Crystal structure optimization
[Definition of energy]
Crystal structure can be built by periodically arranging a unit cell through translational symmetry (Figure 1). The unit cell is defined by an asymmetric unit, lattice constants, and space group symmetry. Therefore, in simulations, the crystal structure is constructed by using the asymmetric unit, the lattice constants, the space group symmetry, and the translational symmetry, and an energy of the crystal is defined by the equation 1 as the energy per the asymmetric unit.
Here, the Eintra is the sum of intramolecular interaction energies in the asymmetric unit, and the Elattice is defined by the equation 2. In the equation 2, the EAUinter is the sum of intermolecular interaction energies in the asymmetric unit. When the number of molecules in the asymmetric unit is one, the the EAUinter is zero. The second term in the equation 2 is the sum of intermolecular interaction energies between the molecule(s) in the asymmetric unit and molecules replicated by symmetry operations within a cut-off radius Rcrystal in the crystal. The Ewald method is applied to the calculation of electrostatic interactions.
The Ewald method calculates coulombic potential by using four terms of real space term, Φreal, reciprocal space term, Φrecip, self energy term, Φself, surface term, Φsurf. In the default setting, the Φsurf term is omitted. You can activate this term through a keyword. Please refer to the manual.
Here, the q is atomic charge, the α is Ewald convergence parameter, the |ri;S,J| is interatomic distance, the V is volume of the unit cell, the n′ is reciprocal lattice vector, and the r is position vector of atom in the unit cell. The Z is the number of the smallest building blocks (the asymmetric unit and replicated units created by applying symmetry operations to the asymmetric unit) in the unit cell. The parameter α and the cutoff distance in the reciprocal lattice space are automatically determined so that the interatomic interaction energy is smaller than 10-8 based on the cutoff distance in the real space. The values of these parameters can be specified by keywords. Please refer to the manual.
[Types of crystal structure optimization]
The program can perform three types of crystal structure optimization shown blow. These optimizations are performed under a specified space group symmetry.
- Molecular geometry optimization under crystal environment (MOL)
- The geometry, orientation, and translation of molecules in the crystal are relaxed. In the calculation, the lattice constants do not change.
- Optimization of crystal structure assuming rigid molecules (RIGID)
- The orientation and translation of molecules in the crystal and the lattice constants are relaxed. In the calculation, the molecular geometry does not change.
- Full crystal structure optimization (ALL)
- The all degree of freedoms for expressing the crystal structure, that is, the geometry, orientation and translation of molecules in the crystal and the lattice constants are relaxed.
[Execution of crystal structure optimization]
This section explains how to execute the crystal structure optimization. For the execution, as input data, atomic coordinates of asymmetric unit, lattice constants, and space group are necessary. Here, we use a crystal of hydroxy malonic acid which is one of malonic acid derivatives (Roelofsen, G.; Kanters, J.A.; Kroon, J.; Doesburg, H.M.; Koops, T. Acta Cryst.1978, B34, 2565.).
In case of using CMF file
We prepare tartronicacid.cmf shown below as input file. The tartronicacid.cmf has the crystal structure data of hydroxy malonic acid in CIFMIF (Combined CIF and MIF file, CIF：Crystallographic Information File, MIF： Molecular Information File) file format. You can find the tartronicacid.cmf in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\optimization\cmf_file\tartronicacid.cmf).
tartronicacid.cmf file
data_Tartronicacid _symmetry_cell_setting ORTHORHOMBIC _symmetry_space_group_name_H-M 'P212121 ' _ccdc_symmetry_space_group_name P212121 _symmetry_Int_Tables_number 19 loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 x,y,z 2 1/2+x,1/2-y,-z 3 -x,1/2+y,1/2-z 4 1/2-x,-y,1/2+z _cell_length_a 4.49400 _cell_length_b 8.81900 _cell_length_c 10.88200 _cell_angle_alpha 90.00000 _cell_angle_beta 90.00000 _cell_angle_gamma 90.00000 _cell_formula_units_Z 4 _cell_volume 431.28180 _exptl_crystal_density_diffrn 1.84821 loop_ _ccdc_atom_site_atom_id_number _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _ccdc_atom_site_symmetry _ccdc_atom_site_base 1 O1 O 1.12990 -0.13910 0.36040 1_555 1 2 O2 O 0.97510 0.09280 0.30700 1_555 2 3 O3 O 1.01480 0.11550 0.66290 1_555 3 4 O4 O 1.13030 -0.12820 0.62810 1_555 4 5 O5 O 0.57240 0.09790 0.48970 1_555 5 6 C1 C 0.97750 -0.01540 0.37600 1_555 6 7 C2 C 0.78810 -0.01520 0.49230 1_555 7 8 C3 C 0.99010 -0.00160 0.60420 1_555 8 9 H1 H 0.66800 -0.11200 0.49600 1_555 9 10 H2 H 0.60500 0.14900 0.45600 1_555 10 11 H3 H 1.23700 -0.13800 0.31000 1_555 11 12 H4 H 1.27100 -0.12000 0.68000 1_555 12 loop_ _atom_id _atom_type _atom_attach_nh _atom_attach_h _atom_charge 1 O 1 1 0 2 O 1 0 0 3 O 1 0 0 4 O 1 1 0 5 O 1 1 0 6 C 3 0 0 7 C 3 1 0 8 C 3 0 0 loop_ _bond_id_1 _bond_id_2 _bond_type_ccdc _bond_environment 1 6 S chain 1 11 S chain 2 6 D chain 3 8 D chain 4 8 S chain 4 12 S chain 5 7 S chain 5 10 S chain 6 7 S chain 7 8 S chain 7 9 S chain
[Execution by Interface]
Open the tartronicacid.cmf file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed.
Next, in [General Settings] dialog on the detail setting dialog, select [Molecular Crystal] in the pull-down menu of [Calculation Type:].
Settings of the crystal calculation are made in [Crystal calculation] dialog.
We can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:]. The default setting is "ALL". In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on.
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 tartronicacid.ini file.
tartronicacid.ini file
CRYSTAL MMFF94S
[CRYSTAL] means to execute a crystal calculation, and in the default, CONFLEX executes full crystal structure optimization (ALL) of the input structure. If you change the type of crystal structure optimization, add [CRYSTAL_OPTIMIZATION=] keyword, for example, [CRYSTAL_OPTIMIZATION=MOL].
[MMFF94s] means to use MMFF94s force field.
Store the two files of tartronicacid.cmf and tartronicacid.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par tartronicacidenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
In the case of using CIF file
In CIF file, bond information (bond order) are not included, although information which are necessary for the crystal calculation, that is, atomic coordinates of molecule in the asymmetric unit, lattice constants, and space group are described.
Here, we prepare input data, tartronicacid.cif, of crystal structure of hydroxy malonic acid based on CIF file format. The tartronicacid.cif is in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\optimization\cif_file\tartronicacid.cif).
tartronicacid.cif file
data_Tartronicacid _symmetry_cell_setting ORTHORHOMBIC _symmetry_space_group_name_H-M 'P212121 ' _symmetry_Int_Tables_number 19 loop_ _symmetry_equiv_pos_as_xyz x,y,z -x+1/2,-y,z+1/2 -x,y+1/2,-z+1/2 x+1/2,-y+1/2,-z _cell_length_a 4.49400 _cell_length_b 8.81900 _cell_length_c 10.88200 _cell_angle_alpha 90.00000 _cell_angle_beta 90.00000 _cell_angle_gamma 90.00000 _cell_formula_units_Z 4 _cell_volume 431.28180 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z O1 O 1.12990 -0.13910 0.36040 O2 O 0.97510 0.09280 0.30700 O3 O 1.01480 0.11550 0.66290 O4 O 1.13030 -0.12820 0.62810 O5 O 0.57240 0.09790 0.48970 C1 C 0.97750 -0.01540 0.37600 C2 C 0.78810 -0.01520 0.49230 C3 C 0.99010 -0.00160 0.60420 H1 H 0.66800 -0.11200 0.49600 H2 H 0.60500 0.14900 0.45600 H3 H 1.23700 -0.13800 0.31000 H4 H 1.27100 -0.12000 0.68000
[Execution by Interface]
Open tartronicacid.cif file by CONFLEX Interface
Select [CONFLEX] in Calculation menu, click in the calculation setting dialog displayed.
Next, in [General Settings] dialog on the detail setting dialog, select [Molecular Crystal] in the pull-down menu of [Calculation Type:].
Settings of the crystal calculation are made in [Crystal calculation] dialog.
We can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:]. The default setting is "ALL". In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on. When the calculation settings are complete, click .
A dialog with the keywords for the calculation settings is displayed.
Here, we will modify bond order.
CONFLEX Interface automatically creates [CIF_BOND=] keyword with 1 bond order for all atomic pairs that are considered to be bonded from the interatomic distance.
The bond order between atom 2 and atom 6 and between atom 3 and atom 8 in the hydroxy malonic acid molecule is 2 (refer to the below figure). Therefore, we have to change CIF_BOND=(2,6,1) and CIF_BOND=(3,8,1) to CIF_BOND=(2,6,2) and CIF_BOND=(3,8,2), respectively.
When you want to set a bond with n bond order to an atomic pair of atom i and atom j, CIF_BOND=(i,j,n) keyword should be described. The serial number of each atom are shown in the below figure.
When you complete the modifications, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the tartronicacid.ini file.
tartronicacid.ini file
CRYSTAL MMFF94S CIF_BOND=(1,6,1) CIF_BOND=(1,11,1) CIF_BOND=(2,6,2) CIF_BOND=(3,8,2) CIF_BOND=(4,8,1) CIF_BOND=(4,12,1) CIF_BOND=(5,7,1) CIF_BOND=(5,10,1) CIF_BOND=(6,7,1) CIF_BOND=(7,8,1) CIF_BOND=(7,9,1)
[CRYSTAL] means to execute a crystal calculation, and in the default, CONFLEX executes full crystal structure optimization (ALL) of the input structure. If you change the type of crystal structure optimization, add [CRYSTAL_OPTIMIZATION=] keyword, for example, [CRYSTAL_OPTIMIZATION=MOL].
[MMFF94s] means to use MMFF94s force field.
[CIF_BOND=] sets bond information of hydroxy malonic acid molecule. When you want to set a bond with n bond order to an atomic pair of atom i and atom j, CIF_BOND=(i,j,n) keyword should be described.
Store the two files of tartronicacid.cif and tartronicacid.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par tartronicacidenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
In case of using MOL file
The molecule in MDL-MOL file is used as the asymmetric unit. Therefore, when you use MDL-MOL file for the crystal calculation, you should care orientation and spatial position of the molecule. Depending on the orientation and spatial position of the molecule, the molecules in the crystal possible to be sterically clashed due to symmetry operations.
Here, we prepare input data, tartronicacid.mol, of hydroxy malonic acid molecule based on MDL-MOL file format. The tartronicacid.mol is in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\optimization\mol_file\tartronicacid.mol).
tartronicacid.mol file
Tartronicacid.mol
12 11 0 0 0 0 0 0 0 0 1 V2000
5.0778 -1.2267 3.9219 O 0 0 0 0 0
4.3821 0.8184 3.3408 O 0 0 0 0 0
4.5605 1.0186 7.2137 O 0 0 0 0 0
5.0796 -1.1306 6.8350 O 0 0 0 0 0
2.5724 0.8634 5.3289 O 0 0 0 0 0
4.3929 -0.1358 4.0916 C 0 0 0 0 0
3.5417 -0.1340 5.3572 C 0 0 0 0 0
4.4495 -0.0141 6.5749 C 0 0 0 0 0
3.0020 -0.9877 5.3975 H 0 0 0 0 0
2.7189 1.3140 4.9622 H 0 0 0 0 0
5.5591 -1.2170 3.3734 H 0 0 0 0 0
5.7119 -1.0583 7.3998 H 0 0 0 0 0
1 6 1 0 0
1 11 1 0 0
2 6 2 0 0
3 8 2 0 0
4 8 1 0 0
4 12 1 0 0
5 7 1 0 0
5 10 1 0 0
6 7 1 0 0
7 8 1 0 0
7 9 1 0 0
M END
[Execution by Interface]
Open the tartronicacid.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, click in the calculation setting dialog displayed.
Next, in [General Settings] dialog on the detail setting dialog, select [Molecular Crystal] in the pull-down menu of [Calculation Type:].
Settings of the crystal calculation are made in [Crystal calculation] dialog.
We can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:]. The default setting is "ALL".
In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on.
The data of space group and lattice constants are not included in the tartronicacid.mol file. Therefore, these parameters should set in this dialog.
First, to set space group, select P212121 from the pull-down menu of [Space group:]. Next, to set lattice constants, check the check box of [Lattice Constants], and input values of lattice constants. The lattice constants of crystal structure of hydroxy malonic acid are a=4.494 Å，b=8.819 Å，c=10.882 Å，α=90.0 °，β=90.0 °，γ=90.0 °.
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 tartronicacid.ini file.
tartronicacid.ini file
CRYSTAL MMFF94S SPACE_GROUP=P212121 LATTICE_CONSTANT=(4.494,8.819,10.882,90.0,90.0,90.0)
[CRYSTAL] means to execute a crystal calculation, and in the default, CONFLEX executes full crystal structure optimization (ALL) of the input structure. If you change the type of crystal structure optimization, add [CRYSTAL_OPTIMIZATION=] keyword, for example, [CRYSTAL_OPTIMIZATION=MOL].
[MMFF94s] means to use MMFF94s force field.
The data of space group and lattice constants are not included in MDL-MOL file. The [SPACE_GROUP=] and [LATTICE_CONSTANT=] keywords are for setting space group and lattice constants, respectively. The space group of crystal structure of hydroxy malonic acid is P212121, and the lattice constants are a=4.494 Å，b=8.819 Å，c=10.882 Å，α=90.0 °，β=90.0 °，γ=90.0 °.
Store the two files of tartronicacid.mol and tartronicacid.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par tartronicacidenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
[Optimization while fixing structure and position of a specified molecule]
CONFLEX can perform the crystal structure optimization while fixing structure and position of a specified molecule, when there is more than one molecule in the asymmetric unit. Here, for explaining this function, we employ co-crystal butylparaben-isonicotinamide.
From supporting information of Bhardwaj’s paper [R. M. Bhardwaj, H. Yang and A. J. Florence, Acta Cryst. (2016). E72, 53-55], we can get “cv5494sup1.cif” which is for structure of the co-crystal. The “cv5494sup1.cif” is modified for treating by CONFLEX program, and the modified data is saved as “BPN-ISN.cif”. The BPN-ISN.cif is in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\molecular.fixing\BPN-ISN.cif).
BPN-ISN.cif file
data_I _symmetry_cell_setting triclinic _symmetry_Int_Tables_number 2 _symmetry_space_group_name_H-M 'P-1' loop_ _symmetry_equiv_pos_as_xyz x,y,z -x,-y,-z _cell_length_a 5.6257(6) _cell_length_b 9.8661(11) _cell_length_c 14.3979(15) _cell_angle_alpha 90.834(7) _cell_angle_beta 91.431(7) _cell_angle_gamma 91.645(7) _cell_volume 798.47(15) _cell_formula_units_Z 2 loop_ _atom_site_type_symbol _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_calc_flag _atom_site_occupancy _atom_site_disorder_assembly _atom_site_disorder_group H H1N -0.623(3) 1.480(2) 1.4226(13) 0.019(5) Uiso d 1 . . H H2N -0.626(4) 1.399(2) 1.3256(16) 0.035(6) Uiso d 1 . . H H3O 0.140(5) 0.939(3) 1.1807(17) 0.054(7) Uiso d 1 . . O O4 0.1197(2) 0.47988(13) 0.82145(8) 0.0227(3) Uani d 1 . . O O1 -0.2641(2) 1.38157(14) 1.49057(9) 0.0275(3) Uani d 1 . . N N1 -0.5594(3) 1.41555(17) 1.38514(11) 0.0238(4) Uani d 1 . . O O2 0.2637(2) 0.88155(15) 1.16227(9) 0.0308(4) Uani d 1 . . N N2 -0.0392(3) 1.05682(16) 1.24155(10) 0.0234(4) Uani d 1 . . O O3 -0.2134(2) 0.59634(14) 0.80166(9) 0.0297(3) Uani d 1 . . C C13 -0.0315(3) 0.57543(19) 0.84578(12) 0.0207(4) Uani d 1 . . C C7 0.2633(3) 0.63083(19) 0.97609(12) 0.0220(4) Uani d 1 . . H H8 0.3619 0.5641 0.9542 0.026 Uiso calc 1 . . C C6 -0.3631(3) 1.35566(18) 1.41440(12) 0.0194(4) Uani d 1 . . C C12 0.0462(3) 0.65243(18) 0.93023(12) 0.0190(4) Uani d 1 . . C C14 0.0586(3) 0.40447(19) 0.73615(12) 0.0223(4) Uani d 1 . . H H15A 0.0438 0.4660 0.6845 0.027 Uiso calc 1 . . H H15B -0.0918 0.3552 0.7423 0.027 Uiso calc 1 . . C C8 0.3330(3) 0.7076(2) 1.05364(13) 0.0239(4) Uani d 1 . . H H9 0.4775 0.6920 1.0839 0.029 Uiso calc 1 . . C C2 -0.0520(3) 1.18936(19) 1.38204(13) 0.0234(4) Uani d 1 . . H H2 0.0162 1.2121 1.4399 0.028 Uiso calc 1 . . C C10 -0.0302(3) 0.83018(19) 1.04128(12) 0.0229(4) Uani d 1 . . H H11 -0.1290 0.8969 1.0631 0.027 Uiso calc 1 . . C C16 0.2264(3) 0.2420(2) 0.62252(13) 0.0242(4) Uani d 1 . . H H17A 0.0722 0.1955 0.6171 0.029 Uiso calc 1 . . H H17B 0.2306 0.3126 0.5764 0.029 Uiso calc 1 . . C C5 -0.3533(3) 1.21153(19) 1.26476(12) 0.0213(4) Uani d 1 . . H H6 -0.4918 1.2498 1.2420 0.026 Uiso calc 1 . . C C15 0.2548(3) 0.30708(19) 0.71924(12) 0.0220(4) Uani d 1 . . H H16A 0.2511 0.2370 0.7658 0.026 Uiso calc 1 . . H H16B 0.4075 0.3551 0.7248 0.026 Uiso calc 1 . . C C1 -0.2580(3) 1.25031(18) 1.35125(12) 0.0185(4) Uani d 1 . . C C9 0.1866(3) 0.80852(19) 1.08652(12) 0.0221(4) Uani d 1 . . C C11 -0.0986(3) 0.75279(19) 0.96404(12) 0.0223(4) Uani d 1 . . H H12 -0.2437 0.7680 0.9342 0.027 Uiso calc 1 . . C C3 0.0504(3) 1.0945(2) 1.32551(13) 0.0251(4) Uani d 1 . . H H3 0.1888 1.0544 1.3467 0.030 Uiso calc 1 . . C C4 -0.2387(3) 1.11486(19) 1.21283(13) 0.0240(4) Uani d 1 . . H H5 -0.3042 1.0892 1.1551 0.029 Uiso calc 1 . . C C17 0.4194(4) 0.1414(2) 0.60224(14) 0.0314(5) Uani d 1 . . H H18A 0.5725 0.1869 0.6068 0.047 Uiso calc 1 . . H H18B 0.3946 0.1042 0.5407 0.047 Uiso calc 1 . . H H18C 0.4130 0.0696 0.6465 0.047 Uiso calc 1 . .
[Execution by Interface]
Open the BPN-ISN.cif file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed.
Next, in [General Settings] dialog on the detail setting dialog, select [Molecular Crystal] in the pull-down menu of [Calculation Type:].
Settings of the crystal calculation are made in [Crystal calculation] dialog.
Select [Molecule] of the pull-down menu of [Crystal optimization:] on this dialog. We can not use other methods in the case of the optimization with the restrictions. Next, click in the detail setting dialog.
A dialog with the keywords for the calculation settings is displayed.
The molecule to be frozen in the crystal structure optimization is defined by [CRYSTAL_FIXED_MOL=] keyword.
Molecular ID of each molecule in the input file are automatically determined according to atom serial number. In case of “BPN-ISN.cif”, the molecular ID of isonicotinamide is 1, and that of butylparaben is 2. Here, to freeze structure and position of buthlparaben, we add [CRYSTAL_FIXED_MOL=2] keyword to this dialog. If you want to optimize hydrogen atom positions of buthylparaben, you should also add [CRYSTAL_FIXED_MOL=EXCLUDE_HYDROGEN] keyword to this dialog.
Next, we will modify bond order.
CONFLEX Interface automatically creates [CIF_BOND=] keyword with 1 bond order for all atomic pairs that are considered to be bonded from the interatomic distance. Here, you should modify bond order of atomic pairs with double bond. When you want to set a bond with n bond order to an atomic pair of atom i and atom j, CIF_BOND=(i,j,n) keyword should be described. The serial number of each atom are shown in the below figure.
CIF_BOND=(5,13,1) → CIF_BOND=(5,13,2) CIF_BOND=(8,38,1) → CIF_BOND=(8,38,2) CIF_BOND=(9,10,1) → CIF_BOND=(9,10,2) CIF_BOND=(11,14,1) → CIF_BOND=(11,14,2) CIF_BOND=(18,33,1) → CIF_BOND=(18,33,2) CIF_BOND=(20,36,1) → CIF_BOND=(20,36,2) CIF_BOND=(22,34,1) → CIF_BOND=(22,34,2) CIF_BOND=(27,32,1) → CIF_BOND=(27,32,2)
The dialog modified is shown below.
When you complete the modifications, click . The calculation will start. The structure and position of buthlparaben in the crystal after and before the optimization are equivalent.
[Execution by command line]
The calculation settings are defined by describing keywords in the BPN-ISN.ini file.
BPN-ISN.ini file
CRYSTAL MMFF94S CRYSTAL_OPTIMIZATION=MOL CRYSTAL_FIXED_MOL=2 CIF_BOND=(1,6,1) CIF_BOND=(2,6,1) CIF_BOND=(3,7,1) CIF_BOND=(4,10,1) CIF_BOND=(4,15,1) CIF_BOND=(5,13,2) CIF_BOND=(6,13,1) CIF_BOND=(7,33,1) CIF_BOND=(8,38,2) CIF_BOND=(8,36,1) CIF_BOND=(9,10,2) CIF_BOND=(10,14,1) CIF_BOND=(11,12,1) CIF_BOND=(11,18,1) CIF_BOND=(11,14,2) CIF_BOND=(13,32,1) CIF_BOND=(14,34,1) CIF_BOND=(15,17,1) CIF_BOND=(15,16,1) CIF_BOND=(15,29,1) CIF_BOND=(18,19,1) CIF_BOND=(18,33,2) CIF_BOND=(20,21,1) CIF_BOND=(20,36,2) CIF_BOND=(20,32,1) CIF_BOND=(22,23,1) CIF_BOND=(22,34,2) CIF_BOND=(22,33,1) CIF_BOND=(24,26,1) CIF_BOND=(24,25,1) CIF_BOND=(24,40,1) CIF_BOND=(24,29,1) CIF_BOND=(27,28,1) CIF_BOND=(27,38,1) CIF_BOND=(27,32,2) CIF_BOND=(29,31,1) CIF_BOND=(29,30,1) CIF_BOND=(34,35,1) CIF_BOND=(36,37,1) CIF_BOND=(38,39,1) CIF_BOND=(40,42,1) CIF_BOND=(40,41,1) CIF_BOND=(40,43,1)
The molecule to be frozen in the crystal structure optimization is defined by [CRYSTAL_FIXED_MOL=] keyword.
Molecular ID of each molecule in the input file are automatically determined according to atom serial number. In case of “BPN-ISN.cif”, the molecular ID of isonicotinamide is 1, and that of butylparaben is 2. Here, to freeze structure and position of buthlparaben, we add [CRYSTAL_FIXED_MOL=2] keyword to the BPN-ISN.ini file. If you want to optimize hydrogen atom positions of buthylparaben, you should also add [CRYSTAL_FIXED_MOL=EXCLUDE_HYDROGEN] keyword to the BPN-ISN.ini file.
We can select only the crystal structure optimization of [CRYSTAL_OPTIMIZATION=MOL] in the case of the optimization with the restrictions.
[CRYSTAL] means to execute a crystal calculation. [MMFF94s] means to use MMFF94s force field. The bond information for isonicotinamide and butylparaben molecules are set by [CIF_BOND=] keywords. When you want to set a bond with n bond order to an atomic pair of atom i and atom j, CIF_BOND=(i,j,n) keyword should be described.
Store the two files of BPN-ISN.cif and BPN-ISN.ini in an one folder, and execute below command. The calculation will start. The structure and position of buthlparaben in the crystal after and before the optimization are equivalent.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par BPN-ISNenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
[Output files]
After the calculation, you can get output files below.
| File type | Explanation |
|---|---|
| (Input file name).bso | Detail information on the crystal calculation is described to this file. |
| (Input file name).ical | Powder X-ray diffraction data of initial and optimized structures are described to this file. |
| (Input file name)-F.cmf | Crystal structure data after the optimization is described to this file in CIFMIF file format (In case of using cmf/mol file as input). |
| (Input file name)-F.cif | Crystal structure data after the optimization is described to this file in CIF file format (In case of using cif file as input). |
[CRYSTAL STRUCTURE INFORMATION] part in the bso file shows information of crystal structure model built and each energy value. In the bso file, these data of both initial and optimized structures are shown.
A part of "tartronicacid.bso" is shown below.
-------------------------- CRYSTAL STRUCTURE INFORMATION --------------------------
CRYSTAL SYSTEM: ORTHORHOMBIC
SPACE GROUP NAME: P212121
NUMBER: 19
SYMMETRY EQUIVALENT POSITION 1: x,y,z
2: 1/2+x,1/2-y,-z
3: -x,1/2+y,1/2-z
4: 1/2-x,-y,1/2+z
CELL LENGTHS a: 4.4940 ANGSTROM
b: 8.8190
c: 10.8820
CELL ANGLES alpha: 90.0000 DEGREE
beta: 90.0000
gamma: 90.0000
CELL VOLUME: 431.2818 ANGSTROM**3
CELL DENSITY: 1.8482 MG/M**3
Z : 4 (ZCFX: 4)
CRYSTAL RADIUS (VDW): 20.00 ANGSTROM
CRYSTAL RADIUS (COULOMBIC): 20.00 ANGSTROM
CRYSTAL PACKING GA: 15 (PGA: 8 NGA: -7)
GB: 11 (PGB: 6 NGB: -5)
GC: 9 (PGC: 5 NGC: -4)
NUM. OF ATOMS IN ASYMMETRIC UNIT: 12
NUM. OF MOLS IN ASYMMETRIC UNIT: 1
NUM. OF ATOMS IN UNIT CELL: 48
NUM. OF CALCULATED UNIT CELLS: 195
NUM. OF CALCULATED MOLECULES (VDW): 513
NUM. OF CALCULATED ATOMS (VDW): 6156
NUM. OF CALCULATED MOLECULES (COULOM.): 513
NUM. OF CALCULATED ATOMS (COULOM.): 6156
INTRAMOLECULAR ENERGY: 258.8731 KCAL/MOL
LATTICE ENERGY: -22.4774 KCAL/MOL
CRYSTAL ENERGY: 236.3957 KCAL/MOL
| Item | Explanation |
|---|---|
| CRYSTAL RADIUS(VDW): | Cutoff distance of vdW interaction |
| CRYSTAL RADIUS(COULOMBIC): | Cutoff distance of coulombic interaction on a real space |
| CRYSTAL PACKING GA GB GC: | Packing area of unit cell along a, b, and c axes |
| NUM. OF ATOMS IN ASYMMETRIC UNIT: | Total the number of atoms in the asymmetric unit |
| NUM. OF MOLS IN ASYMMETRIC UNIT: | Total the number of molecules in the asymmetric unit |
| NUM. OF ATOMS IN UNIT CELL: | Total the number of atoms in the unit cell |
| NUM. OF CALCULATED UNIT CELLS: | Total the number of unit cells in the crystal model |
| NUM. OF CALCULATED MOLECULES (VDW): | Total the number of molecules including in the calculation of vdW interactions |
| NUM. OF CALCULATED ATOMS (VDW): | Total the number of atoms including in the calculation of vdW interactions |
| NUM. OF CALCULATED MOLECULES (COULOM.) | Total the number of molecules including in the calculation of coulombic interactions (real space) |
| NUM. OF CALCULATED ATOMS (COULOM.): | Total the number of atoms including in the calculation of coulombic interactions (real space) |
| INTRAMOLECULAR ENERGY: | Eintra |
| LATTICE ENERGY: | Elattice |
| CRYSTAL ENERGY: | Ecrystal |
The powder X-ray diffraction data of initial (NAME: INITIAL STRUCTURE) and optimized (NAME: FINAL STRUCTURE) structures are outputted to the ical file.
A part of "tartronicacid.ical" is shown below.
------------ SIMULATED POWDER PATTERNS ------------
CID: 1
NAME: INITIAL STRUCTURE
X-RAY: Cu (KA1)
WAVE: 1.54059290
2*THETA: 0.000 - 50.000 , 0.020 STEP
H K L 2*THETA INTENSITY d
(DEGREE) (ANGSTROME)
0 0 0 0.000 0.000 0.00000
0 0 0 0.020 0.000 0.00000
0 0 0 0.040 0.000 0.00000
0 0 0 0.060 0.000 0.00000
0 0 0 0.080 0.000 0.00000
0 0 0 0.100 0.000 0.00000
* snip *
------------ SIMULATED POWDER PATTERNS ------------
CID: 2
NAME: FINAL STRUCTURE
X-RAY: Cu (KA1)
WAVE: 1.54059290
2*THETA: 0.000 - 50.000 , 0.020 STEP
H K L 2*THETA INTENSITY d
(DEGREE) (ANGSTROME)
0 0 0 0.000 0.000 0.00000
0 0 0 0.020 0.000 0.00000
0 0 0 0.040 0.000 0.00000
0 0 0 0.060 0.000 0.00000
0 0 0 0.080 0.000 0.00000
0 0 0 0.100 0.000 0.00000
* snip *
[Visualization of calculation results]
[If you executed the calculation by using Interface]
After the submission, the Job Manager will appear at the bottom of CONFLEX Interface window. The Job Manager shows a state of the calculation job executed. When the state of the job changed to "Finished", double-click the row of job finished (the red frame part). The output file (-F.cmf or -F.cif file) will open and the structure optimized will be displayed.
After the open of output file (-F.cmf or -F.cif file), you can show the powder X-ray diffraction pattern by selecting [Spectra_Analyzer] in [Application] menu.
[If you executed the calculation by using command line]
The all output files will be stored in the folder contained input files. If you open the -F.cmf or -F.cif file, you can visualize the optimized crystal structure.
After the open of output file (-F.cmf or -F.cif file), you can show the powder X-ray diffraction pattern by selecting [Spectra_Analyzer] in [Application] menu.
[Available space groups]
| International Table Number | Space group name | |
|---|---|---|
| 1 | P1 | |
| 2 | P-1 | |
| 3 | P2 | unique axis b |
| 3 | P2 | unique axis c |
| 4 | P21 | unique axis b |
| 4 | P21 | unique axis c |
| 5 | C2 | unique axis b |
| 5 | C2 | unique axis c |
| 6 | PM | unique axis b |
| 6 | PM | unique axis c |
| 7 | PC | unique axis b |
| 7 | PC | unique axis c |
| 8 | CM | unique axis b |
| 8 | CM | unique axis c |
| 9 | CC | unique axis b |
| 9 | CC | unique axis c |
| 10 | P2/M | unique axis b |
| 10 | P2/M | unique axis c |
| 11 | P21/M | unique axis b |
| 11 | P21/M | unique axis c |
| 12 | C2/M | unique axis b |
| 12 | C2/M | unique axis c |
| 13 | P2/C | unique axis b |
| 13 | P2/C | unique axis c |
| 14 | P21/C | unique axis b |
| 14 | P21/C | unique axis c |
| 15 | C2/C | unique axis b |
| 15 | C2/C | unique axis c |
| 16 | P222 | |
| 17 | P2221 | |
| 18 | P21212 | |
| 19 | P212121 | |
| 20 | C2221 | |
| 21 | C222 | |
| 22 | F222 | |
| 23 | I222 | |
| 24 | I212121 | |
| 25 | PMM2 | |
| 26 | PMC21 | |
| 27 | PCC2 | |
| 28 | PMA2 | |
| 29 | PCA21 | |
| 30 | PNC2 | |
| 31 | PMN21 | |
| 32 | PBA2 | |
| 33 | PNA21 | |
| 34 | PNN2 | |
| 35 | CMM2 | |
| 36 | CMC21 | |
| 37 | CCC2 | |
| 38 | AMM2 | |
| 39 | ABM2 | |
| 40 | AMA2 | |
| 41 | ABA2 | |
| 42 | FMM2 | |
| 43 | FDD2 | |
| 44 | IMM2 | |
| 45 | IBA2 | |
| 46 | IMA2 | |
| 47 | PMMM | |
| 48 | PNNN | origin choice 1 |
| 48 | PNNN | origin choice 2 |
| 49 | PCCM | |
| 50 | PBAN | origin choice 1 |
| 50 | PBAN | origin choice 2 |
| 51 | PMMA | |
| 52 | PNNA | |
| 53 | PMNA | |
| 54 | PCCA | |
| 55 | PBAM | |
| 56 | PCCN | |
| 57 | PBCM | |
| 58 | PNNM | |
| 59 | PMMN | origin choice 1 |
| 59 | PMMN | origin choice 2 |
| 60 | PBCN | |
| 61 | PBCA | |
| 62 | PNMA | |
| 63 | CMCM | |
| 64 | CMCA | |
| 65 | CMMM | |
| 66 | CCCM | |
| 67 | CMMA | |
| 68 | CCCA | origin choice 1 |
| 68 | CCCA | origin choice 2 |
| 69 | FMMM | |
| 70 | FDDD | origin choice 1 |
| 70 | FDDD | origin choice 2 |
| 71 | IMMM | |
| 72 | IBAM | |
| 73 | IBCA | |
| 74 | IMMA | |
| 75 | P4 | |
| 76 | P41 | |
| 77 | P42 | |
| 78 | P43 | |
| 79 | I4 | |
| 80 | I41 | |
| 81 | P-4 | |
| 82 | I-4 | |
| 83 | P4/M | |
| 84 | P42/M | |
| 85 | P4/N | origin choice 1 |
| 85 | P4/N | origin choice 2 |
| 86 | P42/N | origin choice 1 |
| 86 | P42/N | origin choice 2 |
| 87 | I4/M | |
| 88 | I41/A | origin choice 1 |
| 88 | I41/A | origin choice 2 |
| 89 | P422 | |
| 90 | P4212 | |
| 91 | P4122 | |
| 92 | P41212 | |
| 93 | P4222 | |
| 94 | P42212 | |
| 95 | P4322 | |
| 96 | P43212 | |
| 97 | I422 | |
| 98 | I4122 | |
| 99 | P4MM | |
| 100 | P4BM | |
| 101 | P42CM | |
| 102 | P42NM | |
| 103 | P4CC | |
| 104 | P4NC | |
| 105 | P42MC | |
| 106 | P42BC | |
| 107 | I4MM | |
| 108 | I4CM | |
| 109 | I41MD | |
| 110 | I41CD | |
| 111 | P-42M | |
| 112 | P-42C | |
| 113 | P-421M | |
| 114 | P-421C | |
| 115 | P-4M2 | |
| 116 | P-4C2 | |
| 117 | P-4B2 | |
| 118 | P-4N2 | |
| 119 | I-4M2 | |
| 120 | I-4C2 | |
| 121 | I-42M | |
| 122 | I-42D | |
| 123 | P4/MMM | |
| 124 | P4/MCC | |
| 125 | P4/NBM | origin choice 1 |
| 125 | P4/NBM | origin choice 2 |
| 126 | P4/NNC | origin choice 1 |
| 126 | P4/NNC | origin choice 2 |
| 127 | P4/MBM | |
| 128 | P4/MNC | |
| 129 | P4/NMM | origin choice 1 |
| 129 | P4/NMM | origin choice 2 |
| 130 | P4/NCC | origin choice 1 |
| 130 | P4/NCC | origin choice 2 |
| 131 | P42/MMC | |
| 132 | P42/MCM | |
| 133 | P42/NBC | origin choice 1 |
| 133 | P42/NBC | origin choice 2 |
| 134 | P42/NNM | origin choice 1 |
| 134 | P42/NNM | origin choice 2 |
| 135 | P42/MBC | |
| 136 | P42/MNM | |
| 137 | P42/NMC | origin choice 1 |
| 137 | P42/NMC | origin choice 2 |
| 138 | P42/NCM | origin choice 1 |
| 138 | P42/NCM | origin choice 2 |
| 139 | I4/MMM | |
| 140 | I4/MCM | |
| 141 | I41/AMD | origin choice 1 |
| 141 | I41/AMD | origin choice 2 |
| 142 | I41/ACD | origin choice 1 |
| 142 | I41/ACD | origin choice 2 |
| 143 | P3 | |
| 144 | P31 | |
| 145 | P32 | |
| 146 | R3 | hexagonal axes |
| 146 | R3 | rhombohedral axes |
| 147 | P-3 | |
| 148 | R-3 | hexagonal axes |
| 148 | R-3 | rhombohedral axes |
| 149 | P312 | |
| 150 | P321 | |
| 151 | P3112 | |
| 152 | P3121 | |
| 153 | P3212 | |
| 154 | P3221 | |
| 155 | R32 | hexagonal axes |
| 155 | R32 | rhombohedral axes |
| 156 | P3M1 | |
| 157 | P31M | |
| 158 | P3C1 | |
| 159 | P31C | |
| 160 | R3M | hexagonal axes |
| 160 | R3M | rhombohedral axes |
| 161 | R3C | hexagonal axes |
| 161 | R3C | rhombohedral axes |
| 162 | P-31M | |
| 163 | P-31C | |
| 164 | P-3M1 | |
| 165 | P-3C1 | |
| 166 | R-3M | hexagonal axes |
| 166 | R-3M | rhombohedral axes |
| 167 | R-3C | hexagonal axes |
| 167 | R-3C | rhombohedral axes |
| 168 | P6 | |
| 169 | P61 | |
| 170 | P65 | |
| 171 | P62 | |
| 172 | P64 | |
| 173 | P63 | |
| 174 | P-6 | |
| 175 | P6/M | |
| 176 | P63/M | |
| 177 | P622 | |
| 178 | P6122 | |
| 179 | P6522 | |
| 180 | P6222 | |
| 181 | P6422 | |
| 182 | P6322 | |
| 183 | P6MM | |
| 184 | P6CC | |
| 185 | P63CM | |
| 186 | P63MC | |
| 187 | P-6M2 | |
| 188 | P-6C2 | |
| 189 | P-62M | |
| 190 | P-62C | |
| 191 | P6/MMM | |
| 192 | P6/MCC | |
| 193 | P63/MCM | |
| 194 | P63/MMC | |
| 195 | P23 | |
| 196 | F23 | |
| 197 | I23 | |
| 198 | P213 | |
| 199 | I213 | |
| 200 | PM-3 | |
| 201 | PN-3 | origin choice 1 |
| 201 | PN-3 | origin choice 2 |
| 202 | FM-3 | |
| 203 | FD-3 | origin choice 1 |
| 203 | FD-3 | origin choice 2 |
| 204 | IM-3 | |
| 205 | PA-3 | |
| 206 | IA-3 | |
| 207 | P432 | |
| 208 | P4232 | |
| 209 | F432 | |
| 210 | F4132 | |
| 211 | I432 | |
| 212 | P4332 | |
| 213 | P4132 | |
| 214 | I4132 | |
| 215 | P-43M | |
| 216 | F-43M | |
| 217 | I-43M | |
| 218 | P-43N | |
| 219 | F-43C | |
| 220 | I-43D | |
| 221 | PM-3M | |
| 222 | PN-3N | origin choice 1 |
| 222 | PN-3N | origin choice 2 |
| 223 | PM-3N | |
| 224 | PN-3M | origin choice 1 |
| 224 | PN-3M | origin choice 2 |
| 225 | FM-3M | |
| 226 | FM-3C | |
| 227 | FD-3M | origin choice 1 |
| 227 | FD-3M | origin choice 2 |
| 228 | FD-3C | origin choice 1 |
| 228 | FD-3C | origin choice 2 |
| 229 | IM-3M | |
| 230 | IA-3D |
[Available X-ray sources]
| Kα1 wavelength (Ang.) | |
|---|---|
| Mg | 9.889554 |
| Al | 8.339514 |
| Si | 7.125588 |
| S | 5.3722 |
| Cl | 4.727818 |
| Ar | 4.191938 |
| K | 3.7412838 |
| Cr | 2.289726 |
| Mn | 2.101854 |
| Fe | 1.936041 |
| Co | 1.788996 |
| Ni | 1.65793 |
| Cu | 1.5405929 |
| Ga | 1.340127 |
| As | 1.175956 |
| Se | 1.10478 |
| Br | 1.039756 |
| Kr | 0.980267 |
| Zr | 0.7859579 |
| Mo | 0.70931715 |
| Ru | 0.6430994 |
| Rh | 0.6132937 |
| Pd | 0.5854639 |
| Ag | 0.55942178 |
| Cd | 0.5350147 |
| In | 0.5121251 |
| Sn | 0.4906115 |
| Sb | 0.47037 |
| Xe | 0.4163508 |
| Ba | 0.38512464 |
| Nd | 0.33185689 |
| Pm | 0.3201648 |
| Sm | 0.30904506 |
| Ho | 0.2607608 |
| Er | 0.25237359 |
| Tm | 0.24434486 |
| W | 0.20901314 |
| Au | 0.1801978 |
| Pb | 0.16537816 |
| Bi | 0.1607903 |