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Article

The X-Ray Crystal Structures of Primary Aryl Substituted Selenoamides

School of Chemistry, University of St Andrews, St Andrews, Fife, Scotland, KY16 9ST, UK
*
Author to whom correspondence should be addressed.
Molecules 2009, 14(2), 884-892; https://doi.org/10.3390/molecules14020884
Submission received: 18 December 2008 / Revised: 13 February 2009 / Accepted: 19 February 2009 / Published: 23 February 2009
(This article belongs to the Special Issue Selenium and Tellurium Chemistry)

Abstract

:
The X-ray structures of 12 primary selenoamides are reported. Metric parameters are provided, together with an illustration of the range of hydrogen bonding motifs.

Graphical Abstract

Introduction

Selenium is an essential element for life; e.g, selenocysteine is recognised as the 21st amino acid and the importance of selenium containing enzymes in redox processes has is now recognized [1,2,3]. Many organoselenium compounds have been studied as biological models that simulate catalytic functions demonstrated by natural enzymes [4,5,6,7,8,9,10,11,12,13,14]. For example, ebselen (I, Figure 1) acts as a glutathione peroxidase (GPx) mimic and as a scavenger of peroxinitrite and the activity of the sulfur analogue of ebselen was 15-fold lower than that of ebselen [5,6]. Selenazofurin (II) has been reported to be a potent inhibitor of phlebovirus infections [10]. Selenophenfurin (III) exhibits antiproliferative and inosine 5-monophosphate dehydrogenase (IMPDH)-inhibition activity. Leukotrienes such as leukotriene B4 (LTB4) are important mediators of asthma, allergy, arthritis, psoriasis, and inflammatory bowel disease [11,12]. Galetet al. showed that benzoselenazolinones of type IV and the corresponding diselenides V dramatically decrease the formation of LTB4 [13]. Phenylseleno-substituted pyrimidines of type VI exhibit significant inhibitory properties on Urd Pase and TMS. Se-methyl selenocysteine (VII) was found to be an antitumor agent, and it has been shown that β-elimination reaction is important for this activity [14].
Figure 1. Some biologically active selenium compounds.
Figure 1. Some biologically active selenium compounds.
Molecules 14 00884 g001
We have a long term interest in selenium chemistry [15,16,17,18,19,20]. Woollins reagent (WR, 2,4-bis(phenyl)-1,3-diselenadiphosphetane-2,4-diselenide, [PhP(Se)(µ-Se)]2), which is isostructural with the thionation agent [(p-MeOC6H4)P(S)(µ-S)]2 (Lawesson’s reagent), and may be obtained readily from PhPCl2, Na2Se and Se [21], is an excellent selenation reagent for converting a range of unsaturated organic substrates into unusual phosphorus containing heterocycles [22,23,24,25,26,27,28,29,30,31]. We have recently reported the use of WR for organic transformations and for the facile synthesis of primary arylselenoamides from WR and ArCN [32]. Although the X-ray crystal structures of some tertiary and secondary selenoamides have been documented [33,34,35,36,37,38,39], surprisingly, no structural information has been published on primary arylselenoamides ArC(Se)NH2. We here provide a comparative study of a range of these systems.

Results and Discussion

Selected metric parameters for compounds A - L are given in Table 1. The C=Se bond lengths range from 1.822(5) to 1.856(4) Å whilst the C-N bond lengths are in the range 1.270(7) to 1.324(8) Å. This compares with literature values from the Cambridge Database for amide C-Se distances of 1.787-1.885 and C-N of 1.29-1.34 Å. The amide functionality is not particularly coplanar with the aryl backbone, with the selenium atom lying up to 1.406 Å from the aryl ring mean plane with the C(7)-N(7)-Se(7) plane being up to 87o from the aryl mean plane in this case. This maximum deviation from coplanarity may be a function of the presence of two ortho chlorine substituents in compound L causing repulsion. However, it is interesting to note that in compound F the two independent molecules have quite different degrees of coplanarity for the selenoamide functional group and the aryl ring suggesting that there is little electronic reason for coplanarity.
Figure 2. Examples of H-bonding motifs. (a) 1 ladder (b) 2 linked dimer (c) 7 Herring-bone dimers (d) 6 tetrameric sheets (e) 10 Chains (f) 9 Helical Chains.
Figure 2. Examples of H-bonding motifs. (a) 1 ladder (b) 2 linked dimer (c) 7 Herring-bone dimers (d) 6 tetrameric sheets (e) 10 Chains (f) 9 Helical Chains.
Molecules 14 00884 g002
Although hydrogen bonding is well understood for N-H···O and N-H···S systems, there is less data available for N-H···Se systems. We have previously noted that Ph2P(Se)NHP(Se)Ph2 forms dimers via N-H···Se hydrogen bonds (Se···N 3.19, Se···H 2.52 Å) [40] and it is interesting to note the range of motifs that we have observed in compounds AL (Figure 2). We have broadly classified the pattern of hydrogen bonding in compounds A - L and give selected parameters in Table 2 and provide illustrative examples in Figure 1. It is clear that N-H···Se hydrogen bonding is an important feature of the solid state packing of these molecules and may be a significant influence in biological systems.
Table 1. Selected 77Se NMR data, bond lengths (Å) and angles (o) (Rows containing multiple entries are a.consequence of the presence of more than one independent molecule in the asymmetric unit).
Table 1. Selected 77Se NMR data, bond lengths (Å) and angles (o) (Rows containing multiple entries are a.consequence of the presence of more than one independent molecule in the asymmetric unit).
δSe (ppm*)C=Se (Å)C-N (Å)Aryl/Scene interplanar angle (°)Deviation of Se from aryl Mean plane (°)
A602.11.856(4)1.311(5)210.469
B641.21.848(3)1.314(3)361.118
C628.61.829(7)1.318(9)270.619
D608.71.843(5)1.316(7)140.343
E579.51.848(5)1.317(6)170.576
F703.71.840(11)1.292(15)70.157
1.846(14)1.332(17)401.087
G646.51.855(10)1.310(13)100.173
1.844(12)1.295(17)30.104
H*647.21.81(5)1.27(7)8-320.299 [-0.963]
I629.61.829(6) 1.324(8) 37 [18]1.018 [0.361]
[1.838(6)][1.305(8)]
J529.01.829(6)1.324(10)390.786
K649.91.838(3)1.317(4)481.346
L715.81.822(5)1.298(7)871.406
*Five independent molecules in the asymmetric unit, average bond lengths and ranges of Se deviations/interplanar angles are given.
Table 2. Major N-H···Se hydrogen bonding distances (Å).
Table 2. Major N-H···Se hydrogen bonding distances (Å).
TypeSe···HSe···NSe···H-NSe···HSe···NSe···H-N
ALadder2.55(1)3.512(3)167(3)2.72(4)3.403(3)127(3)
BLinked dimers2.527(7)3.489(2)168(2)2.539(10)3.491(2)164(3)
CLinked dimers2.59(3)3.510(6)156(6)2.58(3)3.491(5)155(5)
DLinked dimers (sheets)2.55(1)3.517(4)170(5)2.71(5)3.408(4)129(4)
ELinked dimers (sheets)2.55(7)3.527(4)174(4)2.82(5)3.415(4)120(4)
FTetramers (sheets)2.57(2)3.58(11)171(11)2.63(6)3.527(11)152(11)
2.90(14)3.430(12)115(1)2.69(10)3.466(10)136(10)
GHerringbone dimers2.68(10)3.502(8)142(12)2.85(12)3.509(8)125(1)
HDimers2.50(17)3.43(4)158(4)2.49(16)3.43(3)160(4)
2.48(9)3.45(5)169(5)2.58(8)3.43(3)169(5)
IHelical chain2.63(3)3.513(5)150(4)2.97(3)3.628(5)125(4)
2.74(4)3.566(5)143(5)2.62(3)3.512(5)151(5)
JChain2.52(2)3.483(6)168(6)
KDimers2.69(1)3.63(3)162(3)
LLinked dimers2.535(8)3.511(4)174(5)2.579(14)3.533(4)165(4)
N-H···O hydrogen bonding: a H···O 2.09(4) Å, N…O 3.016(7) Å, N-H…O 156(7) Å; bH···O 2.32(3) Å, 2.24(3) Å; N···O 3.076(4), 2.923(3) Å; N-H···O 133(3), 126(3) Å.

Experimental

Primary arylselenoamides AL (Figure 3) were prepared as described previously [32]. Their X-ray crystal data (Table 3) were collected at 93 K by using a Rigaku MM007 High brilliance RA generator/confocal optics and Mercury CCD system. Intensities were corrected for Lorentz-polarisation and for absorption. The structures were solved by direct methods. Hydrogen atoms bound to carbon were idealised. Structural refinements were obtained with full-matrix least-squares based on F2 by using the program SHELXTL [41]. CCDC 611494 & 611495 CCDC 713559 - 713568 contain the supplementary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retrieving.html or from the Cambridge Crystallographic Data centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax (+44) 1223-336-033; E-mail: [email protected].
Figure 3. The chemical structures of primary arylselenoamides AL.
Figure 3. The chemical structures of primary arylselenoamides AL.
Molecules 14 00884 g003
Table 3. Details of data collections and refinements for A - L.
Table 3. Details of data collections and refinements for A - L.
CompoundABCDEF
Empirical formulaC8H9NOSeC8H9NSeC8H9NOSeC8H9NSeC8H9NOSeC8H6N2Se
Crystal color, habitYellow, prismOrange, needleOrange, prismOrange, needleYellow, plateletOrange, needle
Crystal dimensions/mm0.20 × 0.15 × 0.050.15 × 0.15 × 0.080.20 × 0.20 × 0.100.25 × 0.05 × 0.010.20 × 0.05 × 0.020.30 × 0.06 × 0.03
Crystal systemMonoclinicMonoclinicOrthorhombicMonoclinicMonoclinicOrthorhombic
Space groupP2(1) / cP21(1) / cPbcaP21(1) / cP2(1) / cP2(1)2(1)2(1)
a5.9600(11)7.5986(15)8.4086(17)9.869(2)10.108(4)7.4345(15)
b9.9600(18)10.464(2)11.586(2)6.0039(13)6.016(2)6.0647(12)
c14.114(3)10.163(2)16.960(4)13.658(3)13.765(6)34.203(6)
β 95.506(5)96.303(6) 105.485(6)106.907(13)
U/ Å3833.9(3)803.2(3)1652.3(6)779.9(3)800.9(6)1542.1(5)
Z448448
M214.1198.1214.1198.1214.1209.1
Dc/g cm-31.7051.6381.7221.6871.7761.801
µ/mm-14.4414.5954.4834.7324.6254.796
F(000)424392848392424816
Measured reflections444743086679289941708341
Independent reflections (Rint)1498 (0.0393)1502 (0.0396)1377 (0.0908)1057 (0.0393)1385 (0.0629)2715 (0.0562)
Final R1, wR2[I>2σ(I)]0.0316, 0.09710.0269, 0.06800.0604, 0.12520.0371, 0.09240.0458, 0.09110.0752, 0.1501
Compound GHIJKL
Empirical formulaC7H6ClNSeC7H6BrNSeC7H6FNSeC9H11NO2SeC9H11NO2SeC9H11NO2Se
Crystal color, habitOrange, prismOrange, prismYellow, prismYellow, pateletYellow, prismYellow, patelet
Crystal dimentions/mm0.30 × 0.20 × 0.050.10 × 0.08 × 0.050.30 × 0.20 × 0.100.20 × 0.20 × 0.050.20 × 0.20 × 0.150.20 × 0.20 × 0.05
Crystal systemTriclinicTriclinicMonoclinicMonoclinicMonoclinicMonoclinic
Space groupP-1P-1C2 / cCcP2(1) /nCc
a4.0219(8)12.532(3)31.874(4)9.905(2)10.7387(17)9.905(2)
b10.774(2)12.720(3)3.9871(6)14.311(3)7.0242(11)14.311(3)
c17.939(4)17.285(6)22.322(3)7.1924(16)13.539(2)7.1924(16)
α92.421(6)101.69(2)90909090
β 92.548(6)99.83(2)97.724104.360(6)106.225(4)104.360(6)
γ91.464(6)113.572(17)90909090
U/ Å3775.6(3)2373.8(11)2811.1(7)987.7(4)980.6(3)987.7(4)
Z41216444
M218.5263.00202.1244.1244.1244.1
Dc/g cm-31.8722.2081.9101.6421.6541.642
µ/mm-15.1029.7135.2743.7683.7963.768
F(000)42414881568488488488
Measured reflections201145317115268651992686
Independent reflections (Rint)1480 (0.0348)3567 (0.0412)2503 (0.1074)1393 (0.0717)1748 (0.0449)1393(0.0717)
Final R1, wR2[I>2σ(I)]0.0728, 0.18530.0744, 0.17230.0637, 0.15400.0431, 0.12500.0322, 0.08190.0431, 0.1250

Acknowledgements

The authors are grateful to the University of St Andrews and the Engineering and Physical Science Research Council (EPSRC, U.K.) for financial support.

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Li, Y.; Hua, G.-X.; Slawin, A.M.Z.; Woollins, J.D. The X-Ray Crystal Structures of Primary Aryl Substituted Selenoamides. Molecules 2009, 14, 884-892. https://doi.org/10.3390/molecules14020884

AMA Style

Li Y, Hua G-X, Slawin AMZ, Woollins JD. The X-Ray Crystal Structures of Primary Aryl Substituted Selenoamides. Molecules. 2009; 14(2):884-892. https://doi.org/10.3390/molecules14020884

Chicago/Turabian Style

Li, Yang, Guo-Xiong Hua, Alexandra M. Z. Slawin, and J. Derek Woollins. 2009. "The X-Ray Crystal Structures of Primary Aryl Substituted Selenoamides" Molecules 14, no. 2: 884-892. https://doi.org/10.3390/molecules14020884

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