organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 5| May 2012| Pages o1441-o1442

3-Carbamoyl-1-(2-nitro­benzyl)pyridin­ium bromide

aDepartment of Fine Chemistry, Seoul National University of Science & Technology, Seoul 139-743, Republic of Korea, bClean Energy Research Center, Korea Institute of Science & Technology, Seoul 130-650, Republic of Korea, and cDepartment of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Republic of Korea
*Correspondence e-mail: chealkim@seoultech.ac.kr, ymeekim@ewha.ac.kr

(Received 3 April 2012; accepted 12 April 2012; online 18 April 2012)

In the title compound, C13H12N3O3+·Br, the benzene and pyridinium rings form a dihedral angle of 82.0 (1)°. In the crystal, N—H⋯Br and N—H⋯O hydrogen bonds link the components into chains along [001]. In addition, weak C—H⋯O and C—H⋯Br hydrogen bonds are observed.

Related literature

The title compound was prepared as an NAD+ (nicotinamide adenine dinucleotide) model. For effective regeneration systems for co-enzymes (e.g. NADH), see: Hollmann et al. (2001[Hollmann, F., Schmid, A. & Steckhan, E. (2001). Angew. Chem. Int. Ed. 40, 169-171.]); Lee et al. (2011[Lee, H. J., Lee, S. H., Park, C. B. & Won, K. (2011). Chem. Commun. 47, 12538-12540.]); Maenaka et al. (2012[Maenaka, Y., Suenobu, T. & Fukuzumi, S. (2012). J. Am. Chem. Soc. 134, 367-374.]); Park et al. (2008[Park, C. B., Lee, S. H., Subramanian, E., Kale, B. B., Lee, S. M. & Baeg, J.-O. (2008). Chem. Commun. pp. 5423-5425.]); Ruppert et al. (1988[Ruppert, R., Herrmann, S. & Steckhan, E. (1988). J. Chem. Soc. Chem. Commun. pp. 1150-1151.]); Zhu et al. (2006[Zhu, X.-Q., Zhang, J.-Y. & Cheng, J.-P. (2006). J. Org. Chem. 71, 7007-7015.]). For the mechanisms of redox inter­conversions (NADH/NAD+), see: Zhu et al. (2003[Zhu, X.-Q., Yang, Y., Zhang, M. & Cheng, J.-P. (2003). J. Am. Chem. Soc. 125, 15298-15299.]); Song et al. (2008[Song, H.-K., Lee, S. H., Won, K., Park, J. H., Kim, J. K., Lee, H., Moon, S.-J., Kim, D. K. & Park, C. B. (2008). Angew. Chem. Int. Ed. 47, 1749-1752.]).

[Scheme 1]

Experimental

Crystal data
  • C13H12N3O3+·Br

  • Mr = 338.17

  • Monoclinic, P 21 /c

  • a = 17.576 (4) Å

  • b = 7.9990 (16) Å

  • c = 10.152 (2) Å

  • β = 105.88 (3)°

  • V = 1372.8 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 3.01 mm−1

  • T = 293 K

  • 0.15 × 0.15 × 0.10 mm

Data collection
  • Bruker SMART CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 1997[Bruker (1997). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.661, Tmax = 0.753

  • 7399 measured reflections

  • 2684 independent reflections

  • 2081 reflections with I > 2σ(I)

  • Rint = 0.034

Refinement
  • R[F2 > 2σ(F2)] = 0.036

  • wR(F2) = 0.086

  • S = 1.04

  • 2684 reflections

  • 187 parameters

  • 2 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.36 e Å−3

  • Δρmin = −0.38 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1B⋯O1i 0.86 (1) 2.30 (1) 3.143 (4) 168 (4)
N1—H1A⋯Br1ii 0.86 (1) 2.61 (1) 3.454 (3) 166 (3)
C4—H4⋯Br1 0.93 2.82 3.743 (3) 173
C7—H7B⋯Br1iii 0.97 2.82 3.595 (3) 137
C5—H5⋯O2iv 0.93 2.36 3.271 (4) 167
C3—H3⋯O1i 0.93 2.27 3.150 (4) 157
Symmetry codes: (i) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (ii) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iii) x, y, z+1; (iv) [x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}].

Data collection: SMART (Bruker, 1997[Bruker (1997). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 1997[Bruker (1997). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

One of the most important challenges in applying mono-oxygenases reactions in vitro is to find an effective regeneration system for the necessary co-enzyme (mostly NAD(P)H) (Hollmann et al., 2001; Lee et al.,2011; Maenaka et al., 2012; Park et al., 2008; Ruppert et al., 1988; Zhu et al., 2006). The well established methods for the regeneration of the nicotinamide co-enzyme mainly consist of an enzyme-coupled approach utilizing formate dehydrogenase or glucose-6-phosphate dehydrogenase. Because the redox coenzyme couple NADH/NAD+ is ubiquitous and controls so much of our oxidation/reduction nature, there has been a long-standing interest in the mechanisms of the redox interconversions (Zhu et al., 2003). The high cost of these co-factors, however, is prohibitive of industrialization of many promising enzymatic processes. An efficient method of their in situ regeneration is the only means for making the processes economically and industrially feasible (Song et al., 2008). Therefore, many researchers have given considerable attention to the chemistry of NADH and its models (Hollmann et al., 2001). In this work, we have synthesized the title compound as a NAD+ model and report herein its crystal structure.

The molecular structure of the title compound is shown in Fig. 1. The benzene ring (C8-C13) and pyridine ring (N3/C2-C6) form a dihedral angle of 82.0 (1)°. In the crystal, intermolecular N—H···Br and N—H···O hydrogen bonds link the components to form chains along [001]. In addition, weak C—H···O and C—H···Br hydrogen bonds are observed.

Related literature top

The title compound was prepared as an NAD+ (nicotinamide adenine dinucleotide) model. For effective regeneration systems for co-enzymes (e.g. NADH), see: Hollmann et al. (2001); Lee et al. (2011); Maenaka et al. (2012); Park et al. (2008); Ruppert et al. (1988); Zhu et al. (2006). For the mechanisms of redox interconversions (NADH/NAD+), see: Zhu et al. (2003); Song et al. (2008).

Experimental top

Nicotinamide (123.4 mg, 1 mmol) was dissolved in 10 ml acetonitrile. After stirring for a few minutes, 2-nitrobenzyl bromide (220.4 mg, 1 mmol) was carefully added to the reaction mixture. The solution was stirred for 3 h at 353K. The precipitate was filtered, washed three times with methylene chloride, and dried under vacuum. Crystals suitable for X-ray analysis were obtained from a methanol soution of the title compound in a few days.

Refinement top

H atoms bonded to C atoms were placed in calculated positions with C—H distances of 0.93 Å for aromatic C atoms and 0.97 Å for a methylene C atoms. They were included in the refinement in riding-motion approximation with Uiso(H) = 1.2Ueq(C). The positions of N—H atoms of the amine were refined with N—H = 0.860 (2) Å and Uiso(H) =1.2Ueq(N).

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure with displacement ellipsoids shown at the 50% probability level.
3-Carbamoyl-1-(2-nitrobenzyl)pyridinium bromide top
Crystal data top
C13H12N3O3+·BrF(000) = 680
Mr = 338.17Dx = 1.636 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 11909 reflections
a = 17.576 (4) Åθ = 2.7–27.6°
b = 7.9990 (16) ŵ = 3.01 mm1
c = 10.152 (2) ÅT = 293 K
β = 105.88 (3)°Block, colorless
V = 1372.8 (5) Å30.15 × 0.15 × 0.10 mm
Z = 4
Data collection top
Bruker SMART CCD
diffractometer
2684 independent reflections
Radiation source: fine-focus sealed tube2081 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.034
ϕ and ω scansθmax = 26.0°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Bruker, 1997)
h = 2121
Tmin = 0.661, Tmax = 0.753k = 99
7399 measured reflectionsl = 1012
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.086H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0287P)2 + 0.3626P]
where P = (Fo2 + 2Fc2)/3
2684 reflections(Δ/σ)max = 0.001
187 parametersΔρmax = 0.36 e Å3
2 restraintsΔρmin = 0.38 e Å3
Crystal data top
C13H12N3O3+·BrV = 1372.8 (5) Å3
Mr = 338.17Z = 4
Monoclinic, P21/cMo Kα radiation
a = 17.576 (4) ŵ = 3.01 mm1
b = 7.9990 (16) ÅT = 293 K
c = 10.152 (2) Å0.15 × 0.15 × 0.10 mm
β = 105.88 (3)°
Data collection top
Bruker SMART CCD
diffractometer
2684 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 1997)
2081 reflections with I > 2σ(I)
Tmin = 0.661, Tmax = 0.753Rint = 0.034
7399 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0362 restraints
wR(F2) = 0.086H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 0.36 e Å3
2684 reflectionsΔρmin = 0.38 e Å3
187 parameters
Special details top

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 (Å2) top
xyzUiso*/Ueq
Br10.299001 (18)0.53711 (4)0.36253 (3)0.04487 (13)
N10.51901 (17)0.2174 (4)0.9902 (3)0.0556 (7)
H1A0.5634 (10)0.181 (4)1.041 (3)0.067*
H1B0.506 (2)0.193 (5)0.9045 (10)0.067*
N20.09788 (14)0.6339 (3)1.1536 (2)0.0374 (6)
N30.27770 (14)0.5158 (3)0.9346 (2)0.0333 (5)
O10.48818 (12)0.3289 (3)1.1724 (2)0.0515 (6)
O20.11894 (12)0.7569 (3)1.1007 (2)0.0468 (5)
O30.06762 (15)0.6449 (3)1.2487 (3)0.0648 (7)
C10.47318 (17)0.3051 (4)1.0485 (3)0.0396 (7)
C20.40031 (16)0.3825 (3)0.9549 (3)0.0330 (6)
C30.38718 (18)0.3982 (4)0.8142 (3)0.0411 (7)
H30.42490.35920.77280.049*
C40.31891 (19)0.4710 (4)0.7355 (3)0.0444 (8)
H40.31010.48110.64120.053*
C50.26429 (18)0.5282 (4)0.7981 (3)0.0397 (7)
H50.21750.57600.74590.048*
C60.34414 (16)0.4456 (3)1.0136 (3)0.0329 (6)
H60.35230.43961.10800.040*
C70.21733 (16)0.5811 (3)0.9988 (3)0.0340 (7)
H7A0.18590.66570.93980.041*
H7B0.24360.63351.08540.041*
C80.16318 (15)0.4428 (3)1.0230 (3)0.0298 (6)
C90.16802 (17)0.2812 (4)0.9765 (3)0.0372 (7)
H90.20300.25850.92460.045*
C100.12235 (18)0.1532 (4)1.0052 (3)0.0443 (8)
H100.12670.04640.97170.053*
C110.07044 (18)0.1813 (4)1.0828 (3)0.0429 (7)
H110.04040.09411.10280.051*
C120.06342 (17)0.3402 (4)1.1305 (3)0.0394 (7)
H120.02840.36151.18250.047*
C130.10931 (15)0.4683 (3)1.1001 (3)0.0307 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0467 (2)0.0500 (2)0.0367 (2)0.00517 (15)0.00936 (14)0.00137 (15)
N10.0406 (17)0.066 (2)0.0561 (19)0.0114 (15)0.0063 (15)0.0072 (16)
N20.0361 (14)0.0353 (15)0.0415 (15)0.0064 (11)0.0120 (11)0.0022 (12)
N30.0364 (14)0.0322 (13)0.0346 (13)0.0001 (10)0.0152 (11)0.0025 (10)
O10.0402 (12)0.0710 (16)0.0435 (14)0.0001 (11)0.0117 (10)0.0118 (12)
O20.0491 (13)0.0332 (12)0.0613 (15)0.0007 (10)0.0202 (11)0.0023 (11)
O30.0894 (19)0.0559 (16)0.0689 (16)0.0129 (13)0.0549 (15)0.0026 (13)
C10.0320 (16)0.0412 (18)0.047 (2)0.0050 (13)0.0134 (14)0.0044 (15)
C20.0314 (15)0.0317 (16)0.0369 (16)0.0060 (12)0.0111 (12)0.0002 (13)
C30.0445 (18)0.0419 (17)0.0431 (18)0.0009 (14)0.0224 (15)0.0049 (15)
C40.053 (2)0.0526 (19)0.0301 (16)0.0042 (16)0.0158 (14)0.0022 (15)
C50.0418 (17)0.0398 (17)0.0348 (17)0.0044 (14)0.0056 (14)0.0070 (14)
C60.0343 (15)0.0359 (17)0.0289 (15)0.0028 (13)0.0092 (12)0.0045 (12)
C70.0352 (16)0.0331 (16)0.0373 (16)0.0037 (12)0.0160 (13)0.0013 (12)
C80.0278 (14)0.0323 (16)0.0274 (14)0.0010 (11)0.0044 (11)0.0011 (12)
C90.0395 (16)0.0374 (17)0.0363 (17)0.0032 (13)0.0131 (13)0.0050 (13)
C100.0530 (19)0.0298 (17)0.0490 (19)0.0039 (14)0.0121 (15)0.0054 (14)
C110.0438 (18)0.0368 (18)0.0486 (19)0.0129 (14)0.0134 (15)0.0015 (15)
C120.0330 (16)0.0449 (19)0.0425 (18)0.0027 (13)0.0141 (13)0.0028 (14)
C130.0307 (14)0.0283 (14)0.0320 (15)0.0001 (12)0.0067 (12)0.0019 (12)
Geometric parameters (Å, º) top
N1—C11.324 (4)C4—H40.9300
N1—H1A0.860 (2)C5—H50.9300
N1—H1B0.860 (2)C6—H60.9300
N2—O21.226 (3)C7—C81.523 (4)
N2—O31.227 (3)C7—H7A0.9700
N2—C131.466 (4)C7—H7B0.9700
N3—C51.344 (4)C8—C91.387 (4)
N3—C61.345 (4)C8—C131.398 (4)
N3—C71.484 (3)C9—C101.381 (4)
O1—C11.227 (4)C9—H90.9300
C1—C21.503 (4)C10—C111.377 (4)
C2—C61.381 (4)C10—H100.9300
C2—C31.389 (4)C11—C121.377 (4)
C3—C41.376 (4)C11—H110.9300
C3—H30.9300C12—C131.390 (4)
C4—C51.367 (4)C12—H120.9300
C1—N1—H1A119 (2)C2—C6—H6120.0
C1—N1—H1B124 (3)N3—C7—C8111.6 (2)
H1A—N1—H1B118 (4)N3—C7—H7A109.3
O2—N2—O3122.4 (3)C8—C7—H7A109.3
O2—N2—C13118.3 (2)N3—C7—H7B109.3
O3—N2—C13119.3 (3)C8—C7—H7B109.3
C5—N3—C6121.6 (2)H7A—C7—H7B108.0
C5—N3—C7118.8 (2)C9—C8—C13116.1 (2)
C6—N3—C7119.6 (2)C9—C8—C7121.5 (2)
O1—C1—N1123.7 (3)C13—C8—C7122.2 (2)
O1—C1—C2119.4 (3)C10—C9—C8121.8 (3)
N1—C1—C2116.9 (3)C10—C9—H9119.1
C6—C2—C3118.3 (3)C8—C9—H9119.1
C6—C2—C1117.6 (3)C11—C10—C9120.9 (3)
C3—C2—C1124.1 (3)C11—C10—H10119.5
C4—C3—C2120.6 (3)C9—C10—H10119.5
C4—C3—H3119.7C10—C11—C12119.3 (3)
C2—C3—H3119.7C10—C11—H11120.4
C5—C4—C3118.9 (3)C12—C11—H11120.4
C5—C4—H4120.6C11—C12—C13119.3 (3)
C3—C4—H4120.6C11—C12—H12120.4
N3—C5—C4120.5 (3)C13—C12—H12120.4
N3—C5—H5119.8C12—C13—C8122.6 (3)
C4—C5—H5119.8C12—C13—N2115.9 (2)
N3—C6—C2120.1 (3)C8—C13—N2121.4 (2)
N3—C6—H6120.0
O1—C1—C2—C614.2 (4)N3—C7—C8—C13170.4 (2)
N1—C1—C2—C6167.5 (3)C13—C8—C9—C100.2 (4)
O1—C1—C2—C3164.0 (3)C7—C8—C9—C10176.1 (3)
N1—C1—C2—C314.3 (4)C8—C9—C10—C110.6 (5)
C6—C2—C3—C41.7 (4)C9—C10—C11—C120.9 (5)
C1—C2—C3—C4179.9 (3)C10—C11—C12—C130.5 (5)
C2—C3—C4—C50.2 (5)C11—C12—C13—C80.3 (4)
C6—N3—C5—C40.8 (4)C11—C12—C13—N2179.5 (3)
C7—N3—C5—C4179.3 (3)C9—C8—C13—C120.7 (4)
C3—C4—C5—N31.0 (5)C7—C8—C13—C12175.6 (3)
C5—N3—C6—C20.7 (4)C9—C8—C13—N2179.2 (2)
C7—N3—C6—C2179.2 (2)C7—C8—C13—N24.6 (4)
C3—C2—C6—N31.9 (4)O2—N2—C13—C12160.2 (3)
C1—C2—C6—N3179.8 (2)O3—N2—C13—C1219.6 (4)
C5—N3—C7—C897.2 (3)O2—N2—C13—C819.7 (4)
C6—N3—C7—C882.7 (3)O3—N2—C13—C8160.5 (3)
N3—C7—C8—C95.6 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1B···O1i0.86 (1)2.30 (1)3.143 (4)168 (4)
N1—H1A···Br1ii0.86 (1)2.61 (1)3.454 (3)166 (3)
C4—H4···Br10.932.823.743 (3)173
C7—H7B···Br1iii0.972.823.595 (3)137
C5—H5···O2iv0.932.363.271 (4)167
C3—H3···O1i0.932.273.150 (4)157
Symmetry codes: (i) x, y+1/2, z1/2; (ii) x+1, y1/2, z+3/2; (iii) x, y, z+1; (iv) x, y+3/2, z1/2.

Experimental details

Crystal data
Chemical formulaC13H12N3O3+·Br
Mr338.17
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)17.576 (4), 7.9990 (16), 10.152 (2)
β (°) 105.88 (3)
V3)1372.8 (5)
Z4
Radiation typeMo Kα
µ (mm1)3.01
Crystal size (mm)0.15 × 0.15 × 0.10
Data collection
DiffractometerBruker SMART CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 1997)
Tmin, Tmax0.661, 0.753
No. of measured, independent and
observed [I > 2σ(I)] reflections
7399, 2684, 2081
Rint0.034
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.086, 1.04
No. of reflections2684
No. of parameters187
No. of restraints2
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.36, 0.38

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1B···O1i0.860 (2)2.296 (9)3.143 (4)168 (4)
N1—H1A···Br1ii0.860 (2)2.614 (9)3.454 (3)166 (3)
C4—H4···Br10.932.823.743 (3)173.2
C7—H7B···Br1iii0.972.823.595 (3)137.3
C5—H5···O2iv0.932.363.271 (4)166.7
C3—H3···O1i0.932.273.150 (4)157.2
Symmetry codes: (i) x, y+1/2, z1/2; (ii) x+1, y1/2, z+3/2; (iii) x, y, z+1; (iv) x, y+3/2, z1/2.
 

Acknowledgements

Financial support from the Converging Research Center Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2011 K000675 and 2011 K000660), and Seoul National University of Science & Technology is gratefully acknowledged.

References

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Volume 68| Part 5| May 2012| Pages o1441-o1442
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