When calculating derivatives of structure factors, there is one particular term (the derivatives of the atomic form factors) that will always be zero in the case of tabulated spherical atomic form factors. What happens if the form factors are non-spherical? The assumption that this particular term is very close to zero is generally made in non-spherical refinements (for example, implementations of Hirshfeld atom refinement or transferable aspherical atom models), unless the form factors are refinable parameters (for example multipole modelling). To evaluate this general approximation for one specific method, a numerical differentiation was implemented within the NoSpherA2 framework to calculate the derivatives of the structure factors in a Hirshfeld atom refinement directly as accurately as possible, thus bypassing the approximation altogether. Comparing wR2 factors and atomic parameters, along with their uncertainties from the approximate and numerically differentiating refinements, it turns out that the impact of this approximation on the final crystallographic model is indeed negligible.
Supporting information
| Crystallographic Information File (CIF) https://doi.org/10.1107/S2053273321009086/pl5014sup1.cif Contains datablocks epoxide_app, epoxide_hyb, epoxide_num, epoxide_spher, L-Ala_23K_tonto_IAM_app, L-Ala_23K_tonto_IAM_hyb, L-Ala_23K_tonto_IAM_num, L-Ala_23K_tonto_IAM_spher, nh30r_app, nh30r_hyb, nh30r_num, nh30r_spher |
| Portable Document Format (PDF) file https://doi.org/10.1107/S2053273321009086/pl5014sup2.pdf Supporting information |
| Zip compressed file https://doi.org/10.1107/S2053273321009086/pl5014sup3.zip Code used for calculations |
For all structures, program(s) used to refine structure: olex2.refine 1.5-dev (Bourhis et al., 2015); molecular graphics: Olex2 1.5-dev (Dolomanov et al., 2009); software used to prepare material for publication: Olex2 1.5-dev (Dolomanov et al., 2009).
Crystal data top
C2H4O | V = 251.8 (3) Å3 |
Mr = 44.05 | Z = 4 |
Monoclinic, P21/n | F(000) = 96.064 |
a = 4.633 (5) Å | Dx = 1.162 Mg m−3 |
b = 8.400 (1) Å | Mo Kα radiation, λ = 0.71068 Å |
c = 6.577 (3) Å | µ = 0.09 mm−1 |
β = 100.37 (6)° | T = 100 K |
Data collection top
2081 measured reflections | θmax = 35.0°, θmin = 4.0° |
1109 independent reflections | h = −9→6 |
899 reflections with I ≥ 2u(I) | k = 0→16 |
Rint = 0.0000 | l = −6→13 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | 0 constraints |
R[F2 > 2σ(F2)] = 0.023 | All H-atom parameters refined |
wR(F2) = 0.047 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.47 | (Δ/σ)max = −0.0003 |
1109 reflections | Δρmax = 0.15 e Å−3 |
64 parameters | Δρmin = −0.19 e Å−3 |
Special details top
Refinement. Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. DOI 10.1039/D0SC05526C - 2020
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fregment can be embedded in an electrostatic crystal field by employing cluster charges.
The following options were used:
SOFTWARE: ORCA
PARTITIONING: NoSpherA2
INT ACCURACY: High
METHOD: PBE
BASIS SET: def2-TZVPP
CHARGE: 0
MULTIPLICITY: 1
DATE: 2021-06-07_11-39-49 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.11630 (7) | 0.83106 (3) | 0.12462 (5) | 0.02954 (8) | |
C2 | 0.14861 (9) | 0.93867 (5) | 0.29600 (7) | 0.02822 (9) | |
H2a | 0.2818 (18) | 0.8900 (8) | 0.4368 (10) | 0.065 (2) | |
H2b | 0.1738 (15) | 1.0619 (7) | 0.2565 (12) | 0.053 (2) | |
C3 | −0.13420 (10) | 0.86455 (6) | 0.21817 (7) | 0.03217 (10) | |
H3a | −0.3087 (18) | 0.9333 (9) | 0.1202 (12) | 0.069 (3) | |
H3b | −0.2035 (18) | 0.7647 (10) | 0.3037 (13) | 0.069 (2) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.03540 (16) | 0.02562 (12) | 0.02939 (14) | 0.00304 (12) | 0.01060 (12) | −0.00355 (11) |
C2 | 0.03242 (19) | 0.02498 (16) | 0.02736 (18) | 0.00039 (14) | 0.00569 (15) | −0.00209 (13) |
H2a | 0.081 (6) | 0.072 (5) | 0.031 (4) | 0.022 (5) | −0.015 (4) | 0.009 (4) |
H2b | 0.064 (6) | 0.026 (4) | 0.071 (5) | −0.008 (3) | 0.018 (4) | −0.003 (4) |
C3 | 0.0306 (2) | 0.0338 (2) | 0.0343 (2) | −0.00344 (16) | 0.01197 (17) | 0.00000 (16) |
H3a | 0.049 (5) | 0.104 (7) | 0.051 (5) | 0.028 (5) | 0.001 (4) | 0.013 (5) |
H3b | 0.072 (6) | 0.063 (5) | 0.077 (5) | −0.034 (5) | 0.028 (5) | 0.004 (5) |
Geometric parameters (Å, º) top
O1—C2 | 1.4316 (7) | C2—C3 | 1.4577 (14) |
O1—C3 | 1.4359 (13) | C3—H3a | 1.102 (8) |
C2—H2a | 1.095 (7) | C3—H3b | 1.090 (7) |
C2—H2b | 1.079 (6) | | |
| | | |
C3—O1—C2 | 61.11 (3) | C2—C3—O1 | 59.30 (3) |
H2a—C2—O1 | 113.1 (4) | H3a—C3—O1 | 114.6 (4) |
H2b—C2—O1 | 114.6 (4) | H3a—C3—C2 | 120.0 (4) |
H2b—C2—H2a | 119.5 (6) | H3b—C3—O1 | 114.0 (4) |
C3—C2—O1 | 59.59 (3) | H3b—C3—C2 | 118.5 (5) |
C3—C2—H2a | 118.1 (4) | H3b—C3—H3a | 116.8 (7) |
C3—C2—H2b | 117.0 (4) | | |
Crystal data top
C2H4O | V = 251.8 (3) Å3 |
Mr = 44.05 | Z = 4 |
Monoclinic, P21/n | F(000) = 96.064 |
a = 4.633 (5) Å | Dx = 1.162 Mg m−3 |
b = 8.400 (1) Å | Mo Kα radiation, λ = 0.71068 Å |
c = 6.577 (3) Å | µ = 0.09 mm−1 |
β = 100.37 (6)° | T = 100 K |
Data collection top
2081 measured reflections | θmax = 35.0°, θmin = 4.0° |
1109 independent reflections | h = −9→6 |
899 reflections with I ≥ 2u(I) | k = 0→16 |
Rint = 0.0000 | l = −6→13 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | 0 constraints |
R[F2 > 2σ(F2)] = 0.023 | All H-atom parameters refined |
wR(F2) = 0.047 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.47 | (Δ/σ)max = −0.0003 |
1109 reflections | Δρmax = 0.15 e Å−3 |
64 parameters | Δρmin = −0.19 e Å−3 |
Special details top
Refinement. Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. DOI 10.1039/D0SC05526C - 2020
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fregment can be embedded in an electrostatic crystal field by employing cluster charges.
The following options were used:
SOFTWARE: ORCA
PARTITIONING: NoSpherA2
INT ACCURACY: High
METHOD: PBE
BASIS SET: def2-TZVPP
CHARGE: 0
MULTIPLICITY: 1
DATE: 2021-06-07_11-39-49 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Biso*/Beq | |
O1 | 0.11630 (7) | 0.83105 (3) | 0.12462 (5) | | |
C2 | 0.14860 (10) | 0.93867 (5) | 0.29601 (7) | | |
H2a | 0.2819 (18) | 0.8902 (9) | 0.4368 (10) | | |
H2b | 0.1742 (15) | 1.0620 (7) | 0.2566 (11) | | |
C3 | −0.13422 (11) | 0.86456 (6) | 0.21816 (7) | | |
H3a | −0.30970 (17) | 0.9332 (9) | 0.1197 (11) | | |
H3b | −0.2033 (18) | 0.7645 (10) | 0.3035 (12) | | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.03541 (16) | 0.02562 (12) | 0.02940 (14) | −0.00356 (11) | 0.01061 (12) | 0.00304 (12) |
C2 | 0.0324 (2) | 0.02500 (17) | 0.02736 (18) | −0.00209 (14) | 0.00568 (15) | 0.00038 (14) |
H2a | 0.082 (6) | 0.072 (6) | 0.031 (4) | 0.009 (5) | −0.015 (5) | 0.023 (6) |
H2b | 0.064 (6) | 0.026 (4) | 0.070 (5) | −0.003 (4) | 0.018 (4) | −0.008 (3) |
C3 | 0.0307 (2) | 0.0338 (2) | 0.0344 (2) | −0.00002 (16) | 0.01197 (17) | −0.00346 (16) |
H3a | 0.048 (5) | 0.104 (8) | 0.051 (5) | 0.013 (5) | 0.002 (4) | 0.028 (6) |
H3b | 0.071 (6) | 0.063 (5) | 0.076 (6) | 0.004 (6)6 | 0.027 (5) | −0.034 (5) |
Geometric parameters (Å, º) top
O1—C2 | 1.4316 (5) | C2—C3 | 1.4578 (6) |
O1—C3 | 1.4359 (5) | C3—H3a | 1.106 (7) |
C2—H2a | 1.095 (6) | C3—H3b | 1.090 (7) |
C2—H2b | 1.080 (5) | | |
| | | |
C3—O1—C2 | 61.11 (3) | C2—C3—O1 | 59.30 (3) |
H2a—C2—O1 | 113.2 (4) | H3a—C3—O1 | 114.6 (4) |
H2b—C2—O1 | 114.7 (4) | H3a—C3—C2 | 120.1 (4) |
H2b—C2—H2a | 119.4 (6) | H3b—C3—O1 | 113.8 (4) |
C3—C2—O1 | 59.59 (3) | H3b—C3—C2 | 118.5 (5) |
C3—C2—H2a | 118.2 (4) | H3b—C3—H3a | 116.8 (7) |
C3—C2—H2b | 117.1 (4) | | |
Crystal data top
C2H4O | V = 251.8 (3) Å3 |
Mr = 44.05 | Z = 4 |
Monoclinic, P21/n | F(000) = 96.064 |
a = 4.633 (5) Å | Dx = 1.162 Mg m−3 |
b = 8.400 (1) Å | Mo Kα radiation, λ = 0.71068 Å |
c = 6.577 (3) Å | µ = 0.09 mm−1 |
β = 100.37 (6)° | T = 100 K |
Data collection top
2081 measured reflections | θmax = 35.0°, θmin = 4.0° |
1109 independent reflections | h = −9→6 |
899 reflections with I ≥ 2u(I) | k = 0→16 |
Rint = 0.0000 | l = −6→13 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | 0 constraints |
R[F2 > 2σ(F2)] = 0.023 | All H-atom parameters refined |
wR(F2) = 0.047 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.47 | (Δ/σ)max = −0.0003 |
1109 reflections | Δρmax = 0.15 e Å−3 |
64 parameters | Δρmin = −0.19 e Å−3 |
Special details top
Refinement. Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. DOI 10.1039/D0SC05526C - 2020
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fregment can be embedded in an electrostatic crystal field by employing cluster charges.
The following options were used:
SOFTWARE: ORCA
PARTITIONING: NoSpherA2
INT ACCURACY: High
METHOD: PBE
BASIS SET: def2-TZVPP
CHARGE: 0
MULTIPLICITY: 1
DATE: 2021-06-07_11-39-49 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Biso*/Beq | |
O1 | 0.11630 (6) | 0.83105 (3) | 0.12462 (5) | | |
C2 | 0.14860 (9) | 0.93867 (5) | 0.29601 (7) | | |
H2a | 0.2819 (18) | 0.8902 (8) | 0.4368 (10) | | |
H2b | 0.1742 (15) | 1.0620 (6) | 0.2565 (11) | | |
C3 | −0.13422 (10) | 0.86456 (6) | 0.21816 (7) | | |
H3a | −0.3097 (17) | 0.9333 (8) | 0.1197 (11) | | |
H3b | −0.2033 (18) | 0.7645 (10) | 0.3035 (12) | | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.03541 (16) | 0.02562 (12) | 0.02939 (14) | 0.00304 (12) | 0.01061 (12) | −0.00355 (11) |
C2 | 0.0324 (2) | 0.02500 (17) | 0.02736 (18) | 0.00038 (14) | 0.00568 (15) | −0.00209 (14) |
H2a | 0.082 (6) | 0.072 (6) | 0.031 (4) | 0.023 (5) | −0.015 (4) | 0.009 (5) |
H2b | 0.064 (5) | 0.026 (4) | 0.070 (5) | −0.008 (3) | 0.018 (4) | −0.003 (3) |
C3 | 0.0307 (2) | 0.0338 (2) | 0.0343 (2) | −0.00346 (16) | 0.01197 (17) | −0.00002 (16) |
H3a | 0.049 (5) | 0.104 (7) | 0.051 (5) | 0.028 (5) | 0.002 (4) | 0.013 (5) |
H3b | 0.071 (6) | 0.063 (5) | 0.076 (5) | −0.034 (5) | 0.027 (5) | 0.004 (5) |
Geometric parameters (Å, º) top
O1—C2 | 1.4316 (5) | C2—C3 | 1.4578 (6) |
O1—C3 | 1.4359 (5) | C3—H3a | 1.106 (7) |
C2—H2a | 1.095 (6) | C3—H3b | 1.090 (7) |
C2—H2b | 1.080 (5) | | |
| | | |
C3—O1—C2 | 61.11 (3) | C2—C3—O1 | 59.30 (3) |
H2a—C2—O1 | 113.2 (4) | H3a—C3—O1 | 114.6 (4) |
H2b—C2—O1 | 114.6 (4) | H3a—C3—C2 | 120.1 (4) |
H2b—C2—H2a | 119.4 (6) | H3b—C3—O1 | 113.8 (4) |
C3—C2—O1 | 59.59 (3) | H3b—C3—C2 | 118.5 (5) |
C3—C2—H2a | 118.2 (4) | H3b—C3—H3a | 116.8 (7) |
C3—C2—H2b | 117.1 (4) | | |
Crystal data top
C2H4O | V = 251.8 (3) Å3 |
Mr = 44.05 | Z = 4 |
Monoclinic, P21/n | F(000) = 96.064 |
a = 4.633 (5) Å | Dx = 1.162 Mg m−3 |
b = 8.400 (1) Å | Mo Kα radiation, λ = 0.71068 Å |
c = 6.577 (3) Å | µ = 0.09 mm−1 |
β = 100.37 (6)° | T = 100 K |
Data collection top
2081 measured reflections | θmax = 35.0°, θmin = 4.0° |
1109 independent reflections | h = −9→6 |
899 reflections with I ≥ 2u(I) | k = 0→16 |
Rint = 0.0000 | l = −6→13 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | 0 constraints |
R[F2 > 2σ(F2)] = 0.032 | All H-atom parameters refined |
wR(F2) = 0.068 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
S = 2.14 | (Δ/σ)max = 0.0004 |
1109 reflections | Δρmax = 0.22 e Å−3 |
64 parameters | Δρmin = −0.24 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.11682 (10) | 0.83081 (5) | 0.12407 (7) | 0.03037 (12) | |
C2 | 0.14838 (14) | 0.93866 (7) | 0.29621 (10) | 0.02901 (13) | |
H2a | 0.269 (2) | 0.8926 (10) | 0.4231 (13) | 0.044 (2) | |
H2b | 0.1726 (18) | 1.0511 (10) | 0.2663 (13) | 0.035 (2) | |
C3 | −0.13434 (15) | 0.86489 (8) | 0.21842 (11) | 0.03283 (14) | |
H3a | −0.293 (2) | 0.9233 (11) | 0.1330 (16) | 0.053 (3) | |
H3b | −0.194 (2) | 0.7758 (12) | 0.2944 (17) | 0.053 (3) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0352 (2) | 0.02728 (18) | 0.0306 (2) | 0.00259 (17) | 0.01112 (17) | −0.00520 (16) |
C2 | 0.0340 (3) | 0.0256 (2) | 0.0276 (3) | 0.0007 (2) | 0.0060 (2) | −0.0027 (2) |
H2a | 0.056 (6) | 0.049 (6) | 0.019 (4) | 0.006 (6) | −0.016 (4) | −0.008 (5) |
H2b | 0.041 (6) | 0.034 (6) | 0.031 (5) | −0.012 (4) | 0.007 (4) | −0.003 (4) |
C3 | 0.0314 (3) | 0.0346 (3) | 0.0351 (3) | −0.0028 (2) | 0.0129 (3) | −0.0002 (2) |
H3a | 0.038 (6) | 0.080 (8) | 0.043 (6) | 0.000 (7) | 0.010 (5) | 0.003 (6) |
H3b | 0.060 (7) | 0.040 (6) | 0.063 (7) | −0.018 (6) | 0.025 (6) | −0.009 (6) |
Geometric parameters (Å, º) top
O1—C2 | 1.4367 (9) | C2—C3 | 1.4561 (16) |
O1—C3 | 1.4425 (14) | C3—H3a | 0.975 (11) |
C2—H2a | 0.995 (8) | C3—H3b | 0.968 (10) |
C2—H2b | 0.975 (8) | | |
| | | |
C3—O1—C2 | 60.76 (4) | C2—C3—O1 | 59.42 (4) |
H2a—C2—O1 | 112.2 (5) | H3a—C3—O1 | 115.9 (5) |
H2b—C2—O1 | 116.8 (5) | H3a—C3—C2 | 121.8 (6) |
H2b—C2—H2a | 118.6 (7) | H3b—C3—O1 | 113.4 (6) |
C3—C2—O1 | 59.82 (4) | H3b—C3—C2 | 118.1 (7) |
C3—C2—H2a | 117.5 (6) | H3b—C3—H3a | 115.4 (9) |
C3—C2—H2b | 118.0 (5) | | |
(L-Ala_23K_tonto_IAM_app)
top
Crystal data top
C3H7NO2 | Z = 4 |
Mr = 89.10 | F(000) = 192.122 |
Orthorhombic, P212121 | Dx = 1.405 Mg m−3 |
a = 5.9279 (10) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 12.2597 (17) Å | µ = 0.12 mm−1 |
c = 5.7939 (9) Å | T = 23 K |
V = 421.07 (11) Å3 | |
Data collection top
2519 measured reflections | θmax = 50.1°, θmin = 3.3° |
2519 independent reflections | h = 0→12 |
2393 reflections with I ≥ 2u(I) | k = 0→26 |
Rint = 0.0000 | l = 0→12 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | 0 constraints |
R[F2 > 2σ(F2)] = 0.019 | All H-atom parameters refined |
wR(F2) = 0.032 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.15 | (Δ/σ)max = 0.0001 |
2519 reflections | Δρmax = 0.18 e Å−3 |
118 parameters | Δρmin = −0.21 e Å−3 |
Special details top
Refinement. Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. DOI 10.1039/D0SC05526C - 2020
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fregment can be embedded in an electrostatic crystal field by employing cluster charges.
The following options were used:
SOFTWARE: ORCA
PARTITIONING: NoSpherA2
INT ACCURACY: High
METHOD: PBE
BASIS SET: def2-TZVPP
CHARGE: 0
MULTIPLICITY: 1
DATE: 2021-06-02_13-25-25 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.64729 (4) | 0.13751 (2) | 0.18294 (5) | 0.00530 (3) | |
H1a | 0.7045 (11) | 0.0606 (5) | 0.1982 (14) | 0.0235 (19) | |
H1b | 0.7785 (10) | 0.1895 (5) | 0.2114 (14) | 0.0210 (17) | |
H1c | 0.5838 (12) | 0.1492 (5) | 0.0164 (13) | 0.0280 (19) | |
C1 | 0.46630 (4) | 0.16109 (2) | 0.35442 (5) | 0.00448 (4) | |
H1 | 0.4226 (9) | 0.2473 (4) | 0.3432 (11) | 0.0177 (15) | |
C2 | 0.25987 (5) | 0.09069 (2) | 0.30332 (6) | 0.00694 (4) | |
H2a | 0.1921 (10) | 0.1104 (5) | 0.1315 (12) | 0.0278 (19) | |
H2b | 0.1278 (10) | 0.1056 (5) | 0.4315 (13) | 0.0247 (18) | |
H2c | 0.3041 (10) | 0.0045 (5) | 0.3082 (14) | 0.032 (2) | |
C3 | 0.55403 (5) | 0.14080 (2) | 0.59985 (5) | 0.00423 (3) | |
O1 | 0.72675 (4) | 0.083782 (17) | 0.62427 (4) | 0.00655 (3) | |
O2 | 0.44091 (4) | 0.184042 (17) | 0.76112 (4) | 0.00636 (3) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.00555 (7) | 0.00610 (7) | 0.00424 (8) | 0.00012 (6) | 0.00068 (6) | −0.00016 (6) |
H1a | 0.025 (4) | 0.027 (4) | 0.018 (5) | 0.005 (3) | 0.013 (4) | 0.003 (3) |
H1b | 0.013 (3) | 0.028 (4) | 0.022 (5) | 0.003 (3) | 0.007 (4) | 0.000 (4) |
H1c | 0.037 (4) | 0.022 (4) | 0.026 (5) | −0.009 (4) | 0.027 (4) | −0.012 (4) |
C1 | 0.00519 (8) | 0.00473 (7) | 0.00352 (9) | 0.00044 (6) | −0.00044 (7) | 0.00009 (6) |
H1 | 0.023 (3) | 0.012 (3) | 0.018 (4) | 0.008 (3) | 0.004 (3) | −0.001 (3) |
C2 | 0.00582 (9) | 0.00886 (9) | 0.00614 (10) | −0.00132 (8) | −0.00059 (8) | −0.00047 (8) |
H2a | 0.020 (4) | 0.048 (5) | 0.016 (4) | −0.010 (3) | −0.011 (3) | 0.011 (4) |
H2b | 0.011 (3) | 0.031 (4) | 0.033 (5) | −0.003 (3) | 0.008 (4) | 0.004 (4) |
H2c | 0.032 (5) | 0.016 (3) | 0.048 (6) | −0.004 (3) | 0.001 (4) | −0.005 (3) |
C3 | 0.00487 (7) | 0.00426 (7) | 0.00355 (9) | 0.00023 (7) | −0.00019 (7) | −0.00003 (6) |
O1 | 0.00668 (7) | 0.00705 (7) | 0.00592 (8) | 0.00245 (6) | −0.00064 (6) | 0.00052 (6) |
O2 | 0.00755 (7) | 0.00762 (6) | 0.00392 (8) | 0.00210 (6) | 0.00060 (6) | −0.00056 (6) |
Geometric parameters (Å, º) top
N1—H1a | 1.006 (6) | C1—C3 | 1.5344 (5) |
N1—H1b | 1.019 (6) | C2—H2a | 1.100 (7) |
N1—H1c | 1.045 (8) | C2—H2b | 1.094 (7) |
N1—C1 | 1.4905 (4) | C2—H2c | 1.089 (6) |
C1—H1 | 1.090 (5) | C3—O1 | 1.2478 (4) |
C1—C2 | 1.5264 (4) | C3—O2 | 1.2664 (4) |
| | | |
H1b—N1—H1a | 108.4 (5) | C3—C1—C2 | 111.09 (2) |
H1c—N1—H1a | 109.3 (6) | H2a—C2—C1 | 110.1 (3) |
H1c—N1—H1b | 109.8 (5) | H2b—C2—C1 | 110.3 (3) |
C1—N1—H1a | 111.5 (4) | H2b—C2—H2a | 108.4 (4) |
C1—N1—H1b | 108.7 (4) | H2c—C2—C1 | 110.5 (3) |
C1—N1—H1c | 109.2 (4) | H2c—C2—H2a | 108.9 (5) |
H1—C1—N1 | 108.6 (3) | H2c—C2—H2b | 108.5 (5) |
C2—C1—N1 | 109.76 (2) | O1—C3—C1 | 118.30 (2) |
C2—C1—H1 | 110.2 (3) | O2—C3—C1 | 115.88 (2) |
C3—C1—N1 | 110.02 (2) | O2—C3—O1 | 125.83 (3) |
C3—C1—H1 | 107.0 (3) | | |
| | | |
N1—C1—C3—O1 | −18.19 (2) | N1—C1—C3—O2 | 162.16 (2) |
(L-Ala_23K_tonto_IAM_hyb)
top
Crystal data top
C3H7NO2 | Z = 4 |
Mr = 89.10 | F(000) = 192.122 |
Orthorhombic, P212121 | Dx = 1.405 Mg m−3 |
a = 5.9279 (10) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 12.2597 (17) Å | µ = 0.12 mm−1 |
c = 5.7939 (9) Å | T = 23 K |
V = 421.07 (11) Å3 | |
Data collection top
2519 measured reflections | θmax = 50.1°, θmin = 3.3° |
2519 independent reflections | h = 0→12 |
2393 reflections with I ≥ 2u(I) | k = 0→26 |
Rint = 0.0000 | l = 0→12 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | 0 constraints |
R[F2 > 2σ(F2)] = 0.019 | All H-atom parameters refined |
wR(F2) = 0.032 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.15 | (Δ/σ)max = 0.0001 |
2519 reflections | Δρmax = 0.18 e Å−3 |
118 parameters | Δρmin = −0.21 e Å−3 |
Special details top
Refinement. Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. DOI 10.1039/D0SC05526C - 2020
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fregment can be embedded in an electrostatic crystal field by employing cluster charges.
The following options were used:
SOFTWARE: ORCA
PARTITIONING: NoSpherA2
INT ACCURACY: High
METHOD: PBE
BASIS SET: def2-TZVPP
CHARGE: 0
MULTIPLICITY: 1
DATE: 2021-06-02_13-25-25 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Biso*/Beq | |
N1 | 0.64729 (5) | 0.13751 (2) | 0.18294 (5) | | |
H1a | 0.7049 (11) | 0.0606 (5) | 0.1977 (14) | | |
H1b | 0.7785 (10) | 0.1895 (5) | 0.2112 (14) | | |
H1c | 0.5832 (12) | 0.1493 (6) | 0.0159 (11) | | |
C1 | 0.46630 (5) | 0.16110 (2) | 0.35442 (5) | | |
H1 | 0.4227 (10) | 0.2474 (4) | 0.3435 (12) | | |
C2 | 0.25987 (5) | 0.09069 (3) | 0.30332 (6) | | |
H2a | 0.1922 (10) | 0.1105 (5) | 0.1313 (11) | | |
H2b | 0.1277 (10) | 0.1054 (5) | 0.4317 (12) | | |
H2c | 0.3041 (10) | 0.0044 (4) | 0.3083 (15) | | |
C3 | 0.55403 (5) | 0.14080 (2) | 0.59985 (5) | | |
O1 | 0.72675 (4) | 0.083782 (17) | 0.62427 (5) | | |
O2 | 0.44091 (4) | 0.184043 (17) | 0.76112 (4) | | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.00555 (8) | 0.00610 (8) | 0.00425 (9) | −0.00016 (7) | 0.00068 (7) | 0.00012 (7) |
H1a | 0.026 (5) | 0.027 (4) | 0.018 (5) | 0.003 (4) | 0.013 (4) | 0.005 (4) |
H1b | 0.013 (4) | 0.028 (4) | 0.022 (5) | 0.000 (4) | 0.007 (4) | 0.003 (4) |
H1c | 0.036 (5) | 0.021 (4) | 0.026 (5) | −0.012 (4) | 0.027 (4) | −0.009 (4) |
C1 | 0.00519 (9) | 0.00473 (8) | 0.00352 (10) | 0.00009 (7) | −0.00044 (7) | 0.00044 (7) |
H1 | 0.023 (4) | 0.012 (3) | 0.018 (4) | −0.001 (3) | 0.004 (4) | 0.008 (3) |
C2 | 0.00582 (9) | 0.00886 (9) | 0.00614 (10) | −0.00047 (8) | −0.00059 (8) | −0.00132 (8) |
H2a | 0.019 (4) | 0.047 (5) | 0.016 (5) | 0.010 (4) | −0.011 (4) | −0.010 (4) |
H2b | 0.011 (4) | 0.031 (4) | 0.033 (5) | 0.004 (4) | 0.008 (5) | −0.003 (4) |
H2c | 0.031 (5) | 0.016 (3) | 0.048 (6) | −0.005 (4) | 0.001 (5) | −0.004 (4) |
C3 | 0.00487 (8) | 0.00426 (7) | 0.00355 (9) | −0.00003 (7) | −0.00019 (7) | 0.00023 (7) |
O1 | 0.00668 (7) | 0.00706 (7) | 0.00592 (9) | 0.00052 (7) | −0.00064 (7) | 0.00245 (6) |
O2 | 0.00755 (7) | 0.00762 (7) | 0.00392 (8) | −0.00056 (6) | 0.00060 (7) | 0.00210 (6) |
Geometric parameters (Å, º) top
N1—H1a | 1.007 (6) | C1—C3 | 1.5344 (5) |
N1—H1b | 1.019 (6) | C2—H2a | 1.101 (6) |
N1—H1c | 1.050 (6) | C2—H2b | 1.095 (6) |
N1—C1 | 1.4906 (4) | C2—H2c | 1.090 (5) |
C1—H1 | 1.091 (4) | C3—O1 | 1.2478 (3) |
C1—C2 | 1.5264 (4) | C3—O2 | 1.2664 (3) |
| | | |
H1b—N1—H1a | 108.3 (5) | C3—C1—C2 | 111.09 (2) |
H1c—N1—H1a | 109.3 (6) | H2a—C2—C1 | 110.1 (3) |
H1c—N1—H1b | 109.8 (6) | H2b—C2—C1 | 110.4 (3) |
C1—N1—H1a | 111.7 (4) | H2b—C2—H2a | 108.5 (5) |
C1—N1—H1b | 108.8 (4) | H2c—C2—C1 | 110.5 (3) |
C1—N1—H1c | 109.1 (4) | H2c—C2—H2a | 109.0 (5) |
H1—C1—N1 | 108.7 (3) | H2c—C2—H2b | 108.3 (5) |
C2—C1—N1 | 109.76 (2) | O1—C3—C1 | 118.30 (2) |
C2—C1—H1 | 110.3 (3) | O2—C3—C1 | 115.87 (2) |
C3—C1—N1 | 110.02 (2) | O2—C3—O1 | 125.83 (3) |
C3—C1—H1 | 106.9 (3) | | |
| | | |
N1—C1—C3—O1 | −18.19 (2) | N1—C1—C3—O2 | 162.16 (2) |
(L-Ala_23K_tonto_IAM_num)
top
Crystal data top
C3H7NO2 | Z = 4 |
Mr = 89.10 | F(000) = 192.122 |
Orthorhombic, P212121 | Dx = 1.405 Mg m−3 |
a = 5.9279 (10) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 12.2597 (17) Å | µ = 0.12 mm−1 |
c = 5.7939 (9) Å | T = 23 K |
V = 421.07 (11) Å3 | |
Data collection top
2519 measured reflections | θmax = 50.1°, θmin = 3.3° |
2519 independent reflections | h = 0→12 |
2393 reflections with I ≥ 2u(I) | k = 0→26 |
Rint = 0.0000 | l = 0→12 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | 0 constraints |
R[F2 > 2σ(F2)] = 0.019 | All H-atom parameters refined |
wR(F2) = 0.032 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.15 | (Δ/σ)max = 0.0001 |
2519 reflections | Δρmax = 0.18 e Å−3 |
118 parameters | Δρmin = −0.21 e Å−3 |
Special details top
Refinement. Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. DOI 10.1039/D0SC05526C - 2020
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fregment can be embedded in an electrostatic crystal field by employing cluster charges.
The following options were used:
SOFTWARE: ORCA
PARTITIONING: NoSpherA2
INT ACCURACY: High
METHOD: PBE
BASIS SET: def2-TZVPP
CHARGE: 0
MULTIPLICITY: 1
DATE: 2021-06-02_13-25-25 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Biso*/Beq | |
N1 | 0.64729 (4) | 0.13751 (2) | 0.18294 (5) | | |
H1a | 0.7049 (11) | 0.0606 (5) | 0.1977 (14) | | |
H1b | 0.7785 (10) | 0.1895 (5) | 0.2112 (13) | | |
H1c | 0.5832 (11) | 0.1493 (5) | 0.01595 (11) | | |
C1 | 0.46630 (4) | 0.16109 (2) | 0.35442 (5) | | |
H1 | 0.4227 (9) | 0.2474 (4) | 0.3435 (11) | | |
C2 | 0.25987 (5) | 0.09069 (2) | 0.30332 (6) | | |
H2a | 0.1922 (10) | 0.1105 (5) | 0.1313 (11) | | |
H2b | 0.1277 (10) | 0.1054 (5) | 0.4317 (12) | | |
H2c | 0.3041 (10) | 0.0044 (4) | 0.3083 (14) | | |
C3 | 0.55403 (5) | 0.14080 (2) | 0.59985 (5) | | |
O1 | 0.72675 (4) | 0.083783 (17) | 0.62427 (4) | | |
O2 | 0.44091 (4) | 0.184043 (17) | 0.76112 (4) | | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.00555 (7) | 0.00610 (7) | 0.00425 (9) | 0.00012 (6) | 0.00068 (6) | −0.00016 (6) |
H1a | 0.025 (4) | 0.027 (4) | 0.018 (5) | 0.005 (3) | 0.013 (4) | 0.003 (4) |
H1b | 0.013 (3) | 0.028 (4) | 0.022 (5) | 0.003 (3) | 0.007 (4) | 0.000 (4) |
H1c | 0.036 (4) | 0.021 (4) | 0.026 (5) | −0.009 (4) | 0.027 (4) | −0.012 (4) |
C1 | 0.00519 (8) | 0.00473 (7) | 0.00352 (9) | 0.00044 (6) | −0.00044 (7) | 0.00009 (6) |
H1 | 0.023 (3) | 0.012 (3) | 0.018 (4) | 0.008 (3) | 0.004 (3) | −0.001 (3) |
C2 | 0.00582 (9) | 0.00886 (9) | 0.00614 (10) | −0.00132 (8) | −0.00059 (8) | −0.00047 (8) |
H2a | 0.019 (4) | 0.047 (5) | 0.016 (4) | −0.010 (3) | −0.011 (3) | 0.010 (4) |
H2b | 0.011 (3) | 0.031 (4) | 0.033 (5) | −0.003 (3) | 0.008 (4) | 0.004 (4) |
H2c | 0.031 (5) | 0.016 (3) | 0.048 (6) | −0.004 (3) | 0.001 (4) | −0.005 (3) |
C3 | 0.00487 (7) | 0.00426 (7) | 0.00355 (9) | 0.00023 (7) | −0.00019 (7) | −0.00003 (6) |
O1 | 0.00668 (7) | 0.00706 (7) | 0.00592 (8) | 0.00245 (6) | −0.00064 (6) | 0.00052 (6) |
O2 | 0.00755 (7) | 0.00762 (6) | 0.00392 (8) | 0.00210 (6) | 0.00060 (6) | −0.00056 (6) |
Geometric parameters (Å, º) top
N1—H1a | 1.007 (6) | C1—C3 | 1.5344 (4) |
N1—H1b | 1.019 (6) | C2—H2a | 1.101 (6) |
N1—H1c | 1.050 (6) | C2—H2b | 1.095 (6) |
N1—C1 | 1.4906 (4) | C2—H2c | 1.090 (5) |
C1—H1 | 1.091 (4) | C3—O1 | 1.2478 (3) |
C1—C2 | 1.5264 (4) | C3—O2 | 1.2664 (3) |
| | | |
H1b—N1—H1a | 108.3 (5) | C3—C1—C2 | 111.09 (2) |
H1c—N1—H1a | 109.3 (6) | H2a—C2—C1 | 110.1 (3) |
H1c—N1—H1b | 109.8 (6) | H2b—C2—C1 | 110.4 (3) |
C1—N1—H1a | 111.7 (4) | H2b—C2—H2a | 108.5 (5) |
C1—N1—H1b | 108.8 (4) | H2c—C2—C1 | 110.5 (3) |
C1—N1—H1c | 109.1 (4) | H2c—C2—H2a | 109.0 (5) |
H1—C1—N1 | 108.7 (3) | H2c—C2—H2b | 108.3 (5) |
C2—C1—N1 | 109.76 (2) | O1—C3—C1 | 118.29 (2) |
C2—C1—H1 | 110.3 (3) | O2—C3—C1 | 115.88 (2) |
C3—C1—N1 | 110.02 (2) | O2—C3—O1 | 125.83 (3) |
C3—C1—H1 | 106.9 (3) | | |
| | | |
N1—C1—C3—O1 | −18.19 (2) | N1—C1—C3—O2 | 162.16 (2) |
(L-Ala_23K_tonto_IAM_spher)
top
Crystal data top
C3H7NO2 | Z = 4 |
Mr = 89.10 | F(000) = 192.122 |
Orthorhombic, P212121 | Dx = 1.405 Mg m−3 |
a = 5.9279 (10) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 12.2597 (17) Å | µ = 0.12 mm−1 |
c = 5.7939 (9) Å | T = 23 K |
V = 421.07 (11) Å3 | |
Data collection top
2519 measured reflections | θmax = 50.1°, θmin = 3.3° |
2519 independent reflections | h = 0→12 |
2393 reflections with I ≥ 2u(I) | k = 0→26 |
Rint = 0.0000 | l = 0→12 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | 0 constraints |
R[F2 > 2σ(F2)] = 0.027 | All H-atom parameters refined |
wR(F2) = 0.061 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
S = 2.15 | (Δ/σ)max = 0.0003 |
2519 reflections | Δρmax = 0.46 e Å−3 |
118 parameters | Δρmin = −0.28 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.64715 (8) | 0.13748 (4) | 0.18297 (9) | 0.00562 (6) | |
H1a | 0.6958 (17) | 0.0659 (11) | 0.186 (2) | 0.025 (3) | |
H1b | 0.7692 (17) | 0.1850 (9) | 0.202 (2) | 0.021 (3) | |
H1c | 0.571 (2) | 0.1479 (8) | 0.014 (3) | 0.056 (6) | |
C1 | 0.46618 (8) | 0.16103 (4) | 0.35484 (9) | 0.00493 (7) | |
H1 | 0.4249 (15) | 0.2401 (7) | 0.3429 (18) | 0.007 (2) | |
C2 | 0.25985 (9) | 0.09071 (5) | 0.30330 (11) | 0.00738 (8) | |
H2a | 0.2027 (17) | 0.1081 (8) | 0.146 (2) | 0.020 (3) | |
H2b | 0.1448 (16) | 0.1075 (8) | 0.419 (2) | 0.015 (3) | |
H2c | 0.2996 (17) | 0.0111 (8) | 0.310 (2) | 0.018 (3) | |
C3 | 0.55406 (9) | 0.14076 (4) | 0.59995 (9) | 0.00462 (6) | |
O1 | 0.72708 (7) | 0.08373 (3) | 0.62429 (8) | 0.00683 (6) | |
O2 | 0.44093 (7) | 0.18410 (3) | 0.76120 (8) | 0.00666 (6) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.00577 (14) | 0.00662 (14) | 0.00447 (16) | 0.00018 (12) | 0.00064 (12) | −0.00018 (12) |
H1a | 0.006 (6) | 0.068 (9) | 0.002 (7) | −0.009 (6) | 0.007 (5) | 0.016 (7) |
H1b | 0.009 (5) | 0.039 (7) | 0.015 (8) | 0.027 (6) | 0.012 (6) | 0.010 (6) |
H1c | 0.067 (9) | 0.000 (5) | 0.102 (15) | −0.036 (6) | 0.079 (11) | −0.028 (7) |
C1 | 0.00551 (15) | 0.00538 (14) | 0.00390 (17) | 0.00045 (12) | 0.00002 (13) | −0.00009 (12) |
H1 | 0.004 (5) | 0.015 (5) | 0.002 (6) | 0.010 (4) | 0.011 (5) | −0.004 (4) |
C2 | 0.00614 (16) | 0.00939 (16) | 0.00661 (19) | −0.00130 (15) | −0.00065 (15) | −0.00042 (15) |
H2a | 0.008 (6) | 0.024 (7) | 0.027 (9) | −0.007 (5) | −0.004 (6) | 0.001 (6) |
H2b | 0.002 (5) | 0.016 (6) | 0.028 (9) | −0.005 (5) | −0.003 (6) | 0.004 (6) |
H2c | 0.022 (7) | 0.018 (6) | 0.014 (7) | −0.011 (5) | 0.002 (6) | −0.002 (5) |
C3 | 0.00548 (14) | 0.00431 (13) | 0.00408 (17) | −0.00032 (13) | −0.00040 (13) | 0.00007 (12) |
O1 | 0.00674 (13) | 0.00691 (12) | 0.00685 (16) | 0.00218 (11) | −0.00058 (12) | 0.00067 (12) |
O2 | 0.00796 (13) | 0.00783 (12) | 0.00417 (14) | 0.00172 (11) | 0.00100 (12) | −0.00070 (11) |
Geometric parameters (Å, º) top
N1—H1a | 0.923 (13) | C1—C3 | 1.5329 (8) |
N1—H1b | 0.936 (12) | C2—H2a | 0.993 (13) |
N1—H1c | 1.085 (17) | C2—H2b | 0.978 (11) |
N1—C1 | 1.4919 (7) | C2—H2c | 1.005 (10) |
C1—H1 | 1.002 (9) | C3—O1 | 1.2493 (7) |
C1—C2 | 1.5260 (8) | C3—O2 | 1.2668 (7) |
| | | |
H1b—N1—H1a | 110.3 (8) | C3—C1—C2 | 111.23 (4) |
H1c—N1—H1a | 105.1 (9) | H2a—C2—C1 | 109.3 (6) |
H1c—N1—H1b | 111.1 (9) | H2b—C2—C1 | 107.8 (6) |
C1—N1—H1a | 113.2 (7) | H2b—C2—H2a | 110.1 (8) |
C1—N1—H1b | 110.8 (7) | H2c—C2—C1 | 110.7 (6) |
C1—N1—H1c | 106.1 (6) | H2c—C2—H2a | 108.8 (9) |
H1—C1—N1 | 108.5 (5) | H2c—C2—H2b | 110.1 (8) |
C2—C1—N1 | 109.66 (4) | O1—C3—C1 | 118.31 (5) |
C2—C1—H1 | 109.7 (5) | O2—C3—C1 | 115.81 (4) |
C3—C1—N1 | 110.04 (4) | O2—C3—O1 | 125.88 (5) |
C3—C1—H1 | 107.7 (6) | | |
| | | |
N1—C1—C3—O1 | −18.18 (5) | N1—C1—C3—O2 | 162.11 (4) |
Crystal data top
H3N | F(000) = 40.004 |
Mr = 17.03 | Dx = 0.838 Mg m−3 |
Cubic, P213 | Mo Kα radiation, λ = 0.71069 Å |
a = 5.1305 (8) Å | µ = 0.06 mm−1 |
V = 135.05 (4) Å3 | T = 160 K |
Z = 4 | |
Data collection top
1762 measured reflections | θmax = 30.0°, θmin = 5.6° |
136 independent reflections | h = −7→7 |
133 reflections with I ≥ 2u(I) | k = −5→7 |
Rint = 0.030 | l = −7→7 |
Refinement top
Refinement on F2 | 0 constraints |
Least-squares matrix: full | All H-atom parameters refined |
R[F2 > 2σ(F2)] = 0.009 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.020 | (Δ/σ)max = 0.0003 |
S = 2.24 | Δρmax = 0.04 e Å−3 |
136 reflections | Δρmin = −0.02 e Å−3 |
13 parameters | Absolute structure: Hooft, R.W.W., Straver, L.H., Spek, A.L. (2010). J. Appl. Cryst., 43, 665-668. |
0 restraints | Absolute structure parameter: 5 (2) |
Special details top
Refinement. Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. Chem. Sci. DOI 10.1039/D0SC05526C - 2021
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fragment can be embedded in an electrostatic crystal field by employing cluster charges
or modelled using implicit solvation models, depending on the software used.
The following options were used:
SOFTWARE: ORCA
PARTITIONING: NoSpherA2
INT ACCURACY: High
METHOD: PBE
BASIS SET: def2-TZVPP
CHARGE: 0
MULTIPLICITY: 1
DATE: 2021-06-02_22-18-50 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N | −0.21056 (4) | −0.21056 (4) | −0.21056 (4) | 0.03619 (17) | |
H | −0.3639 (10) | −0.2677 (12) | −0.1168 (8) | 0.0678 (11) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N | 0.03619 (17) | 0.03619 (17) | 0.03619 (17) | −0.00128 (7) | −0.00128 (7) | −0.00128 (7) |
H | 0.070 (3) | 0.068 (3) | 0.065 (3) | −0.009 (2) | 0.008 (2) | −0.008 (2) |
Geometric parameters (Å, º) top
N—H | 0.967 (5) | N—Hii | 0.967 (5) |
N—Hi | 0.967 (5) | | |
| | | |
Hii—N—H | 108.0 (3) | Hi—N—H | 108.0 (3) |
Hi—N—Hii | 108.0 (3) | | |
Symmetry codes: (i) z, x, y; (ii) y, z, x. |
Crystal data top
H3N | F(000) = 40.004 |
Mr = 17.03 | Dx = 0.838 Mg m−3 |
Cubic, P213 | Mo Kα radiation, λ = 0.71069 Å |
a = 5.1305 (8) Å | µ = 0.06 mm−1 |
V = 135.05 (4) Å3 | T = 160 K |
Z = 4 | |
Data collection top
1762 measured reflections | θmax = 30.0°, θmin = 5.6° |
136 independent reflections | h = −7→7 |
133 reflections with I ≥ 2u(I) | k = −5→7 |
Rint = 0.030 | l = −7→7 |
Refinement top
Refinement on F2 | 0 constraints |
Least-squares matrix: full | All H-atom parameters refined |
R[F2 > 2σ(F2)] = 0.009 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.020 | (Δ/σ)max = 0.0003 |
S = 2.24 | Δρmax = 0.04 e Å−3 |
136 reflections | Δρmin = −0.02 e Å−3 |
13 parameters | Absolute structure: Hooft, R.W.W., Straver, L.H., Spek, A.L. (2010). J. Appl. Cryst., 43, 665-668. |
0 restraints | Absolute structure parameter: 5 (2) |
Special details top
Refinement. Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. Chem. Sci. DOI 10.1039/D0SC05526C - 2021
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fragment can be embedded in an electrostatic crystal field by employing cluster charges
or modelled using implicit solvation models, depending on the software used.
The following options were used:
SOFTWARE: ORCA
PARTITIONING: NoSpherA2
INT ACCURACY: High
METHOD: PBE
BASIS SET: def2-TZVPP
CHARGE: 0
MULTIPLICITY: 1
DATE: 2021-06-02_22-18-50 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Biso*/Beq | |
N | −0.21065 (5) | −0.21065 (5) | −0.21065 (5) | | |
H | −0.3656 (9) | −0.2688 (10) | −0.1157 (9) | | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N | 0.03654 (19) | 0.03654 (19) | 0.03654 (19) | −0.00141 (8) | −0.00141 (8) | −0.00141 (8) |
H | 0.066 (3) | 0.071 (3) | 0.068 (3) | −0.008 (3) | 0.010 (3) | −0.012 (3) |
Geometric parameters (Å, º) top
N—H | 0.979 (5) | N—Hii | 0.979 (5) |
N—Hi | 0.979 (5) | | |
| | | |
Hii—N—H | 108.0 (3) | Hi—N—H | 108.0 (3) |
Hi—N—Hii | 108.0 (3) | | |
Symmetry codes: (i) z, x, y; (ii) y, z, x. |
Crystal data top
H3N | F(000) = 40.004 |
Mr = 17.03 | Dx = 0.838 Mg m−3 |
Cubic, P213 | Mo Kα radiation, λ = 0.71069 Å |
a = 5.1305 (8) Å | µ = 0.06 mm−1 |
V = 135.05 (4) Å3 | T = 160 K |
Z = 4 | |
Data collection top
1762 measured reflections | θmax = 30.0°, θmin = 5.6° |
136 independent reflections | h = −7→7 |
133 reflections with I ≥ 2u(I) | k = −5→7 |
Rint = 0.030 | l = −7→7 |
Refinement top
Refinement on F2 | 0 constraints |
Least-squares matrix: full | All H-atom parameters refined |
R[F2 > 2σ(F2)] = 0.009 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.019 | (Δ/σ)max = 0.0003 |
S = 2.24 | Δρmax = 0.04 e Å−3 |
136 reflections | Δρmin = −0.02 e Å−3 |
13 parameters | Absolute structure: Hooft, R.W.W., Straver, L.H., Spek, A.L. (2010). J. Appl. Cryst., 43, 665-668. |
0 restraints | Absolute structure parameter: 5 (2) |
Special details top
Refinement. Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. Chem. Sci. DOI 10.1039/D0SC05526C - 2021
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors. The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fragment can be embedded in an electrostatic crystal field by employing cluster charges
or modelled using implicit solvation models, depending on the software used.
The following options were used:
SOFTWARE: ORCA
PARTITIONING: NoSpherA2
INT ACCURACY: High
METHOD: PBE
BASIS SET: def2-TZVPP
CHARGE: 0
MULTIPLICITY: 1
DATE: 2021-06-02_22-18-50 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Biso*/Beq | |
N | −0.21064 (5) | −0.21064 (5) | −0.21064 (5) | | |
H | −0.3655 (9) | −0.2689 (10) | −0.1158 (9) | | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N | 0.03654 (18) | 0.03654 (18) | 0.03654 (18) | −0.00141 (8) | −0.00141 (8) | −0.00141 (8) |
H | 0.066 (3) | 0.071 (3) | 0.066 (2) | −0.012 (3) | 0.010 (2) | −0.008 (2) |
Geometric parameters (Å, º) top
N—H | 0.969 (5) | N—Hii | 0.969 (5) |
N—Hi | 0.969 (5) | | |
| | | |
Hii—N—H | 107.7 (3) | Hi—N—H | 107.7 (3) |
Hi—N—Hii | 107.7 (3) | | |
Symmetry codes: (i) z, x, y; (ii) y, z, x. |
Crystal data top
H3N | F(000) = 40.004 |
Mr = 17.03 | Dx = 0.838 Mg m−3 |
Cubic, P213 | Mo Kα radiation, λ = 0.71069 Å |
a = 5.1305 (8) Å | µ = 0.06 mm−1 |
V = 135.05 (4) Å3 | T = 160 K |
Z = 4 | |
Data collection top
1762 measured reflections | θmax = 30.0°, θmin = 5.6° |
136 independent reflections | h = −7→7 |
133 reflections with I ≥ 2u(I) | k = −5→7 |
Rint = 0.030 | l = −7→7 |
Refinement top
Refinement on F2 | 0 constraints |
Least-squares matrix: full | All H-atom parameters refined |
R[F2 > 2σ(F2)] = 0.013 | w = 1/[σ2(Fo2) + (0.P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.032 | (Δ/σ)max = −0.001 |
S = 3.65 | Δρmax = 0.04 e Å−3 |
136 reflections | Δρmin = −0.03 e Å−3 |
13 parameters | Absolute structure: Hooft, R.W.W., Straver, L.H., Spek, A.L. (2010). J. Appl. Cryst., 43, 665-668. |
0 restraints | Absolute structure parameter: 5 (2) |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N | −0.21005 (9) | −0.21005 (9) | −0.21005 (9) | 0.0354 (3) | |
H | −0.3383 (17) | −0.2467 (18) | −0.1341 (12) | 0.0568 (19) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N | 0.0354 (3) | 0.0354 (3) | 0.0354 (3) | 0.00004 (13) | 0.00004 (13) | 0.00004 (13) |
H | 0.076 (4) | 0.051 (4) | 0.044 (4) | 0.030 (4) | −0.006 (4) | −0.001 (3) |
Geometric parameters (Å, º) top
N—H | 0.787 (9) | N—Hii | 0.787 (9) |
N—Hi | 0.787 (9) | | |
| | | |
Hii—N—H | 109.4 (5) | Hi—N—H | 109.4 (5) |
Hi—N—Hii | 109.4 (5) | | |
Symmetry codes: (i) z, x, y; (ii) y, z, x. |