# Crystal Structure of [Bis(L-Alaninato)Diaqua]Nickel(II) Dihydrate

Authors: Awni Khatib; Fathi Aqra; David Deamer; Allen Oliver
Journal: Research Letters in Inorganic Chemistry
 (2009)

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## Abstract

The title complex, [Ni(C3H6O2N)2(H2O)2]⋅2H2O, has been prepared from nickel(II) chloride in aqueous solution by adding L-alanine and potassium hydroxide. It has been crystallized from aqueous solution, and its structure was determined by X-ray structure analysis. The nickel(II) ion adopts distorted octahedral coordination geometry with two bidentate L-alanine molecules and two water molecules. The complex is neutral and dihydrated. The crystal structure shows the hydrogen bonding between water and amide hydrogens within the lattice, and each fragment of the complex contains two water molecules as hydrated water. The L-alaninato ligand skeleton of the compound adopts the most stable trans-III configuration in the solid state. The alternating two five-membered chelate rings are in the stable gauche conformation.


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## Body

## 1. Introduction

Complexes formed
by metal cations and organic species are incorporated in many biochemical
structures, such as cytochromes of mitochondrial membranes, hemoglobin, and
chlorophyll. Transition metal complexes with Schiff-base  ligand containing the carboxylate
group have been of great interest due to their importance as essentially
biologically active [1–3] models
for metalloproteins [4] and their various geometry aspects [5]. Metals
bound to amino acids are essential for the catalytic function of certain
enzymes, and their chemistry has received a great deal of research interest due
to their significant  interaction with enzymes and with
different organic ligands which enables a better understanding of the antitumor/viral
activities of this class of compounds and for modeling substrates involved in
enzyme inhibition [6, 7].  A number of complexes of amino acids with many
transition metal ions have been prepared and thoroughly studied [8–14].  A
complex of alanine with nickel(II) was reported [15] and described as a
neutral bis(alaninato)diaqua nickel(II),
and its X-ray crystal structure seems not to have been explicitly studied. Therefore, it was considered worthwhile and of
great significant chemical interest to synthesize this complex and to study
thoroughly its crystal structure in order to get greater depth into its composition.Study
of the structures of metal-amino acid complexes is a classical problem initiated
by the school of Pauling
in the 40s, with the
nickel-glycine compound. Many authors have worked in this direction with
increasing resolution and details. This paper describes the single-crystal
structure of  [bis(L-alaninato)diaqua]Nickel(II) dihydrate.


## 2. Experimental

## 2.1. Chemicals and Instrumentation

All chemicals
were of reagent grade and used as purchased from commercial source. The single-crystal
X-ray diffraction data in this paper were recorded on an instrument Bruker
APEX-II 3-circle diffractometer, a CCD area detector with graphite
monochromated Mo-Kα radiation supported by the National Science Foundation,
Major Research Instrumentation (MRI) Program under Grant no. CHE-0521569.


## 2.2. Preparation Procedures

NiCl2⋅6H2O
(20 mL, 0.1 M), KOH (20 mL, 1.0 M), and L-alanine
(20 mL, 0.2 M) were mixed. The mixture was made basic with pH = 8 and turned from
green to pale blue. The flask solution was left at room temperature. After
standing for two weeks, pale-blue tablet-shaped crystals were obtained, removed,
and dried under vacuum. The isolated crystals were subjected to X-ray studies.


## 2.3. Crystal Structure Determination

The structure
was solved by direct methods and expanded routinely. The model was refined by
full-matrix least-squares analysis ofF2 against all reflections.
All nonhydrogen atoms were refined with anisotropic thermal displacement
parameters. The hydrogens  on
the water oxygens
and amide nitrogens
were located from a difference
Fourier map and included in their observed
positions with thermal parameters tied to that of the atoms to which they are
bonded. The hydrogen atoms bonded to carbon were included in calculated
positions with thermal parameters tied to that of the carbon to which they are
bonded. The crystallographic data and parameters are given in Table 1. The
softwares used for direct method, least-squares analysis, molecular drawing,
and preparing the crystallographic materials are APEX-II [16], SAINT [17],
XPREP [18], SADABS [19], SHELXTL [20], and ORTEPII [21].Table 1
Crystal  data and structure refinement of the title compound.
Empirical formulaC6H20N2NiO8Formula weight306.95Temperature150(2) KWavelength0.71073 ÅCrystal  systemMonoclinicSpace groupC2Unit cell
dimensionsa = 20.162(4) Åb = 6.5089(13) Åc = 9.6476(19) Åβ = 94.823(2)°Volume1261.6(4)  Å3Z4Density
(calculated)1.616 g.cm−3Absorption
coefficient (μ)1.570 mm−1F(000)648Crystal  size0.16 × 0.10 × 0.09
mm3ω range for data
collection2.03 to 28.28°Index ranges−26 ≤h ≤ 6−8  ≤k ≤  8−12  ≤l ≤  12Reflections
collected7100Independent
reflections3070 [Rint= 0.0218]Completeness toθ
= 28.28°99.6%Absorption
correctionNumericalMax. and min.
transmission0.8716 and 0.7873Refinement methodFull-matrix
least-squares on F2Data/restraints/parameters3070/3/192Goodness-of-fit on
F21.013Final R indices
[I>2σ(I)]R1=
0.0232, wR2= 0.0528Absolute structure
parameter0.018(13)Largest diff. peak
and hole0.400 and −0.251 e−⋅Å−3


## 3. Results and Discussion

The title
complex was prepared by the reaction ofNiCl2⋅6H2O, KOH,
and L-alanine. The presence of
KOH has two roles: the first is to adjust the pH of the resulting solution from
6 to 8 and the second is to convert the carboxylic group of alanine to
carboxylate ion in favor to bind readily with nickel(II) ion.There
are four molecules of the nickel complex and eight water of
crystallization in the unit cell of the C-centered, acentric, and monoclinic
space group C2.  The correct enantiomorph
of the space group and handedness of the molecule were determined by comparison
of the intensities of Friedel pairs of reflections (Flack parameter
= 0.018(13)) and   and by the known stereochemistry of the L-alanine ligands. Both
techniques agreed, and the correct configuration is shown in the Figure1.The chemical diagram and the crystal structure of the title compound showing
the atomic numbering scheme.The
title compoundis crystallized from aqueous solution as pale-blue
prismatic crystals. The structure
consists of an  [Ni(L-alaninato)2(H2O)2]  and two water molecules. The nickel ion resides at the center of symmetry of
the octahedron and is surrounded by two oxygen atoms of two alanine molecules,
two oxygen atoms of two water molecules, and two nitrogen atoms of the same two
alanine molecules. The carboxylato oxygens and the amido nitrogens of the two
alanine molecules define the equatorial positions, whereas the two oxygen atoms
of the two water molecules occupy the axial ones. It is observed that the axial
Ni–O bond distances (Table 2) of 2.0706(18) and 2.1006(16) Å are
significantly longer than the equatorial Ni–O bonds of 2.0422(17) and 2.0567(17) Å. All the Ni–O distances are in agreement with those found in six coordinate
nickel(II) complexes [22]. The average Ni–N bond distance of 2.073(17) Å is in the normal range for Ni–N primary
amines of high-spin octahedral nickel(II) complexes with chelating ligands [23].
The axial angle O–Ni–O is 178.36(9)°, whereas the equatorial O–Ni–O is 179.33(7)°
(Table 2) that are close to linearity. The
average Ni–O and Ni–N bond lengths
are in accordance to that known for nickel(II) distorted octahedral geometry.
Therefore, two alanine molecules and two water  molecules are directly involved
in coordination. The coordination geometry around the nickel(II) ion is a six-coordinated
tending toward distorted octahedral,
with a metal center not lying exactly within the N2O2 plane because the bond angles are not perfect [24, 25]. The two apical positions are occupied by
water molecules, and the equatorial plane is occupied by the
chelating alanine ligands. Distortions
about nickel atom are observed, in which slightly different bond distances to
the coordinating water molecules; essentially identical bond distances to the
nitrogens and slightly different bond distances to the chelating oxygens O1 and
O3. The enforced distortion about the equatorial plane due to the formation
of the two five-membered chelate rings is seen. The two ligands adopt an
envelope and a planar geometry, with respect to the mean equatorial plane about
the nickel (Table 3).Table 2
Important bond lengths [Å]  and angles [°]  of the title compound.
Bond
distanceNi(1)–O(3)2.0422(17)Ni(1)–O(1)2.0567(17)Ni(1)–N(1)2.0703(17)Ni(1)–O(6)2.0706(18)Ni(1)–N(2)2.0758(16)Ni(1)–O(5)2.1006(16)Bond
anglesO(3)–Ni(1)–O(1)179.33(7)O(3)–Ni(1)–N(1)99.35(8)O(1)–Ni(1)–N(1)80.30(8)O(3)–Ni(1)–O(6)90.09(7)O(1)–Ni(1)–O(6)89.33(6)N(1)–Ni(1)–O(6)88.07(7)O(3)–Ni(1)–N(2)82.32(9)O(1)–Ni(1)–N(2)98.03(9)N(1)–Ni(1)–N(2)178.29(15)O(6)–Ni(1)–N(2)92.29(7)O(3)–Ni(1)–O(5)88.27(7)O(1)–Ni(1)–O(5)92.31(7)N(1)–Ni(1)–O(5)92.22(7)O(6)–Ni(1)–O(5)178.36(9)N(2)–Ni(1)–O(5)87.46(7)C(1)–O(1)–Ni(1)115.63(13)Table 3
Deviation
from the mean plane.
Deviations.u.AtomDeviations.u.Atom(Å)(Å)*0.0000(0.0000)Ni1*0.0000(0.0000)Ni1*0.0000(0.0000)O1*0.0000(0.0000)O3*0.0000(0.0000)N1*0.0000(0.0000)N2−0.1711(0.0028)C1−0.0050(0.0029)C4−0.5880(0.0033)C20.0376(0.0034)C5Atom* defining mean plane.It is seen that there are two water molecules
not chemically bonded to Ni(II) and located at the opposite site of alanine
group, and have no
significant interaction with the metal atom. A hydrogen bonding is observed
between the hydrogen atoms of coordinated and hydrated waters with the oxygen
atoms of the carboxylato groups,
there are many hydrogen bonds
responsible of the packing, and the values of these interactions are shown in
Table4. Also, the hydrogen bonds are seen between the hydrogen of the
amide nitrogen and the oxygen atoms of the hydrated water molecules and
carboxylato groups (Figure 2). The
hydrogen atoms on the water molecules and the amide nitrogens were all located
from a difference Fourier map. All are involved in an extensive
three-dimensional network of hydrogen bonds within the lattice.Table 4
Hydrogen bonds of the title
compound [Å and°].
D–H…Ad(D–H)d(H…A)d(D…A)<(DHA)O(5)–H(5OA)…O(4)#10.92(3)1.85(3)2.724(4)158(2)O(5)–H(5OB)…O(3)#20.77(2)1.97(2)2.732(2)175(3)O(6)–H(6OA)…O(2)#30.60(3)2.11(3)2.712(3)171(3)O(6)–H(6OB)…O(1)#40.81(2)2.11(3)2.687(2)169(3)N(1)–H(1NA)…O(10)#30.88(2)2.44(2)3.274(3)159(2)N(1)–H(1NB)…O(4)#20.75(3)2.31(2)3.022(2)159(4)N(2)–H(2NA)…O(11)#50.92(2)2.36(2)3.227(3)157(2)N(2)–H(2NB)…O(2)#40.90(2)2.28(2)3.183(2)173(3)O(10)–H(10A)…O(2)0.777(18)2.043(19)2.803(3)166(3)O(10)–H(10B)…O(10)#60.745(17)2.158(18)2.860(3)157(3)O(11)–H(11A)…O(11)#70.745(17)2.170(19)2.843(3)151(3)O(11)–H(11B)…O(4)#80.784(19)1.994(19)2.750(3)162(3)Symmetry transformations
used to generate equivalent atoms:#1x,y−1,z;#2−x+3/2,y−1/2,−z;#3x,y+1,z;#4−x+3/2,y+1/2,−z+1;#5x−1/2,y+1/2,z;#6−x+2,y,−z+1;#7−x+2,y,−z;#8x+1/2,y−3/2,z.Figure 2
Hydrogen bonding network of the
title compound.


## 4. Conclusions

This
communication describes the crystallographic characterization of a complex of
nickel(II) with L-alanine.
The method illustrated for the preparation of this complex must be extended to
other metal ions such as iron, copper, and zinc. In fact, nickel(II) was chosen
for our synthesis because it forms well-defined crystals that can be studied by X-ray
crystallography. The complex is a chelate with two bidentate alanine ligands
bonding through N and O and two water molecules. The oxygen of the carboxylato
groups of alanine is deprotonated by removal of its hydrogen with the hydroxyl
group of KOH producing water molecule.Supplementary Material
Crystallographic data for the structure
reported in this paper have been deposited at the Cambridge
Crystallographic Data Centre (CCDC) and allocated
deposition no. CCDC 718341 for the title compound and
can be obtained free of charge on application to CCDC
12 Union Road, Cambridge CB2 1EZ, UK (Fax: (internat.)
44(1223)336-033; E-mail:deposit@ccdc.cam.ac.uk).



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*Source: 168416-2009-03-18.xml*