Literature DB >> 21579154

N-[Bis(dimethyl-amino)phosphinoyl]-2,2,2-trichloro-acetamide.

Oleksiy V Amirkhanov1, Olesia V Moroz, Kateryna O Znovjyak, Elizaveta A Trush, Tetyana Yu Sliva.   

Abstract

In the title compound, C(6)H(13)Cl(3)N(3)O(2)P or CCl(3)C(O)NHP(O)(N(CH(3))(2)), the phosphinoyl group is synclinal to the carbonyl group and acts as an acceptor for an inter-molecular N-H⋯O hydrogen bond from the amide group as the donor.

Entities:  

Year:  2010        PMID: 21579154      PMCID: PMC2979112          DOI: 10.1107/S1600536810013589

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the biological and pharmacological properties of carbacyl­amido­phosphate derivatives, see: Adams et al. (2002 ▶); Grimes et al. (2008 ▶). For structural and conformation studies of related mol­ecules, see: Gholivand et al. (2008a ▶,b ▶); Skopenko et al. (2004 ▶); Znovjyak et al. (2009a ▶,b ▶). For details of the synthesis, see: Kirsanov & Derkach (1956 ▶). For P—O bond lengths in compounds with amide substituents close to phospho­rus atoms, see: Rebrova et al. (1982 ▶).

Experimental

Crystal data

C6H13Cl3N3O2P M = 296.51 Orthorhombic, a = 15.794 (3) Å b = 15.820 (3) Å c = 9.739 (2) Å V = 2433.4 (8) Å3 Z = 8 Mo Kα radiation μ = 0.87 mm−1 T = 100 K 0.60 × 0.40 × 0.20 mm

Data collection

Oxford Diffraction Xcalibur Sapphire2 (large Be window) diffractometer Absorption correction: Gaussian (Coppens et al., 1965 ▶) T min = 0.624, T max = 0.845 35140 measured reflections 5631 independent reflections 4869 reflections with I > 2σ(I) R int = 0.032

Refinement

R[F 2 > 2σ(F 2)] = 0.030 wR(F 2) = 0.072 S = 1.15 5631 reflections 144 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.46 e Å−3 Δρmin = −0.40 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2006 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2006 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶). Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810013589/jh2144sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810013589/jh2144Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C6H13Cl3N3O2PF(000) = 1216
Mr = 296.51Dx = 1.619 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 35140 reflections
a = 15.794 (3) Åθ = 3.6–36.1°
b = 15.820 (3) ŵ = 0.87 mm1
c = 9.739 (2) ÅT = 100 K
V = 2433.4 (8) Å3Block, white
Z = 80.60 × 0.40 × 0.20 mm
Oxford Diffraction Xcalibur Sapphire2 (large Be window) diffractometer5631 independent reflections
Radiation source: Enhance (Mo) X-ray Source4869 reflections with I > 2σ(I)
graphiteRint = 0.032
Detector resolution: 8.3359 pixels mm-1θmax = 36.1°, θmin = 3.6°
ω scansh = −26→26
Absorption correction: gaussian Coppens et al. (1965)k = −25→25
Tmin = 0.624, Tmax = 0.845l = −12→15
35140 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.030Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.072H atoms treated by a mixture of independent and constrained refinement
S = 1.15w = 1/[σ2(Fo2) + (0.0336P)2 + 0.5268P] where P = (Fo2 + 2Fc2)/3
5631 reflections(Δ/σ)max = 0.001
144 parametersΔρmax = 0.46 e Å3
0 restraintsΔρmin = −0.40 e Å3
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes.
xyzUiso*/Ueq
P10.285320 (15)0.522358 (14)0.42665 (2)0.00982 (5)
C10.14518 (6)0.60952 (6)0.48883 (9)0.01181 (14)
C20.06928 (6)0.62610 (5)0.58869 (9)0.01177 (15)
Cl10.033556 (15)0.534225 (14)0.67522 (3)0.01615 (5)
Cl20.104133 (16)0.701650 (14)0.71094 (2)0.01672 (5)
Cl3−0.015884 (16)0.668869 (15)0.49346 (3)0.01985 (6)
O10.26191 (5)0.51406 (5)0.28033 (7)0.01480 (12)
O20.15469 (5)0.65692 (5)0.39188 (8)0.02050 (15)
N10.19672 (5)0.54418 (5)0.52192 (8)0.01086 (13)
N20.35444 (5)0.59761 (5)0.45503 (8)0.01341 (14)
N30.32000 (5)0.43758 (5)0.50197 (9)0.01413 (14)
C30.36307 (7)0.63290 (7)0.59326 (10)0.01877 (18)
H3A0.34490.59080.66100.028*
H3B0.32770.68350.60140.028*
H3C0.42240.64790.60990.028*
C40.37770 (7)0.65551 (6)0.34435 (11)0.01709 (17)
H4A0.34340.70700.35100.026*
H4B0.36750.62820.25560.026*
H4C0.43780.67020.35230.026*
C50.40306 (6)0.42489 (7)0.56243 (11)0.01898 (18)
H5A0.43710.47620.55070.028*
H5B0.43130.37740.51690.028*
H5C0.39690.41260.66050.028*
C60.26438 (7)0.36368 (6)0.51134 (12)0.01950 (19)
H6A0.29060.31580.46360.029*
H6B0.20980.37670.46860.029*
H6C0.25560.34910.60810.029*
H1N0.1961 (10)0.5241 (9)0.6005 (17)0.023 (4)*
U11U22U33U12U13U23
P10.01062 (9)0.01090 (9)0.00794 (9)0.00005 (7)0.00106 (7)−0.00067 (7)
C10.0138 (4)0.0121 (3)0.0095 (3)0.0019 (3)−0.0007 (3)−0.0001 (3)
C20.0123 (3)0.0113 (3)0.0117 (4)0.0021 (3)−0.0013 (3)−0.0018 (3)
Cl10.01546 (10)0.01469 (9)0.01831 (11)−0.00068 (7)0.00464 (8)0.00048 (7)
Cl20.02070 (10)0.01642 (10)0.01304 (10)−0.00216 (7)−0.00055 (8)−0.00503 (7)
Cl30.01663 (10)0.01936 (10)0.02357 (12)0.00705 (8)−0.00704 (9)−0.00265 (8)
O10.0174 (3)0.0188 (3)0.0082 (3)−0.0010 (2)0.0010 (2)−0.0026 (2)
O20.0275 (4)0.0196 (3)0.0144 (3)0.0069 (3)0.0044 (3)0.0073 (3)
N10.0119 (3)0.0131 (3)0.0076 (3)0.0026 (2)0.0013 (2)0.0018 (2)
N20.0165 (3)0.0145 (3)0.0092 (3)−0.0034 (3)0.0001 (3)−0.0002 (2)
N30.0116 (3)0.0120 (3)0.0188 (4)0.0006 (2)−0.0001 (3)0.0027 (3)
C30.0226 (5)0.0203 (4)0.0134 (4)−0.0056 (3)−0.0021 (3)−0.0032 (3)
C40.0195 (4)0.0157 (4)0.0160 (4)−0.0041 (3)0.0007 (3)0.0031 (3)
C50.0147 (4)0.0214 (4)0.0208 (5)0.0021 (3)−0.0032 (4)0.0047 (4)
C60.0177 (4)0.0124 (4)0.0284 (5)−0.0003 (3)0.0031 (4)0.0013 (3)
P1—O11.4780 (8)N3—C61.4652 (13)
P1—N31.6239 (8)C3—H3A0.9800
P1—N21.6388 (8)C3—H3B0.9800
P1—N11.7141 (8)C3—H3C0.9800
C1—O21.2151 (11)C4—H4A0.9800
C1—N11.3546 (12)C4—H4B0.9800
C1—C21.5658 (13)C4—H4C0.9800
C2—Cl31.7684 (9)C5—H5A0.9800
C2—Cl11.7723 (10)C5—H5B0.9800
C2—Cl21.7745 (9)C5—H5C0.9800
N1—H1N0.828 (16)C6—H6A0.9800
N2—C41.4614 (13)C6—H6B0.9800
N2—C31.4637 (13)C6—H6C0.9800
N3—C51.4518 (13)
O1—P1—N3116.53 (4)N2—C3—H3A109.5
O1—P1—N2113.19 (4)N2—C3—H3B109.5
N3—P1—N2107.40 (4)H3A—C3—H3B109.5
O1—P1—N1109.61 (4)N2—C3—H3C109.5
N3—P1—N1101.37 (4)H3A—C3—H3C109.5
N2—P1—N1107.83 (4)H3B—C3—H3C109.5
O2—C1—N1125.55 (9)N2—C4—H4A109.5
O2—C1—C2118.29 (8)N2—C4—H4B109.5
N1—C1—C2116.12 (8)H4A—C4—H4B109.5
C1—C2—Cl3108.70 (6)N2—C4—H4C109.5
C1—C2—Cl1113.68 (6)H4A—C4—H4C109.5
Cl3—C2—Cl1108.72 (5)H4B—C4—H4C109.5
C1—C2—Cl2106.98 (6)N3—C5—H5A109.5
Cl3—C2—Cl2109.28 (5)N3—C5—H5B109.5
Cl1—C2—Cl2109.40 (5)H5A—C5—H5B109.5
C1—N1—P1121.03 (7)N3—C5—H5C109.5
C1—N1—H1N120.3 (11)H5A—C5—H5C109.5
P1—N1—H1N115.7 (11)H5B—C5—H5C109.5
C4—N2—C3114.58 (8)N3—C6—H6A109.5
C4—N2—P1119.89 (7)N3—C6—H6B109.5
C3—N2—P1119.62 (7)H6A—C6—H6B109.5
C5—N3—C6113.97 (8)N3—C6—H6C109.5
C5—N3—P1127.02 (7)H6A—C6—H6C109.5
C6—N3—P1119.00 (7)H6B—C6—H6C109.5
O2—C1—C2—Cl332.74 (11)N3—P1—N2—C4138.23 (8)
N1—C1—C2—Cl3−149.48 (7)N1—P1—N2—C4−113.24 (8)
O2—C1—C2—Cl1153.97 (8)O1—P1—N2—C3159.66 (7)
N1—C1—C2—Cl1−28.25 (10)N3—P1—N2—C3−70.29 (8)
O2—C1—C2—Cl2−85.16 (10)N1—P1—N2—C338.24 (9)
N1—C1—C2—Cl292.62 (8)O1—P1—N3—C5118.05 (9)
O2—C1—N1—P11.02 (14)N2—P1—N3—C5−10.10 (10)
C2—C1—N1—P1−176.58 (6)N1—P1—N3—C5−123.08 (9)
O1—P1—N1—C1−53.07 (8)O1—P1—N3—C6−61.17 (9)
N3—P1—N1—C1−176.80 (7)N2—P1—N3—C6170.68 (7)
N2—P1—N1—C170.54 (8)N1—P1—N3—C657.70 (8)
O1—P1—N2—C48.18 (9)
D—H···AD—HH···AD···AD—H···A
N1—H1N···O1i0.828 (16)1.968 (16)2.7586 (11)159.3 (16)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1N⋯O1i0.828 (16)1.968 (16)2.7586 (11)159.3 (16)

Symmetry code: (i) .

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Authors:  Kateryna O Znovjyak; Vladimir A Ovchynnikov; Tetyana Yu Sliva; Svitlana V Shishkina; Vladimir M Amirkhanov
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-10-23

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4.  Novel acyl phosphate mimics that target PlsY, an essential acyltransferase in gram-positive bacteria.

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