Aqua­(L-phenyl­alaninato)(L-prolinato)copper(II) monohydrate

The title compound, [Cu(C₅H₈NO₂)(C₉H₁₀NO₂)(H₂O)]·H₂O, is formed by the chelate coordination of L-prolinate and L-phenyl­alaninate anions. Both ligands bind through carboxyl­ate O and amine N atoms to the Cu^II atom in a trans arrangement. The square pyramid is completed by an aqua ligand in the apical position.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.010 Å
• H-atom completeness 91%
• R factor = 0.057
• wR factor = 0.168
• Data-to-parameter ratio = 11.2

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT306_ALERT_2_A Isolated Oxygen Atom (H-atoms Missing ?) .......         O6

Author Response: Hydrogen atoms from crystallization water molecule were not found in \DF maps and were disregarded in the final model (see text).

Alert level B
PLAT222_ALERT_3_B Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       4.03 Ratio
PLAT430_ALERT_2_B Short Inter D...A Contact  O2     ..  O6      ..       2.78 Ang.

Alert level C
PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings    Differ ....          ?
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)...          ?
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       3.17 Ratio
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         C4
PLAT341_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...         10

Alert level G
FORMU01_ALERT_2_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and the formula from the _atom_site* data.
            Atom count from _chemical_formula_sum:C14 H22 Cu1 N2 O6
            Atom count from the _atom_site data:  C14 H20 Cu1 N2 O6
CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G WARNING: H atoms missing from atom site list. Is this intentional?
           From the CIF: _cell_formula_units_Z    4
           From the CIF: _chemical_formula_sum  C14 H22 Cu N2 O6
           TEST: Compare cell contents of formula and atom_site data

           atom    Z*formula  cif sites diff
           C         56.00     56.00    0.00
           H         88.00     80.00    8.00
           Cu         4.00      4.00    0.00
           N          8.00      8.00    0.00
           O         24.00     24.00    0.00
REFLT03_ALERT_4_G  WARNING: Large fraction of Friedel related reflns may
                     be needed to determine absolute structure
           From the CIF: _diffrn_reflns_theta_max           27.52
           From the CIF: _reflns_number_total               2415
           Count of symmetry unique reflns         2182
           Completeness (_total/calc)            110.68%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       233
           Fraction of Friedel pairs measured     0.107
           Are heavy atom types Z>Si present        yes
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K
PLAT791_ALERT_1_G Confirm the Absolute Configuration of N1     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C7     = .          S

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

  10 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   5 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 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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Computing details

Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1993); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: MSC/AFC Diffractometer Control Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Brandenburg, 1999); software used to prepare material for publication: PLATON (Spek, 2003).

Aqua(L-phenylalaninato)(L-prolinato)copper(II) monohydrate

Crystal data

[Cu(C5H8NO2)(C9H10NO2)(H2O)]·H2O	F(000) = 788
Mr = 377.88	Dx = 1.544 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71069 Å
Hall symbol: P 2ac 2ab	Cell parameters from 25 reflections
a = 12.663 (3) Å	θ = 5.1–11.6°
b = 22.894 (3) Å	µ = 1.38 mm^−1
c = 5.609 (3) Å	T = 293 K
V = 1626.1 (10) Å^3	Needle, blue
Z = 4	0.30 × 0.03 × 0.01 mm

Data collection

Rigaku AFC-7S diffractometer	1983 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.045
Graphite monochromator	θmax = 27.5°, θmin = 2.4°
ω/2θ scans	h = −8→16
Absorption correction: ψ scan (North et al., 1968)	k = −20→29
Tmin = 0.683, Tmax = 0.986	l = −4→7
2508 measured reflections	3 standard reflections every 150 reflections
2415 independent reflections	intensity decay: none

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.057	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.168	w = 1/[σ^2(Fo^2) + (0.118P)^2 + 1.1436P] where P = (Fo^2 + 2Fc^2)/3
S = 1.06	(Δ/σ)max < 0.001
2415 reflections	Δρmax = 1.08 e Å^−3
215 parameters	Δρmin = −0.65 e Å^−3
20 restraints	Absolute structure: Flack (1983), 235 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.01 (3)

Special details

Experimental. Elemental analyses (C,H,N) were performed on a Carlo Erba model 1108 elemental analyzer. IR spectrometry on KBr pellets was performed with a Bomem MB-102 FTIR spectrometer. The spectra show the absorption lines assigned to the aminoacid ligands 1601(s), 1387(m), 1135(m), 1089(w), 937(w), 890(w), 856(w), 828(w), 749(w), 701(m) cm^-1.

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.

———————————————

Interaction among π rings:

C9—C10—C11—C12—C13—C14-

LS-Plane: 0.678 (2)*x - 0.578 (2)*y + 0.454 (3)*z=5.386 (17)

Deviations from plane #C(9) 0.010 (5) #C(10) -0.005 (7) #C(11) -0.006 (7) #C(12) 0.011 (8) #C(13) -0.006 (8) #C(14) -0.005 (7)

Ring centroid (CG) coodinates (x,y,z): (0.5929 (2),0.02425 (12),0.2417 (6))

Closes CG—CG interaction

CG—CGⁱ 4.993 (5) Å perpendicular distance between rings 2.065 Å distance between CG and the projection of CGⁱ in CG's plane 4.613 Å

i=[2655] = 3/2-X,-Y,1/2+Z

NOTE: THIS IS NOT CONSIDERED A π—π STACKING INTERACTION

Refinement. Conformational disorder in the five-membered ring could be invoked to explain the observed behavior together with the observed C—C bond distances between C3, C4 and C5 that are shorter than expected for C(sp³)—C(sp³) (see suplementary material). The use of optically pure L-aminoacids allowed to postulate the absolute structure of the compound, afterwards confirmed by refinement. The needle-shaped crystals obtained showed twinning and the cut piece used for data collection did not diffract adequately. Accordingly, the data set gathered was of poor quality, as evidenced in the rather large R_int factor attained (0.0451) with about 10% of redundant reflections.

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
Cu	0.47313 (5)	0.18848 (3)	0.16380 (12)	0.0338 (2)
O1	0.3717 (3)	0.1901 (2)	0.4263 (8)	0.0459 (11)
C1	0.2762 (5)	0.1785 (3)	0.3711 (10)	0.0344 (12)
O2	0.2026 (3)	0.1801 (2)	0.5147 (9)	0.0467 (11)
C2	0.2544 (5)	0.1609 (3)	0.1113 (11)	0.0374 (14)
H2	0.2083	0.1902	0.0384	0.045*
C3	0.2007 (8)	0.1013 (4)	0.095 (2)	0.077 (3)
H3A	0.2003	0.0822	0.2497	0.115*
H3B	0.1285	0.1053	0.0403	0.115*
C4	0.2648 (8)	0.0672 (4)	−0.079 (3)	0.092 (3)
H4A	0.2720	0.0271	−0.0266	0.137*
H4B	0.2307	0.0673	−0.2342	0.137*
C5	0.3684 (6)	0.0948 (3)	−0.0957 (17)	0.0553 (18)
H5C	0.3958	0.0917	−0.2567	0.083*
H5D	0.4177	0.0760	0.0122	0.083*
N1	0.3542 (4)	0.1574 (2)	−0.0287 (9)	0.0341 (11)
H1	0.3474	0.1792	−0.1636	0.041*
O3	0.5751 (3)	0.1797 (2)	−0.0941 (7)	0.0380 (10)
C6	0.6717 (5)	0.1837 (3)	−0.0295 (10)	0.0315 (11)
O4	0.7465 (3)	0.1855 (2)	−0.1726 (8)	0.0487 (11)
C7	0.6945 (4)	0.1834 (3)	0.2382 (10)	0.0285 (11)
H7	0.7501	0.2121	0.2705	0.034*
N2	0.5985 (4)	0.2017 (2)	0.3650 (9)	0.0322 (10)
H2A	0.6031	0.2399	0.4024	0.039*
H2B	0.5922	0.1813	0.5014	0.039*
C8	0.7357 (4)	0.1229 (2)	0.3098 (12)	0.0356 (12)
H8A	0.7996	0.1151	0.2199	0.053*
H8B	0.7549	0.1240	0.4772	0.053*
C9	0.6594 (5)	0.0725 (2)	0.2714 (11)	0.0334 (12)
C10	0.6666 (6)	0.0390 (3)	0.0682 (13)	0.0433 (15)
H10	0.7153	0.0485	−0.0496	0.065*
C11	0.5997 (6)	−0.0098 (3)	0.0393 (14)	0.0519 (18)
H11	0.6043	−0.0324	−0.0982	0.078*
C12	0.5274 (6)	−0.0243 (3)	0.2152 (16)	0.059 (2)
H12	0.4848	−0.0571	0.1981	0.089*
C13	0.5192 (7)	0.0101 (3)	0.4143 (15)	0.061 (2)
H13	0.4694	0.0012	0.5308	0.092*
C14	0.5849 (6)	0.0582 (3)	0.4426 (13)	0.0476 (16)
H14	0.5787	0.0811	0.5787	0.071*
O5	0.4500 (4)	0.2877 (2)	0.0805 (12)	0.0548 (14)
H5A	0.391 (5)	0.288 (4)	0.09 (2)	0.082*
H5B	0.474 (7)	0.308 (4)	−0.012 (18)	0.082*
O6	0.4911 (5)	0.3293 (3)	0.6092 (12)	0.0752 (17)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu	0.0333 (4)	0.0471 (4)	0.0209 (3)	0.0008 (3)	−0.0062 (3)	−0.0031 (3)
O1	0.042 (2)	0.076 (3)	0.0195 (18)	0.004 (2)	−0.0038 (17)	−0.004 (2)
C1	0.039 (3)	0.039 (3)	0.025 (3)	0.008 (2)	−0.003 (2)	0.000 (2)
O2	0.041 (2)	0.064 (3)	0.034 (2)	0.004 (2)	0.004 (2)	−0.006 (2)
C2	0.040 (3)	0.043 (3)	0.029 (3)	0.000 (2)	−0.004 (3)	−0.008 (3)
C3	0.086 (6)	0.069 (5)	0.075 (6)	−0.032 (4)	0.024 (5)	−0.031 (5)
C4	0.101 (6)	0.051 (4)	0.122 (8)	−0.022 (4)	0.030 (6)	−0.025 (5)
C5	0.061 (4)	0.047 (3)	0.057 (4)	0.009 (3)	0.002 (4)	−0.018 (3)
N1	0.044 (3)	0.039 (2)	0.020 (2)	−0.001 (2)	−0.004 (2)	−0.002 (2)
O3	0.042 (2)	0.055 (3)	0.0170 (16)	−0.002 (2)	−0.0052 (17)	−0.0010 (19)
C6	0.041 (3)	0.034 (3)	0.020 (2)	−0.007 (3)	0.000 (2)	0.001 (2)
O4	0.043 (2)	0.077 (3)	0.027 (2)	−0.011 (2)	0.0027 (19)	0.001 (3)
C7	0.029 (2)	0.034 (3)	0.023 (2)	−0.001 (2)	−0.010 (2)	0.000 (2)
N2	0.036 (2)	0.036 (2)	0.024 (2)	0.0036 (19)	−0.008 (2)	−0.0031 (19)
C8	0.034 (3)	0.042 (3)	0.032 (3)	0.004 (2)	−0.004 (3)	0.007 (3)
C9	0.040 (3)	0.031 (3)	0.029 (3)	0.009 (2)	−0.002 (2)	0.001 (2)
C10	0.052 (4)	0.044 (3)	0.034 (3)	0.008 (3)	0.007 (3)	−0.002 (3)
C11	0.067 (4)	0.038 (3)	0.051 (4)	0.010 (3)	−0.005 (4)	−0.014 (3)
C12	0.063 (4)	0.041 (3)	0.074 (5)	−0.005 (3)	0.000 (5)	0.000 (4)
C13	0.071 (5)	0.059 (4)	0.053 (4)	−0.013 (4)	0.017 (4)	0.000 (4)
C14	0.063 (4)	0.045 (3)	0.035 (3)	−0.005 (3)	0.011 (3)	0.000 (3)
O5	0.042 (2)	0.056 (3)	0.066 (4)	0.007 (2)	−0.010 (3)	0.014 (3)
O6	0.063 (3)	0.097 (4)	0.065 (4)	0.019 (3)	0.000 (3)	−0.009 (3)

Geometric parameters (Å, º)

Cu—O3	1.949 (4)	C6—C7	1.530 (7)
Cu—O1	1.955 (4)	C7—N2	1.470 (7)
Cu—N2	1.971 (5)	C7—C8	1.532 (8)
Cu—N1	1.985 (5)	C7—H7	0.9800
Cu—O5	2.338 (5)	N2—H2A	0.9000
O1—C1	1.276 (7)	N2—H2B	0.9000
C1—O2	1.232 (8)	C8—C9	1.522 (8)
C1—C2	1.537 (8)	C8—H8A	0.9700
C2—N1	1.490 (8)	C8—H8B	0.9700
C2—C3	1.527 (10)	C9—C10	1.377 (9)
C2—H2	0.9800	C9—C14	1.386 (9)
C3—C4	1.493 (14)	C10—C11	1.411 (10)
C3—H3A	0.9700	C10—H10	0.9300
C3—H3B	0.9700	C11—C12	1.386 (11)
C4—C5	1.458 (11)	C11—H11	0.9300
C4—H4A	0.9700	C12—C13	1.370 (11)
C4—H4B	0.9700	C12—H12	0.9300
C5—N1	1.494 (8)	C13—C14	1.389 (10)
C5—H5C	0.9700	C13—H13	0.9300
C5—H5D	0.9700	C14—H14	0.9300
N1—H1	0.9100	O5—H5A	0.75 (6)
O3—C6	1.279 (7)	O5—H5B	0.76 (6)
C6—O4	1.242 (7)
O3—Cu—O1	175.2 (2)	C6—O3—Cu	114.6 (3)
O3—Cu—N2	84.7 (2)	O4—C6—O3	123.3 (5)
O1—Cu—N2	95.46 (19)	O4—C6—C7	119.4 (5)
O3—Cu—N1	93.55 (19)	O3—C6—C7	117.3 (5)
O1—Cu—N1	85.3 (2)	N2—C7—C6	108.5 (4)
N2—Cu—N1	167.86 (18)	N2—C7—C8	114.4 (5)
O3—Cu—O5	92.0 (2)	C6—C7—C8	109.1 (5)
O1—Cu—O5	92.8 (2)	N2—C7—H7	108.2
N2—Cu—O5	93.77 (19)	C6—C7—H7	108.2
N1—Cu—O5	98.3 (2)	C8—C7—H7	108.2
C1—O1—Cu	115.9 (4)	C7—N2—Cu	110.2 (3)
O2—C1—O1	123.5 (6)	C7—N2—H2A	109.6
O2—C1—C2	119.4 (6)	Cu—N2—H2A	109.6
O1—C1—C2	117.0 (5)	C7—N2—H2B	109.6
N1—C2—C3	107.4 (6)	Cu—N2—H2B	109.6
N1—C2—C1	111.2 (5)	H2A—N2—H2B	108.1
C3—C2—C1	111.7 (6)	C9—C8—C7	115.6 (4)
N1—C2—H2	108.8	C9—C8—H8A	108.4
C3—C2—H2	108.8	C7—C8—H8A	108.4
C1—C2—H2	108.8	C9—C8—H8B	108.4
C4—C3—C2	105.2 (7)	C7—C8—H8B	108.4
C4—C3—H3A	110.7	H8A—C8—H8B	107.4
C2—C3—H3A	110.7	C10—C9—C14	119.1 (6)
C4—C3—H3B	110.7	C10—C9—C8	119.9 (6)
C2—C3—H3B	110.7	C14—C9—C8	120.9 (6)
H3A—C3—H3B	108.8	C9—C10—C11	119.8 (7)
C5—C4—C3	107.7 (7)	C9—C10—H10	120.1
C5—C4—H4A	110.2	C11—C10—H10	120.1
C3—C4—H4A	110.2	C12—C11—C10	120.2 (7)
C5—C4—H4B	110.2	C12—C11—H11	119.9
C3—C4—H4B	110.2	C10—C11—H11	119.9
H4A—C4—H4B	108.5	C13—C12—C11	119.6 (7)
C4—C5—N1	106.9 (6)	C13—C12—H12	120.2
C4—C5—H5C	110.3	C11—C12—H12	120.2
N1—C5—H5C	110.3	C12—C13—C14	120.2 (7)
C4—C5—H5D	110.3	C12—C13—H13	119.9
N1—C5—H5D	110.3	C14—C13—H13	119.9
H5C—C5—H5D	108.6	C9—C14—C13	121.1 (7)
C2—N1—C5	106.6 (5)	C9—C14—H14	119.5
C2—N1—Cu	109.7 (4)	C13—C14—H14	119.5
C5—N1—Cu	112.9 (4)	Cu—O5—H5A	96 (7)
C2—N1—H1	109.2	Cu—O5—H5B	133 (8)
C5—N1—H1	109.2	H5A—O5—H5B	117 (10)
Cu—N1—H1	109.2
N2—Cu—O1—C1	−175.1 (5)	N2—Cu—O3—C6	2.2 (4)
N1—Cu—O1—C1	−7.2 (5)	N1—Cu—O3—C6	−165.7 (4)
O5—Cu—O1—C1	90.9 (5)	O5—Cu—O3—C6	95.8 (4)
Cu—O1—C1—O2	−177.0 (5)	Cu—O3—C6—O4	−172.0 (5)
Cu—O1—C1—C2	4.0 (7)	Cu—O3—C6—C7	10.9 (7)
O2—C1—C2—N1	−175.8 (5)	O4—C6—C7—N2	160.4 (5)
O1—C1—C2—N1	3.2 (8)	O3—C6—C7—N2	−22.4 (8)
O2—C1—C2—C3	−55.8 (9)	O4—C6—C7—C8	−74.4 (7)
O1—C1—C2—C3	123.3 (7)	O3—C6—C7—C8	102.8 (6)
N1—C2—C3—C4	−6.9 (10)	C6—C7—N2—Cu	22.4 (6)
C1—C2—C3—C4	−129.1 (8)	C8—C7—N2—Cu	−99.6 (4)
C2—C3—C4—C5	20.1 (12)	O3—Cu—N2—C7	−14.6 (4)
C3—C4—C5—N1	−25.7 (12)	O1—Cu—N2—C7	160.5 (4)
C3—C2—N1—C5	−8.3 (8)	N1—Cu—N2—C7	67.5 (11)
C1—C2—N1—C5	114.2 (6)	O5—Cu—N2—C7	−106.3 (4)
C3—C2—N1—Cu	−130.9 (6)	N2—C7—C8—C9	59.3 (7)
C1—C2—N1—Cu	−8.4 (6)	C6—C7—C8—C9	−62.3 (7)
C4—C5—N1—C2	21.0 (10)	C7—C8—C9—C10	96.9 (7)
C4—C5—N1—Cu	141.5 (8)	C7—C8—C9—C14	−85.6 (7)
O3—Cu—N1—C2	−176.3 (4)	C14—C9—C10—C11	−1.2 (9)
O1—Cu—N1—C2	8.4 (4)	C8—C9—C10—C11	176.3 (6)
N2—Cu—N1—C2	102.5 (10)	C9—C10—C11—C12	−0.3 (10)
O5—Cu—N1—C2	−83.8 (4)	C10—C11—C12—C13	1.8 (12)
O3—Cu—N1—C5	65.0 (5)	C11—C12—C13—C14	−1.7 (13)
O1—Cu—N1—C5	−110.3 (5)	C10—C9—C14—C13	1.3 (10)
N2—Cu—N1—C5	−16.2 (13)	C8—C9—C14—C13	−176.2 (6)
O5—Cu—N1—C5	157.5 (5)	C12—C13—C14—C9	0.2 (12)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^i	0.91	2.33	3.155 (7)	150
N1—H1···O2^i	0.91	2.57	3.243 (7)	131
N2—H2B···O3^ii	0.90	2.28	3.090 (7)	150
N2—H2A···O2^iii	0.90	2.27	3.084 (6)	150
O5—H5A···O4^iv	0.75 (6)	1.98 (7)	2.699 (7)	160 (11)
O5—H5B···O6^i	0.76 (6)	2.19 (9)	2.858 (10)	147 (11)

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