add same keywords on the restart. If the settings for the search calculation do not match, you may not be able to restart the calculation correctly.
[Execution by command line]
Store molecular structure, ini, and cpt files that were used in the search calculation to an one folder. If you used a reference diffraction data, the xrd file is also needed.
Next, change suffix of the cpt file to “rst”, and add “CSP_RESTART” keyword to the ini file. It is note that the you do not change the settings for the search calculation in the ini file. If the settings do not match, you may not be able to restart the calculation correctly.
When you are ready to restart, execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par (Input file name)enter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
[Unavailable space groups]
The following space group can not be used in crystal structure search.
P4MM, P4BM, P42CM, P42NM, I4MM, I4CM, P-42M, P-421M, I-42M, P4/MMM, P4/NBM, P4/MBM,
P4/NMM, P42/MCM, P42/NNM, P42/MNM, P42/NCM, I4MMM, I4/MCM, P3, P31, P32, R3, P-3,
R-3, P312, P321, P3112, P3121, P3212, P3221, R32, P3M1, P31M, P3C1, P31C, R3M, R3C,
P-31M, P-31C, P-3M1, P-3C1, R-3M, R-3C, P6, P61, P65, P62, P64, P63, P-6, P6/M,
P63/M, P622, P6122, P6522, P6222, P6422, P6322, P6MM, P6CC, P63CM, P63MC, P-6M2,
P-6C2, P-62M, P-62C, P6/MMM, P6/MCC, P63/MCM, P63/MMC, P23, F23, I23, P213, I213,
PM-3, PN-3, FM-3, FD-3, IM-3, PA-3, IA-3, P432, P4232, F432, F4132, I432, P4332,
P4132, I4132, P-43M, F-43M, I-43M, P-43N, F-43C, I-43D, PM-3M, PN-3N, PM-3N, PN-3M,
FM-3M, FM-3C, FD-3M, FD-3C, IM-3M, IA-3D