[²H₃]Sarcosine

The crystal structure of [²H₃]sarcosine or meth­yl[²H₃]ammonioacetate, CD₃NH₂⁺CH₂COO⁻ or C₃H₄D₃NO₂, was solved at room temperature. It is isostructural with nondeuterated sarcosine. The amino acid mol­ecules exist as zwitterions. Each mol­ecule is connected to four neighbouring mol­ecules through N—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 286 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.028
• wR factor = 0.075
• Data-to-parameter ratio = 9.5

checkCIF/PLATON results

No syntax errors found



Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           29.41
           From the CIF: _reflns_number_total                734
           Count of symmetry unique reflns          767
           Completeness (_total/calc)             95.70%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   0 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

We determined the crystal structure of sarcosine-d3 (methyl-d3). It is isostructural with sarcosine – P2₁2₁2₁ (Mostad & Natarajan, 1989). The sarcosine molecules are in the form of zwitterions creating helices down the a, b and c axes through the network of N—H···O hydrogen bonds. There are also weak C(3)—D(5)···O(2) interactions with C(3)···O(2) = 3.355 (1) Å and a C(3)—D(5)···O(2) angle of 178.60 (1) °. Figure 1 shows the molecule of the sarcosine. Figure 2 shows the packing of sarcosine-d3 molecules in the crystal as seen down the b axis. Vibrational spectroscopy measurements corroborate the presence of the deuterated methyl group (–CD₃).

Related literature

Undeuterated sarcosine was reported by Mostad & Natarajan (1989).

S2. Experimental

The single crystals of sarcosine-d3 were obtained from Aldrich (99 atom % D).

S3. Refinement

Positions of all hydrogen and deutrium atoms were taken from difference Fourier maps. They were refiened with isotropic displacement parameters correlated with the anisotropic displacement parameters of the atoms to which they were bonded [U_iso(H) = 1.2U_eq(C)]. Friedel pairs were merged prior to refinement

Computing details

Data collection: CrysAlis (Mayer, 2006); cell refinement: CrysAlis (Mayer, 2006); data reduction: CrysAlis (Mayer, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Diamond (Brandenburg, 2005); software used to prepare material for publication: publCIF (Westrip, 2007).

Figures

	Fig. 1. The molecule of sarcosine-d3.
	Fig. 2. The packing of sarcosine-d3 molecules in the crystal as seen down the b axis. The dashed lines represent the hydrogen bonds.

methyl[²H₃]ammoniobenzoate

Crystal data

C3H4D3NO2	F(000) = 192
Mr = 92.11	Dx = 1.323 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 734 reflections
a = 6.7998 (13) Å	θ = 3.8–29.4°
b = 7.9208 (16) Å	µ = 0.11 mm^−1
c = 8.5874 (18) Å	T = 286 K
V = 462.52 (16) Å^3	Prism, colourless
Z = 4	0.15 × 0.1 × 0.1 mm

Data collection

Kuma KM-4 diffractometer with CCD area detector	608 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.030
Graphite monochromator	θmax = 29.4°, θmin = 3.8°
Detector resolution: 1024x1024 with blocks 2x2, 33.133pixel/mm pixels mm^-1	h = −8→9
ω–scan	k = −9→10
5729 measured reflections	l = −11→11
734 independent reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Only H-atom coordinates refined
R[F^2 > 2σ(F^2)] = 0.028	w = 1/[σ^2(Fo^2) + (0.053P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.075	(Δ/σ)max = 0.002
S = 0.96	Δρmax = 0.12 e Å^−3
734 reflections	Δρmin = −0.13 e Å^−3
77 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.077 (15)
Primary atom site location: structure-invariant direct methods

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.21502 (16)	0.18017 (13)	0.32862 (12)	0.0404 (3)
O2	0.2292 (2)	−0.09212 (14)	0.26347 (14)	0.0525 (4)
N1	−0.01173 (18)	−0.06244 (15)	0.01915 (14)	0.0293 (3)
H4	−0.046 (3)	−0.141 (2)	0.084 (2)	0.035*
H3	0.092 (2)	−0.102 (2)	−0.036 (2)	0.035*
C1	0.1734 (2)	0.05453 (18)	0.24312 (17)	0.0314 (3)
C2	0.0441 (2)	0.09257 (18)	0.10361 (17)	0.0320 (3)
H2	−0.074 (3)	0.146 (2)	0.135 (2)	0.038*
H1	0.104 (2)	0.163 (2)	0.030 (2)	0.038*
C3	−0.1714 (3)	−0.0354 (2)	−0.0949 (2)	0.0467 (4)
D5	−0.199 (3)	−0.146 (3)	−0.147 (3)	0.056*
D6	−0.134 (3)	0.056 (3)	−0.170 (2)	0.056*
D7	−0.285 (3)	0.003 (2)	−0.043 (2)	0.056*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0485 (6)	0.0358 (6)	0.0370 (6)	0.0047 (5)	−0.0085 (5)	−0.0113 (5)
O2	0.0736 (8)	0.0307 (6)	0.0532 (7)	0.0042 (5)	−0.0275 (6)	−0.0011 (5)
N1	0.0361 (6)	0.0255 (6)	0.0263 (6)	−0.0012 (5)	−0.0016 (5)	0.0013 (5)
C1	0.0352 (6)	0.0307 (7)	0.0282 (7)	−0.0019 (6)	0.0001 (6)	−0.0012 (6)
C2	0.0417 (7)	0.0256 (7)	0.0289 (7)	0.0003 (6)	0.0001 (6)	−0.0011 (6)
C3	0.0532 (10)	0.0388 (9)	0.0481 (10)	−0.0016 (8)	−0.0219 (8)	0.0011 (8)

Geometric parameters (Å, º)

O1—C1	1.2687 (17)	C1—C2	1.516 (2)
O2—C1	1.2343 (18)	C2—H2	0.949 (18)
N1—C2	1.4757 (18)	C2—H1	0.931 (18)
N1—C3	1.4782 (19)	C3—D5	1.00 (2)
N1—H4	0.867 (18)	C3—D6	1.00 (2)
N1—H3	0.905 (18)	C3—D7	0.94 (2)
C2—N1—C3	113.22 (12)	C1—C2—H2	111.1 (11)
C2—N1—H4	110.9 (11)	N1—C2—H1	106.0 (11)
C3—N1—H4	109.1 (11)	C1—C2—H1	113.5 (10)
C2—N1—H3	110.2 (11)	H2—C2—H1	106.9 (15)
C3—N1—H3	106.2 (10)	D5—C3—D6	113.5 (17)
H4—N1—H3	107.0 (16)	D5—C3—D7	109.8 (16)
O2—C1—O1	126.00 (14)	D6—C3—D7	105.7 (18)
O2—C1—C2	118.49 (12)	D5—C3—N1	107.8 (13)
O1—C1—C2	115.51 (12)	D6—C3—N1	110.2 (12)
N1—C2—C1	111.84 (11)	D7—C3—N1	109.8 (13)
N1—C2—H2	107.0 (11)
C1—C2—N1—C3	167.20 (14)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H4···O1^i	0.867 (18)	1.971 (18)	2.7886 (16)	156.9 (16)
N1—H3···O1^ii	0.905 (18)	1.860 (19)	2.7599 (17)	172.4 (15)
C3—D5···O2^iii	1.00 (2)	2.35 (2)	3.355 (2)	179 (2)

Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x+1/2, −y, z−1/2; (iii) x−1/2, −y−1/2, −z.