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Three complete neutron diffraction datasets have been collected for deuterated malonic acid single crystals, DOOC(CD2)COOD, above (153 K), just below (56 K) and further below (50 K) the low-temperature phase transition (Tc = 57 K). The structural details obtained for this transition, studied previously solely by spectroscopic and calorimetric techniques, clearly establish its first-order nature. At 153 K, the space group is P\bar 1, Z = 2, Z′ = 1. The molecules are packed as linear chains linked end-to-end by asymmetric hydrogen bonds so that the carboxyl groups form cyclic dimers. The deuterons in the carboxyl links are ordered. Neighboring chains are cross-linked through C—D...O hydrogen bonds. Upon cooling through the transition the cell doubles along the a axis. Molecules which are equivalent by symmetry above Tc become independent below Tc owing to conformational changes in alternate chains. At 50 K, the space group is P\bar 1, Z = 4, Z′ = 2. Thermal motion analysis, using for all three temperatures the same segmented rigid-body model, reveals a large torsional motion around the one COOD group associated with the conformational change. Refinements were carried out on all three datasets with an anharmonic structural model, including higher-order displacement tensors (Gram–Charlier expansion up to fourth order). Only atoms involved in torsional motion exhibit a significant anharmonic component which increases with temperature.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768108000268/bk5069sup1.cif
Contains datablocks 50K, 56K, 153K

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108768108000268/bk506950Ksup2.hkl
Contains datablock 50K

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108768108000268/bk506956Ksup3.hkl
Contains datablock 56K

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108768108000268/bk5069153Ksup4.hkl
Contains datablock 153K

pdf

Portable Document Format (PDF) file https://doi.org/10.1107/S0108768108000268/bk5069sup5.pdf
Supplementary material

CCDC references: 685159; 685160; 685161

Computing details top

Program(s) used to refine structure: UPALS(Lundgren,82)&NOOT(Craven et al.,91) for (50K); UPALS (Lundgren,82)& NOOT(Craven et al.,91) for (56K); UPALS(Lundgren,'82)& NOOT(Craven et al.,91) for 153K. For all compounds, molecular graphics: DIAMOND (Brandenburg, 2006).

Figures top
[Figure 1]
[Figure 2]
[Figure 3]
(50K) top
Crystal data top
C3D4O4Z = 4
Mr = 108.03Dx = 1.758 Mg m3
Triclinic, P1Neutron radiation, λ = 1.1588 Å
a = 10.663 (4) ÅCell parameters from 32 reflections
b = 5.142 (2) Åθ = 29–35°
c = 11.234 (2) ŵ = 0.02 mm1
α = 103.39 (3)°T = 50 K
β = 136.81 (2)°Prism, colourless
γ = 85.19 (3)°3.0 × 2.4 × 2.0 mm
V = 406.8 (3) Å3
Data collection top
Four-circle
diffractometers H6S
2307 independent reflections
Radiation source: steady-state reactorRint = 0.019
Ge 022 monochromatorθmax = 54.2°, θmin = 1.8°
θ–2θ scansh = 1414
Absorption correction: analytical
Templeton & Templeton, 1973
k = 77
Tmin = 0.95, Tmax = 0.97l = 1515
2653 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: full w = 1/[s2(Fo2) + (0.02(Fo2)2 + 0.05]
wR(F2) = 0.052
S = 1.53Δρmax = 0.27 e Å3
2300 reflectionsΔρmin = 0.40 e Å3
208 parametersExtinction correction: Becker & Coppens
0 restraintsExtinction coefficient: 0.102 (2)
Primary atom site location: structure-invariant direct methods
Crystal data top
C3D4O4γ = 85.19 (3)°
Mr = 108.03V = 406.8 (3) Å3
Triclinic, P1Z = 4
a = 10.663 (4) ÅNeutron radiation, λ = 1.1588 Å
b = 5.142 (2) ŵ = 0.02 mm1
c = 11.234 (2) ÅT = 50 K
α = 103.39 (3)°3.0 × 2.4 × 2.0 mm
β = 136.81 (2)°
Data collection top
Four-circle
diffractometers H6S
2653 measured reflections
Absorption correction: analytical
Templeton & Templeton, 1973
2307 independent reflections
Tmin = 0.95, Tmax = 0.97Rint = 0.019
Refinement top
wR(F2) = 0.0520 restraints
S = 1.53Δρmax = 0.27 e Å3
2300 reflectionsΔρmin = 0.40 e Å3
208 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C0A0.03930 (9)0.11744 (12)0.23688 (8)0.0148 (2)
C1A0.03043 (8)0.29771 (12)0.35716 (8)0.0111 (2)
C2A0.01821 (8)0.27417 (12)0.12644 (8)0.0122 (2)
O11A0.03285 (10)0.54168 (14)0.37702 (9)0.0169 (2)
O12A0.02100 (10)0.16141 (14)0.43609 (10)0.0218 (2)
O21A0.14782 (10)0.35536 (17)0.16073 (11)0.0318 (2)
O22A0.15367 (10)0.31321 (16)0.01041 (10)0.0236 (2)
D12A0.01040 (13)0.28907 (17)0.51169 (12)0.0334 (2)
D21A0.15710 (12)0.43044 (18)0.07171 (12)0.0336 (2)
D01A0.17288 (13)0.04118 (19)0.32179 (12)0.0487 (2)
D02A0.07034 (13)0.05104 (17)0.15137 (12)0.0314 (2)
C0B0.55989 (9)0.12874 (12)0.25322 (8)0.0142 (2)
C1B0.54465 (8)0.30473 (12)0.36932 (8)0.0119 (2)
C2B0.53347 (8)0.28585 (12)0.13977 (8)0.0113 (2)
O11B0.52689 (10)0.54377 (14)0.37533 (9)0.0192 (2)
O12B0.55247 (11)0.17081 (14)0.46038 (10)0.0239 (2)
O21B0.65638 (10)0.44400 (15)0.19758 (10)0.0213 (2)
O22B0.36557 (10)0.23937 (15)0.02523 (10)0.0186 (2)
D12B0.52762 (12)0.28434 (17)0.52534 (12)0.0408 (2)
D21B0.35396 (12)0.35973 (18)0.09028 (12)0.0331 (2)
D01B0.69712 (13)0.06327 (18)0.34140 (12)0.0488 (2)
D02B0.45644 (17)0.04789 (17)0.17098 (12)0.0248 (2)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C0A0.0091 (3)0.0058 (2)0.0074 (2)0.0015 (2)0.0071 (2)0.0016 (2)
C1A0.0067 (2)0.0051 (2)0.0057 (2)0.0004 (2)0.0053 (2)0.0010 (2)
C2A0.0065 (3)0.0067 (2)0.0057 (2)0.0010 (2)0.0050 (2)0.0013 (2)
O11A0.0096 (3)0.0052 (3)0.0077 (3)0.0009 (2)0.0072 (3)0.0010 (2)
O12A0.0140 (3)0.0057 (3)0.0097 (3)0.0016 (2)0.0105 (3)0.0021 (2)
O21A0.0076 (3)0.0184 (3)0.0120 (3)0.0029 (2)0.0072 (3)0.0089 (3)
O22A0.0072 (3)0.0143 (3)0.0087 (3)0.0004 (2)0.0051 (3)0.0052 (2)
D12A0.0219 (5)0.0134 (4)0.0167 (4)0.0019 (3)0.0168 (4)0.0020 (3)
D21A0.0157 (4)0.0210 (5)0.0156 (5)0.0033 (3)0.0109 (4)0.0094 (3)
D01A0.0181 (5)0.0207 (5)0.0192 (5)0.0105 (3)0.0150 (4)0.0108 (3)
D02A0.0222 (5)0.0121 (4)0.0175 (5)0.0053 (3)0.0153 (4)0.0019 (3)
C0B0.0083 (2)0.0061 (2)0.0063 (2)0.0014 (2)0.0060 (2)0.0015 (2)
C1B0.0065 (2)0.0056 (2)0.0057 (2)0.0009 (2)0.0051 (2)0.0012 (2)
C2B0.0069 (2)0.0063 (2)0.0060 (2)0.0005 (2)0.0055 (2)0.0010 (2)
O11B0.0102 (3)0.0058 (3)0.0087 (3)0.0017 (2)0.0080 (3)0.0019 (2)
O12B0.0145 (3)0.0067 (3)0.0110 (3)0.0033 (2)0.0116 (3)0.0036 (2)
O21B0.0071 (3)0.0128 (3)0.0079 (3)0.0003 (2)0.0048 (2)0.0038 (2)
O22B0.0076 (3)0.0119 (3)0.0070 (3)0.0013 (2)0.0045 (3)0.0027 (2)
D12B0.0211 (5)0.0151 (4)0.0167 (4)0.0039 (3)0.0165 (4)0.0041 (3)
D21B0.0157 (4)0.0201 (5)0.0130 (4)0.0006 (3)0.0095 (4)0.0070 (3)
D01B0.0181 (5)0.0212 (5)0.0187 (5)0.0093 (3)0.0146 (4)0.0097 (3)
D02B0.0229 (5)0.0120 (4)0.0173 (5)0.0046 (3)0.0155 (4)0.0010 (3)
(56K) top
Crystal data top
C3D4O4Z = 4
Mr = 108.03Dx = 1.747 Mg m3
Triclinic, P1Neutron radiation, λ = 1.0411 Å
a = 10.675 (1) ÅCell parameters from 32 reflections
b = 5.152 (1) Åθ = 29–35°
c = 11.238 (1) ŵ = 0.02 mm1
α = 103.35 (1)°T = 56 K
β = 136.68 (1)°Prism, colourless
γ = 85.07 (1)°3.0 × 2.4 × 2.0 mm
V = 409.45 (13) Å3
Data collection top
Four-circle
diffractometers H6M
3203 independent reflections
Radiation source: steady-state reactorRint = 0.022
Be 002 monochromatorθmax = 55.3°, θmin = 1.8°
θ–2θ scansh = 1414
Absorption correction: analytical
Templeton & Templeton, 1973
k = 77
Tmin = 0.95, Tmax = 0.97l = 1515
4641 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: full w = 1/[s2(Fo2) + (0.02(Fo2))2]
wR(F2) = 0.049
S = 1.02Δρmax = 0.45 e Å3
3205 reflectionsΔρmin = 0.50 e Å3
208 parametersExtinction correction: Becker & Coppens
0 restraintsExtinction coefficient: 0.103 (3)
Primary atom site location: structure-invariant direct methods
Crystal data top
C3D4O4γ = 85.07 (1)°
Mr = 108.03V = 409.45 (13) Å3
Triclinic, P1Z = 4
a = 10.675 (1) ÅNeutron radiation, λ = 1.0411 Å
b = 5.152 (1) ŵ = 0.02 mm1
c = 11.238 (1) ÅT = 56 K
α = 103.35 (1)°3.0 × 2.4 × 2.0 mm
β = 136.68 (1)°
Data collection top
Four-circle
diffractometers H6M
4641 measured reflections
Absorption correction: analytical
Templeton & Templeton, 1973
3203 independent reflections
Tmin = 0.95, Tmax = 0.97Rint = 0.022
Refinement top
wR(F2) = 0.0490 restraints
S = 1.02Δρmax = 0.45 e Å3
3205 reflectionsΔρmin = 0.50 e Å3
208 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C0A0.04205 (7)0.11896 (9)0.23879 (6)0.0194 (3)
C1A0.03183 (6)0.29815 (9)0.35818 (6)0.0138 (2)
C2A0.02027 (6)0.27620 (9)0.12820 (6)0.0165 (2)
O11A0.03222 (8)0.54172 (11)0.37671 (7)0.0188 (3)
O12A0.02349 (8)0.16217 (11)0.43784 (8)0.0233 (4)
O21A0.15011 (8)0.36856 (15)0.16683 (9)0.0406 (7)
O22A0.15193 (8)0.30361 (14)0.01291 (8)0.0231 (4)
D12A0.01138 (10)0.28128 (14)0.51244 (9)0.0360 (5)
D21A0.15632 (10)0.42136 (16)0.07479 (10)0.0391 (6)
D01A0.17582 (11)0.04376 (16)0.32382 (10)0.0533 (8)
D02A0.06682 (11)0.05039 (14)0.15360 (10)0.0295 (6)
C0B0.55955 (7)0.12864 (9)0.25266 (6)0.0168 (2)
C1B0.54391 (6)0.30411 (9)0.36861 (6)0.0154 (2)
C2B0.53307 (6)0.28594 (9)0.13935 (6)0.0135 (2)
O11B0.52746 (8)0.54355 (11)0.37560 (7)0.0228 (3)
O12B0.54962 (8)0.16994 (11)0.45802 (8)0.0284 (4)
O21B0.65628 (8)0.43881 (12)0.19565 (8)0.0169 (3)
O22B0.36412 (8)0.24381 (12)0.02455 (7)0.0148 (2)
D12B0.52587 (10)0.28417 (14)0.52391 (10)0.0413 (7)
D21B0.35296 (10)0.36400 (10)0.08948 (9)0.0308 (5)
D01B0.69645 (10)0.06306 (15)0.34061 (10)0.0454 (7)
D02B0.45652 (11)0.04779 (14)0.17057 (10)0.0272 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C0A0.0125 (2)0.0079 (2)0.0092 (2)0.0021 (2)0.0092 (2)0.0030 (1)
C1A0.0087 (2)0.0071 (2)0.0068 (2)0.0009 (1)0.0063 (1)0.0023 (1)
C2A0.0097 (2)0.0091 (2)0.0077 (2)0.0015 (1)0.0072 (2)0.0010 (2)
O11A0.0125 (2)0.0073 (2)0.0098 (2)0.0014 (2)0.0094 (2)0.0027 (2)
O12A0.0161 (2)0.0077 (2)0.0109 (2)0.0022 (2)0.0118 (2)0.0036 (2)
O21A0.0102 (2)0.0290 (3)0.0176 (3)0.0058 (2)0.0101 (2)0.0166 (2)
O22A0.0096 (2)0.0214 (3)0.0106 (2)0.0004 (2)0.0056 (2)0.0086 (2)
D12A0.0244 (4)0.0155 (3)0.0181 (3)0.0028 (2)0.0183 (3)0.0040 (2)
D21A0.0176 (3)0.0271 (4)0.0173 (3)0.0031 (2)0.0117 (3)0.0128 (3)
D01A0.0233 (4)0.0244 (4)0.0224 (4)0.0125 (2)0.0187 (3)0.0134 (3)
D02A0.0283 (4)0.0152 (3)0.0198 (4)0.0054 (2)0.0186 (3)0.0007 (2)
C0B0.0113 (2)0.0077 (2)0.0082 (2)0.0013 (1)0.0081 (2)0.0023 (1)
C1B0.0088 (2)0.0079 (2)0.0073 (2)0.0015 (1)0.0066 (2)0.0030 (1)
C2B0.0085 (2)0.0087 (2)0.0066 (2)0.0004 (1)0.0060 (2)0.0021 (1)
O11B0.0139 (2)0.0080 (2)0.0115 (2)0.0026 (2)0.0110 (2)0.0039 (2)
O12B0.0171 (2)0.0090 (2)0.0130 (2)0.0041 (2)0.0134 (2)0.0055 (2)
O21B0.0087 (2)0.0150 (2)0.0084 (2)0.0010 (2)0.0055 (2)0.0048 (2)
O22B0.0094 (2)0.0133 (2)0.0069 (2)0.0013 (2)0.0049 (2)0.0038 (2)
D12B0.0252 (4)0.0171 (3)0.0197 (3)0.0052 (2)0.0196 (3)0.0063 (2)
D21B0.0179 (3)0.0217 (4)0.0143 (3)0.0008 (2)0.0107 (3)0.0079 (2)
D01B0.0198 (3)0.0233 (4)0.0199 (3)0.0098 (2)0.0156 (3)0.0111 (2)
D02B0.0252 (4)0.0144 (3)0.0186 (3)0.0050 (2)0.0166 (3)0.0000 (2)
(153K) top
Crystal data top
C3D4O4Z = 2
Mr = 108.03Dx = 1.733 Mg m3
Triclinic, P1Neutron radiation, λ = 1.1588 Å
a = 5.333 (2) ÅCell parameters from 32 reflections
b = 5.158 (2) Åθ = 29–35°
c = 11.250 (2) ŵ = 0.02 mm1
α = 103.33 (3)°T = 153 K
β = 136.40 (2)°Prism, colourless
γ = 84.76 (3)°3.0 × 2.4 × 2.0 mm
V = 206.34 (15) Å3
Data collection top
Four-circle
diffractometers H6S
1169 independent reflections
Radiation source: steady-state reactorRint = 0.011
Ge 022 monochromatorθmax = 54.2°, θmin = 1.8°
θ–2θ scansh = 77
Absorption correction: analytical
Templeton & Templeton, 1973
k = 77
Tmin = 0.95, Tmax = 0.97l = 1515
1345 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: full w = 1/[σ2(Fo2) + (0.020 (Fo2))2 + 514]
wR(F2) = 0.040
S = 1.04Δρmax = 0.53 e Å3
1177 reflectionsΔρmin = 0.60 e Å3
105 parametersExtinction correction: Becker & Coppens
0 restraintsExtinction coefficient: 0.125 (3)
Primary atom site location: structure-invariant direct methods
Crystal data top
C3D4O4γ = 84.76 (3)°
Mr = 108.03V = 206.34 (15) Å3
Triclinic, P1Z = 2
a = 5.333 (2) ÅNeutron radiation, λ = 1.1588 Å
b = 5.158 (2) ŵ = 0.02 mm1
c = 11.250 (2) ÅT = 153 K
α = 103.33 (3)°3.0 × 2.4 × 2.0 mm
β = 136.40 (2)°
Data collection top
Four-circle
diffractometers H6S
1345 measured reflections
Absorption correction: analytical
Templeton & Templeton, 1973
1169 independent reflections
Tmin = 0.95, Tmax = 0.97Rint = 0.011
Refinement top
wR(F2) = 0.0400 restraints
S = 1.04Δρmax = 0.53 e Å3
1177 reflectionsΔρmin = 0.60 e Å3
105 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C00.60455 (14)0.12563 (10)0.24685 (7)0.0309 (5)
C10.57591 (13)0.30175 (10)0.36341 (6)0.0247 (4)
C20.55587 (14)0.28324 (10)0.13513 (7)0.0255 (4)
O110.55832 (17)0.54299 (12)0.37553 (8)0.0362 (6)
O120.5723 (5)0.1654 (4)0.4458 (3)0.0531 (8)
O210.8066 (5)0.4133 (4)0.1845 (3)0.0436 (7)
O220.2170 (5)0.2676 (5)0.0190 (3)0.0343 (6)
D120.5371 (2)0.28112 (18)0.51686 (12)0.0552 (8)
D210.1988 (2)0.3852 (2)0.08380 (13)0.0451 (7)
D010.8758 (2)0.05620 (15)0.33327 (10)0.0742 (10)
D020.3974 (2)0.04627 (14)0.16512 (10)0.0431 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C00.0195 (2)0.0123 (2)0.0155 (2)0.0034 (2)0.0145 (2)0.0043 (2)
C10.0136 (2)0.0114 (2)0.0126 (2)0.0025 (2)0.0106 (2)0.0043 (2)
C20.0152 (2)0.0136 (2)0.0126 (2)0.0017 (2)0.0112 (2)0.0035 (2)
O110.0207 (3)0.0115 (2)0.0184 (3)0.0035 (2)0.0167 (3)0.0047 (2)
O120.0285 (3)0.0131 (3)0.0215 (3)0.0055 (2)0.0220 (3)0.0070 (2)
O210.0145 (3)0.0379 (4)0.0210 (3)0.0019 (3)0.0110 (2)0.0171 (3)
O220.0172 (3)0.0313 (3)0.0154 (3)0.0051 (3)0.0082 (3)0.0094 (3)
D120.0337 (5)0.0204 (4)0.0268 (4)0.0055 (3)0.0258 (4)0.0076 (3)
D210.0239 (4)0.0374 (5)0.0211 (4)0.0013 (3)0.0135 (3)0.0123 (3)
D010.0318 (5)0.0314 (4)0.0325 (4)0.0177 (3)0.0266 (4)0.0188 (3)
D020.0410 (5)0.0197 (4)0.0285 (4)0.0066 (3)0.0269 (4)0.0006 (3)

Experimental details

(50K)(56K)(153K)
Crystal data
Chemical formulaC3D4O4C3D4O4C3D4O4
Mr108.03108.03108.03
Crystal system, space groupTriclinic, P1Triclinic, P1Triclinic, P1
Temperature (K)5056153
a, b, c (Å)10.663 (4), 5.142 (2), 11.234 (2)10.675 (1), 5.152 (1), 11.238 (1)5.333 (2), 5.158 (2), 11.250 (2)
α, β, γ (°)103.39 (3), 136.81 (2), 85.19 (3)103.35 (1), 136.68 (1), 85.07 (1)103.33 (3), 136.40 (2), 84.76 (3)
V3)406.8 (3)409.45 (13)206.34 (15)
Z442
Radiation typeNeutron, λ = 1.1588 ÅNeutron, λ = 1.0411 ÅNeutron, λ = 1.1588 Å
µ (mm1)0.020.020.02
Crystal size (mm)3.0 × 2.4 × 2.03.0 × 2.4 × 2.03.0 × 2.4 × 2.0
Data collection
DiffractometerFour-circle
diffractometers H6S
Four-circle
diffractometers H6M
Four-circle
diffractometers H6S
Absorption correctionAnalytical
Templeton & Templeton, 1973
Analytical
Templeton & Templeton, 1973
Analytical
Templeton & Templeton, 1973
Tmin, Tmax0.95, 0.970.95, 0.970.95, 0.97
No. of measured, independent and
observed reflections
2653, 2307, ? [I > 2σ(I)]4641, 3203, ? [ > 0*σ(I)]1345, 1169, ? [ > 0*σ(I)]
Rint0.0190.0220.011
(sin θ/λ)max1)0.7000.7900.700
Refinement
R[F2 > 2σ(F2)], wR(F2), S ?, 0.052, 1.53 ?, 0.049, 1.02 ?, 0.040, 1.04
No. of reflections230032051177
No. of parameters208208105
Δρmax, Δρmin (e Å3)0.27, 0.400.45, 0.500.53, 0.60

Computer programs: UPALS(Lundgren,82)&NOOT(Craven et al.,91), UPALS (Lundgren,82)& NOOT(Craven et al.,91), UPALS(Lundgren,'82)& NOOT(Craven et al.,91), DIAMOND (Brandenburg, 2006).

 

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