8158
J. Phys. Chem. B 2009, 113, 8158–8169
Unusual Noncovalent Interaction Between the Chelated Cu(II) Ion and the π Bond in the
Vitamin B13 Complex, cis-Diammine(orotato)copper(II): Theoretical and Vibrational
Spectroscopy Studies
K. Helios,† R. Wysokiński,† W. Zierkiewicz,† L. M. Proniewicz,‡ and D. Michalska*,†
Faculty of Chemistry, Wrocław UniVersity of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław,
Poland, Faculty of Chemistry, Jagiellonian UniVersity, R. Ingardena 3, 30-060 Kraków, Poland
ReceiVed: March 2, 2009; ReVised Manuscript ReceiVed: April 22, 2009
The crystal structure of the Cu(II) complex with Vitamin B13 (orotic acid), cis-[Cu(oro)(NH3)2] has revealed
the presence of unusual, noncovalent π-type interaction between the chelated Cu(II) ion and the CdC bond
of the uracilate ring [Michalska et al. Polyhedron 2007, 26, 4303]. In this work, the origin and strength of
this interaction is thoroughly investigated. Comprehensive studies of the molecular structures and vibrational
spectra of the title complex have been performed by using the unrestricted density functional theory methods,
B3LYP, and the newly developed M05-2X functional. Calculations at the UMP2 level were also carried out
for comparison. A variety of basis sets have been employed in the DFT calculations, including aug-cc-pVTZ,
D95V(d,p), SDD, and LanL2DZ. The 63Cu/65Cu isotope substitution technique was applied to identify the
copper-ligand vibrations in the infrared spectra. The clear-cut assignment of all the bands in the FT-IR and
Raman spectra of the title complex has been made on the basis of the calculated potential energy distribution,
PED. It is shown that an extremely intense band at 1210 cm-1 in the Raman spectrum of cis-[Cu(oro)(NH3)2]
is diagnostic for the N-1 deprotonation of the uracilate ring and coordination to the copper(II) ion. The B3LYP
functional performs better than M05-2X in predicting vibrational frequencies of this complex in the solid
state. Intermolecular interactions in crystal were modeled by the supramolecular system consisting of cis[Cu(oro)(NH3)2], ethylene (above), and formaldehyde (below the copper coordination plane). The stable
structure of this system has been predicted only by the M05-2X and MP2 methods, which include dispersion
energy, whereas the B3LYP calculations failed in geometry optimization. The distance between the Cu atom
and the CdC bond, predicted by the M05-2X method (3.00 Å) is similar to the van der Waals contacts
between the stacking bases in DNA. The calculated interaction energy between the chelated Cu(II) complex
and ethylene amounts to -7.33 kcal mol-1, which is similar to that determined for stacked uracil dimer. It is
concluded that the London dispersion energy plays a significant role in the noncovalent interaction between
the chelated Cu(II) ion and the uracilate ring in the crystal of cis-[Cu(oro)(NH3)2]. Many copper enzymes in
their active sites contain the chelated Cu(II) ion and the aromatic groups (Phe, Tyr and Trp) as the potential
binding sites; therefore, the noncovalent copper(II)-π interaction can be very important for the structure and
functioning of these enzymes.
1. Introduction
Orotic acid (6-carboxyuracil, vitamin B13) is a key intermediate in biosynthesis of nucleic acids, being the only precursor in
the pathway to formation of all pyrimidine nucleotides in living
organisms.1,2 Vitamin B13 also plays the main role in the
metabolism of vitamins B6 (folic acid) and B12 (cobalamine).
Orotic acid has also attracted growing attention in medicine,
since it is used as the carrier for some metal ions in curing
syndromes associated with a deficiency of Mg2+, Ca2+, Cu2+,
and Zn2+ ions.3-5 The treatment with Mg-orotate yields excellent
results in the prevention and therapy of heart and vessels
diseases,6 and it markedly improves the liver enzymes activity.7
Moreover, platinum(II) complexes with orotic acid and diaminocyclohexane ligands have revealed some antitumor properties.8 In view of the biological importance of orotic acid, the
coordination chemistry of this ligand has been the subject of
very intensive studies.9-18
* Corresponding author. E-mail: [email protected].
†
Wrocław University of Technology.
‡
Jagiellonian University.
Recently,9 we have reported the crystal and molecular
structure of cis-diammine(orotato)copper(II), cis-[Cu(oro)(NH3)2], and demonstrated the presence of unusual, noncovalent
copper(II)-π interaction between the chelated Cu(II) ion and
the CdC double bond of the uracil ring. In this complex, the
copper(II) cation is chelated by the carboxylate oxygen atom
and the deprotonated ring nitrogen atom of the orotate ligand.
Two ammonia nitrogen atoms complete the square-planar
environment around copper in the basal plane. In the crystal,
one carbonyl oxygen atom (O4a) from the neighboring uracil
ring forms a long copper-oxygen axial bond, whereas the sixth
apical copper-binding site is located, surprisingly, at the π(CdC)
bond of the other uracil ring, as illustrated in Figure 1.
The distance between the copper atom and the midpoint of
the CdC bond (3.293 Å) is similar to the van der Waals contacts
between the stacking bases in DNA. It seems that the noncovalent Cu(II)-π binding force is very important in stabilizing
the columnar, polymeric structure of this complex.
In the past decade, much interest has been focused on the
significance of the cation-π noncovalent interactions in protein
folding, the functioning of ionic channels in membranes, and
10.1021/jp901912v CCC: $40.75  2009 American Chemical Society
Published on Web 05/19/2009
Cu(II)-cis-[Cu(oro)(NH3)2] Noncovalent Interaction
J. Phys. Chem. B, Vol. 113, No. 23, 2009 8159
M+ (or M2+) interacting with olefins or aromatic molecules.21-26
Interaction between the chelated copper(II) complex and the
CdC double bond has not been studied as yet. The main goal
of this work is to provide detailed insights into the molecular
and electronic structure and the nature of bonding in cisdiammine (orotato)copper(II).
Ab initio MP2 and density functional theory (DFT) methods,
including the newly developed functional M05-2X,32,33 have
been used to study the structure and vibrational spectra of the
isolated cis-[Cu(oro)(NH3)2] complex. The M05-2X method
belongs to the new generation of DFT methods and shows very
good performance for noncovalent interactions, especially weak
interactions, π · · · π stacking, and hydrogen bonding. Thus, it is
interesting to examine the performance of the M05-2X vs
B3LYP functionals in calculations of the structure and vibrational spectra of the title complex. The clear-cut assignment of
the experimental Raman and FT-IR spectra of cis-[Cu(oro)(NH3)2] has been made on the basis of the calculated
potential energy distribution (PED). To aid the assignment of
the copper-ligand vibrations, the 63Cu/65Cu isotope substitution
method has been applied.
The intermolecular interactions were studied in the supramolecular system consisting of cis-[Cu(oro)(NH3)2], ethylene
(above), and formaldehyde (below the copper coordination
plane). The optimized structure of this system has been obtained
only in calculations by the M05-2X and MP2 methods, which
include dispersion energy.
Figure 1. The view of the dimer unit of cis-[Cu(oro)(NH3)2] displaying
the pseudooctahedral environment around the copper ions.
in various molecular recognition processes involving aromatic
side chains of proteins.19,20 A large number of experimental and
theoretical studies have been carried out on the factors that
control the binding geometry, strength, and specificity of a
cation-π interaction for alkali metal cations 21,22 and transition
metal monocations, including Cu+.23-26
Copper cations play an essential role in many intracellular
metabolic processes.27 Wilson’s and Menkes diseases are two
genetically inherited disorders of Cu metabolism. Copper
deficiency is related to cardiac myopathy and ischemic heart
disease.28 Moreover, it is suggested that the interaction between
copper cations and the β-amyloid peptide (containing aromatic
tyrosine side chain) is associated with the pathogenesis of
Alzheimer’s disease.29 Copper-containing oxidases (amine oxidases, galactose oxidase, tyrosinase, ceruloplasmin, laccase)
catalyze the oxidation of a wide variety of substrates ranging
from small molecules, such as methane, to large peptides.
Elucidation of crystal structures for many of these enzymes has
revealed that the tyrosine residue is coordinated to the Cu(II)
ion, in the active site of enzyme.30,31 For example, in galactose
oxidase, the Tyr residue occupies an axial position in the
distorted square-pyramidal geometry around copper. Additionally, the aromatic indole ring of tryptophan (Trp) is also present
in the active site.31 Hence, it is evident that the aromatic groups
of amino acids (Phe, Tyr, and Trp) in proteins can be viewed
as important binding sites for the copper ion.
It should be emphasized that earlier theoretical studies on
cation-π interaction were carried out for a bare metal cation
2. Methods
2.1. Experimental Section. The crystals of cis-[Cu(oro)(NH3)2] were obtained as described in ref 9. The complex
analogs with pure stable isotopes, 63Cu and 65Cu, were obtained
in a microscale, in a similar way. In each synthesis, 0.05 mmol
of copper(II) isotope (in the form of copper(II) nitrate or
copper(II) sulfate) was added to a solution containing 0.05 mmol
of orotic acid, 5 cm3 of concentrated ammonia, and 5 cm3 of
ethanol. The reaction mixture was heated at 313 K under reflux
for 1 h. Upon cooling, the complex precipitated in the form of
dark-purple crystals.
The FT-infrared (MIR) spectra of cis-[Cu(oro)(NH3)2] were
measured in KBr pellets on a Bruker IFS 113 V spectrometer,
in the range 4000-400 cm-1 (with a resolution of 2 cm-1). The
far-infrared (FIR) spectra (600-50 cm-1) of each isotopic
species, 63Cu and 65Cu, were recorded on IFS 66/S Bruker
spectrometer using Nujoll mull technique and polyethylene
discs. The accuracy of the readings was (1.0 cm-1. The Raman
spectrum of the copper(II) complex was recorded on a Jobin
Yvon spectrometer, model T6400, using a CCD camera as a
detector (Princeton Instruments). Excitation was provided by
an argon laser (514.5 nm line). For the measurements, a few
milligrams of the compound was placed in a capillary tube and
measured with a resolution of 2 cm-1.
2.2. Theoretical. The complex investigated is an open-shell
system (d9 electron configuration of Cu(II) cation), which
requires the use of the unrestricted methods for calculations of
an electronic structure. Since a spin contamination of the UHF
wave function may occur, therefore, the expectation value of
the total spin, Ŝ2, should be examined. The final Ŝ2 was equal
to 0.7503 and 0.7500, in UMP2 and unrestricted DFT calculations, respectively. This is in perfect agreement with the value
of 0.7500 corresponding to the doublet ground state wave
function with no spin contamination and confirms the validity
of the theoretical results. The calculated ground electronic state
for the title complex is doublet, 2A′.
8160
J. Phys. Chem. B, Vol. 113, No. 23, 2009
Helios et al.
In the first part, calculations were performed for the isolated
cis-[Cu(oro)(NH3)2] complex. The optimized geometry, harmonic frequencies, IR intensities and Raman scattering activities
were computed using the density functional gradient corrected
three-parameter hybrid B3LYP functional34,35 and the MöllerPlesset second-order perturbation (MP2) method. The newly
developed DFT method, M05-2X, which has recently become
available to us, is also employed in this study. This new method
includes spin kinetic energy density in both the exchange and
correlation functionals; moreover, it is completely free of selfcorrelation error.32,33 All calculations were based on an unrestricted mechanism; however, for clarity, U will be omitted from
the UMP2, UB3LYP, and UM05-2X abbreviations, in the
remaining text.
A variety of basis sets have been used in computations. The
largest basis set is aug-cc-pVTZ, which is the correlationconsistent, polarized valence, triple-ζ basis set augmented with
diffuse functions on all atoms.36,37 For the title complex, it
employs 875 contracted basis functions (1710 primitives),
including the all electron (21s,17p,9d,3f,2g)/[8s,7p,5d,3f,2g]
contracted basis set for Cu. It should be mentioned that these
calculations were computationally very expensive. The SDD
relativistic effective core potential supplemented by valence
basis sets on all atoms38 and the effective core potential of Hay
and Wadt39 with the concomitant basis set were employed (the
latter basis set is denoted as I). We have also used the combined
basis sets: LanL2DZ for Cu in conjunction with the polarized
valence double-ξ basis set (D95V(d,p))40 for all ligands (denoted
as II). The basis set III utilized the aug-cc-pVTZ basis set for
all nonmetal atoms in conjunction with LanL2DZ for copper.
A natural bond orbital (NBO) analysis was applied separately
to R and β spin density matrices, as described by Carpenter
and Weinhold for open-shell species.41,42 This method has
provided the character of valence hybrid orbitals on atoms. Each
natural bonding orbital, σAB, can be written in terms of two
directed valence hybrids, hA, hB on atoms A and B, with
corresponding polarization coefficients, cA and cB:
σAB ) cAhA + cBhB
(1)
Polarization coefficients vary smoothly from covalent (cA ) cB)
to ionic (cA , cB) limit.
To provide the detailed vibrational assignment of the experimental spectra, a normal-mode analysis was carried out, and
the potential energy distribution was calculated at each level of
theory. The nonredundant set of 60 internal coordinates for the
complex was defined, as recommended by Pulay et al.43 The
symmetrized internal coordinates for the ligands were analogous
to those reported in our earlier studies on 1-methyluracil.44 The
procedure for normal coordinate analysis was described
previously,44,45 and calculations were performed using the Balga
program.46
In the region below 1500 cm-1, the B3LYP-calculated
frequencies show very good agreement with experiment;
therefore, they are not scaled in this work. However, the
calculated harmonic frequencies higher than 1500 cm-1 are all
overestimated in comparison to the experimental ones. This is
mainly caused by the neglect of anharmonicity, the incomplete
treatment of electron correlation, and basis set truncation effects.
To aid comparison between the predicted and observed frequencies, various scaling strategies have been devised.47,48 The
procedure developed by Pulay and co-workers47 uses about a
dozen parameters to scale force constants in internal coordinates.
Schlegel et al.48 have shown that the direct scaling of the
Figure 2. The optimized molecular structure of cis-[Cu(oro)(NH3)2],
and the numbering of atoms.
computed harmonic frequencies by two scaling factors, one
below and one above 1800 cm-1 (dual scaling), greatly improves
the agreement between the theoretical and experimental results.
In this work, we have also employed two scaling factors: 0.920
(above 1800 cm-1) and 0.957 (in the region of 1800-1500
cm-1) for the B3LYP-calculated harmonic frequencies. These
factors were determined by minimizing the root-mean-square
errors between the theoretical and observed frequencies. It
should be mentioned that the B3LYP predicted ν(NH) frequency
of the N-Hi bond involved in the intramolecular hydrogen bond
in the title complex is slightly lower than experimental;
therefore, the frequency of the corresponding mode 8 was not
scaled. The scaling factors for frequencies determined in this
work will be used in our further theoretical study of the
vibrational spectra of the Vitamin B13 complexes with transition
metal ions.
In the second part of our theoretical studies, we performed
full geometry optimization of the supramolecular system
consisting of cis-[Cu(oro)(NH3)2], ethylene (above the copper
complex), and formaldehyde (below the complex). An attempt
to optimize this structure using the unrestricted B3LYP method
was unsuccessful. The stable structure of this supramolecule
has been obtained at the MP2/I, M05-2X/I, and M05-2X/II levels
of theory. The binding energy between the ethylene molecule,
A, and the rest of the supramolecule, B (cis-[Cu(oro)(NH3)2
bonded with formaldehyde), was calculated as the difference
between the total electronic energy of the supramolecular system
and the sum of the energies of A and B. This energy was then
corrected for basis set superposition error (BSSE) using the
counterpoise (CP) method.49 All computations were performed
with the Gaussian 03 (Rev. E.01) set of programs.50
3. Results
3.1. Structure. The optimized molecular structure and the
numbering of atoms of cis-[Cu(oro)(NH3)2] are shown in Figure
2. In this complex, the copper atom is chelated by the
carboxylate oxygen atom O1 and the N1-deprotonated nitrogen
atom of the uracilate ring (the numbering of atoms in the ring
refers to that commonly used for uracil and its derivatives). The
two ammonia nitrogen atoms, N4 and N5, complete the squareplanar basal plane.
Table 1 lists the theoretical bond lengths and angles calculated
by the MP2, M05-2X, and B3LYP methods using various basis
sets and the experimental geometrical parameters obtained from
the X-ray data for crystal.9 As follows from this comparison,
the theoretical Cu-N1 and Cu-O1 bond lengths are slightly
shorter, whereas the Cu-ammonia (Cu-N4 and Cu-N5) bond
lengths are slightly longer than experimental, regardless of the
method used in calculations. This discrepancy can be caused
by the fact that the theoretical values correspond to an isolated
Cu(II)-cis-[Cu(oro)(NH3)2] Noncovalent Interaction
J. Phys. Chem. B, Vol. 113, No. 23, 2009 8161
TABLE 1: Comparison of Experimental and Theoretical Bond Lengths (Å) and Angles (°) of cis-[Cu(oro)(NH3)2], Calculated
by the MP2, M05-2X and B3LYP Methods with Various Basis Sets
Cu-N1
Cu-O1
Cu-N4
Cu-N5
N1-C2
C2-N3
N3-C4
C4-C5
C5-C6
C6-N1
C6-C7
C7-O1
C7-O3
C2-O2
C4-O4
O1-Cu-N1
N1-Cu-N5
N4-Cu-N5
N4-Cu-O1
C7-O1-Cu
C6-N1-Cu
N1-C2-N3
N1-C2-O2
C2-N3-C4
N3-C4-O4
N3-C4-C5
C4-C5-C6
C5-C6-N1
C6-N1-C2
C5-C6-C7
C6-C7-O3
C6-C7-O1
O3-C7-O1
exptla
MP2/Ib
M05-2X/Ib
B3LYP/Ib
B3LYP/SDD
M05-2X/IIc
B3LYP/IIc
B3LYP/IIId
B3LYP/aug-cc-pVTZ
1.999(1)
1.959(1)
1.996(1)
1.955(1)
1.363(1)
1.377(1)
1.372(1)
1.439(1)
1.350(1)
1.365(1)
1.517(1)
1.278(1)
1.230(1)
1.233(1)
1.234(1)
82.5(1)
96.6(1)
90.4(1)
90.5(1)
116.4(1)
112.1(1)
117.6(1)
124.3(1)
126.5(1)
120.3(1)
114.0(2)
118.4(1)
125.2(1)
117.9(1)
121.0(2)
119.6(1)
114.9(1)
125.6(1)
1.985
1.928
2.095
2.055
1.390
1.407
1.436
1.473
1.386
1.420
1.537
1.367
1.265
1.296
1.273
84.5
97.7
96.9
80.9
117.1
112.2
117.2
123.4
127.0
120.0
113.1
119.7
123.8
119.2
122.3
122.1
112.3
125.6
1.970
1.917
2.061
2.026
1.363
1.382
1.413
1.456
1.358
1.391
1.517
1.338
1.238
1.276
1.248
83.6
97.5
97.7
81.3
117.5
112.6
117.4
123.0
125.6
119.8
113.6
119.0
124.2
119.4
121.9
121.8
112.4
125.9
1.979
1.942
2.078
2.041
1.376
1.390
1.425
1.457
1.369
1.394
1.518
1.349
1.246
1.281
1.255
83.3
97.8
98.2
80.7
116.9
113.1
117.0
123.3
126.7
119.9
113.2
119.6
123.9
119.7
122.2
122.7
112.7
124.6
1.964
1.926
2.070
2.025
1.376
1.391
1.425
1.458
1.369
1.395
1.520
1.349
1.246
1.281
1.255
84.0
97.6
97.4
81.0
116.7
112.8
117.2
123.1
126.6
119.9
113.2
119.6
124.0
119.5
122.2
122.5
112.6
124.8
1.967
1.900
2.077
2.032
1.357
1.373
1.404
1.454
1.353
1.378
1.522
1.315
1.214
1.250
1.221
84.5
95.8
96.9
82.7
116.8
111.5
117.0
123.6
127.3
119.9
113.0
118.7
124.8
119.3
121.1
121.2
113.2
125.6
1.977
1.923
2.099
2.049
1.368
1.382
1.414
1.456
1.363
1.380
1.523
1.322
1.221
1.253
1.228
84.0
97.5
97.6
81.9
116.5
112.1
116.6
123.9
127.5
120.0
112.7
119.3
124.4
119.7
121.6
122.2
113.4
124.3
1.958
1.911
2.097
2.036
1.360
1.375
1.407
1.445
1.351
1.375
1.518
1.313
1.211
1.245
1.218
84.3
97.1
96.4
82.2
116.4
112.0
116.7
123.8
127.3
120.0
112.6
119.5
124.4
119.5
121.7
122.2
113.4
124.4
1.968
1.912
2.099
2.039
1.361
1.375
1.407
1.445
1.351
1.375
1.518
1.314
1.211
1.245
1.219
84.1
96.9
96.7
82.3
116.6
112.0
116.6
123.8
127.3
120.0
112.7
119.5
124.3
119.6
121.7
122.1
113.4
124.4
a
X-ray data from ref 9 (the estimated standard deviation in parentheses). b LanL2DZ basis set on all atoms, denoted as I. c D95V(d,p) basis
set on all nonmetal atoms and LanL2DZ basis set on Cu, denoted as II. d aug-cc-pVTZ basis set on all nonmetal atoms and LanL2DZ basis set
on Cu, denoted as III.
cis-[Cu(oro)(NH3)2] in the gas phase; therefore, the intermolecular interactions are neglected.
Both the Cu-N1 and Cu-O1 bond lengths calculated by the
B3LYP functional with two basis sets (I and II) are closer to
experiment than those predicted by the M05-2X functional with
the same basis sets. A further enlargement of the basis set in
the B3LYP calculations (e.g. the use of aug-cc-pVTZ) does not
improve the results. The copper-orotate (Cu-N1 and Cu-O1)
atom distances are underestimated by 0.031 and 0.047 Å,
respectively, whereas the copper-ammonia bond lengths are
overestimated by about 0.1 Å, in comparison with experiment.
It should be noted, however, that the bond lengths in the uracilate
ring predicted at the B3LYP/aug-cc-pVTZ level of theory show
the best agreement with experiment. For example, the calculated
N1-C2 (1.361 Å) and C2-N3 (1.375 Å) bond lengths nearly
reproduce the experimental values, 1.363(1) Å and 1.377(1) Å,
respectively.
As is seen in Table 1, calculations with the MP2 method using
the LanL2DZ basis set seriously overestimate all atom distances
in the orotate ligand. It is evident that the MP2 method requires
a larger basis set for accurate prediction of the molecular
geometry.
All the bond lengths calculated by M05-2X are consistently
shorter than those computed by the B3LYP functional (with
the same basis sets). In some cases, this difference amounts to
nearly 0.01 Å (e.g. for C2-N3, N3-C4, and C5dC6 bonds).
It seems that the M05-2X functional performs better than
B3LYP in prediction of the bond lengths in the uracil ring.
Examination of the results listed in Table 1 clearly indicates
that the accurate atom distances can be obtained only with these
basis sets, which contain the polarization functions (and diffuse
functions) on all nonmetal atoms; for example, the D95V(d,p)
or aug-cc-pVTZ basis sets. This is particularly important for
the bonds involving oxygen or nitrogen atoms. For example,
the C7-O1 distances calculated at the MP2/I and B3LYP/I
levels of theory (without polarization functions), are equal to
1.367 and 1.349 Å, respectively, whereas the experimental value
is much lower, 1.278(1) Å.
The O1-Cu-N1 bond angle in the coordination ring is quite
well predicted in calculations at all levels of theory. Similarly,
the calculated N1-Cu-N5 bond angle shows very good
agreement with experiment. However, the other two bond
angles, N4-Cu-N5 and N4-Cu-O1, show some discrepancies
between the theoretical and experimental values. This is caused
by the fact that in crystal, the N4 nitrogen atom is involved in
the intermolecular hydrogen bonding with other complex unit,
which may lead to some distortions of the geometry around
copper. The calculated bond angles of the uracil ring are accurate
to within 1° in all theoretical methods.
In summary, the new M05-2X density functional method
predicts the copper-orotate (Cu-O1 and Cu-N1) bond lengths
in a slightly worse agreement with experiment in comparison
to the results obtained by the B3LYP method with the same
basis set. On the other hand, M05-2X performs better than
B3LYP in predicting geometrical parameters for the uracil ring.
8162
J. Phys. Chem. B, Vol. 113, No. 23, 2009
Helios et al.
TABLE 2: The NBOa Description of the Bonds between
Copper and Ligands in the cis-[Cu(oro)(NH3)2] Complex
cAhA + cBhBb
σ(A-B) bond
σ(Cu-O1)
σ(Cu-N1)
σ(Cu-N4)
σ(Cu-N5)
0.376
0.386
0.326
0.347
(d1.3sp2)Cu
(d1.0sp2)Cu
(d0.9sp2)Cu
(d0.9sp2)Cu
+
+
+
+
0.926
0.922
0.946
0.938
total occupancyc
(sp3.5)O1
(sp2.5)N1
(sp4)N4
(sp4.5)N5
1.879
1.866
1.930
1.915
a
Calculations performed by the unrestricted M05-2X method
using the D95V(d,p) basis set for nonmetal atoms and LanL2DZ for
Cu. b hB is an average hybrid orbital for R and β spin electrons.
c
The sum for R and β spin electrons.
3.2. NBO Analysis. The natural bond orbital (NBO) analysis
of cis-[Cu(oro)(NH3)2] has provided detailed insight into the
bonding in this complex. The electronic ground state is 2A′. In
calculations performed by the unrestricted M05-2X method
using the II basis set, the natural electron configuration of Cu
is [core] 3d9.284s0.324p0.31. Thus, 18 core electrons and 9.91
valence electrons give the total of 27.91 electrons on the Cu
cation in this complex. This is consistent with the calculated
natural charge on Cu, equal to +1.09e (it corresponds to the
difference between the nuclear charge (Z ) 29) and 27.91e). It
is interesting to note that in cis-[Cu(oro)(NH3)2], the effective
natural charge on the chelated copper(II) ion is close to +1.
In the case of an open-shell system, the NBO analysis is
performed separately for R and β-spin electrons.42,51 The results
obtained for R-spin electrons show strong donations from
various spn natural hybrid orbitals on N1, O1, N4, and N5 atoms
to the Cu acceptor molecular orbitals. Each donation corresponds
to a chemical picture of the L f Cu coordination bond from a
lone pair orbital on the ligand atom to copper. Calculations
performed for β-spin electrons have revealed the hybridization
of Cu atomic orbitals and formation of strongly polarized σ
bonds between Cu and the ligand atoms. Thus, the NBO results
for R and β-spin electrons complement each other in the
description of the copper-ligand bonds in the planar complex.
These results are collected in Table 2.
The hybrid orbitals on Cu correspond to an idealized dsp2
hybridization of transition metal M2+ cations in square-planar
complexes. According to NBO, the hybrids are a mixture of
4s, 4px, 4py, and 3dxy atomic orbitals (with a minor contribution
from the 3dx2-dy2 orbital). As is seen in this table, σ(Cu-O1)
is a bond resulting from the overlap of a d1.3sp2 hybrid on Cu
with an sp3.5 hybrid on the O1 atom. Similarly, the σ(Cu-N1)
bond is formed by an overlap of a dsp2 hybrid on copper with
an sp2.5 hybrid on N1. Both the σ bonds are strongly polarized
toward the O1 and N1 atoms. The calculated total electron
population (occupancy) on each bond is much lower than the
idealized occupancy of 2e. This indicates a strong electron
delocalization within the chelate ring. Two ammonia nitrogen
atoms, N4 and N5, donate electron density from the sp4- and
sp4.5-type hybrids, respectively, to two d0.9sp2 hybrid orbitals
on Cu.
The NBO method provides the donor-acceptor interaction
energy between the orbitals of the conjugated bonds. The
strength of this interaction can be estimated by the second-order
perturbation theory.41 The selected interacting orbitals and the
interaction energies (E2) are available in the Supporting
Information. As follows from these results, the π orbitals of
the C7dO3, C5dC6, and C4dO4 bonds are strongly conjugated. This leads to a relatively high occupancy of the
π*(C5dC6) antibonding orbital, which should be formally
empty. A gain of electron population in the π*(CdC) orbital
can be directly correlated with a weakening of the corresponding
CdC bond.41 Thus, it is expected that the C5dC6 bond in the
orotate ligand is weaker than that in uracil, which will be
confirmed by the vibrational spectra (see the next section).
Furthermore, NBO analysis shows that π electron delocalization builds a partial double bond between the N1 and C2
atoms. All these results indicate that the N1-deprotonated
uracilate ring displays strong π-donating capability, and the
strength of the copper-N1 bond should be similar to that between
Cu(II) and pyridine.
3.3. Vibrational Spectra. Theoretical vibrational spectra
were computed by the unrestricted B3LYP method using several
basis sets: SDD, LanL2DZ, D95V(d,p), and aug-cc-pVTZ.
Moreover, calculations of the spectra were also performed by
the novel M05-2X functional using the D95V(d,p) basis set on
all nonmetal atoms, and the LanL2DZ basis set on Cu (II basis
set). To allow the comparison of the corresponding vibrational
frequencies, normal coordinate analysis was carried out at each
level of theory. The detailed examination of all the theoretical
results has revealed that the best overall agreement between
the experimental and theoretical spectra gives the B3LYP
method with the II or III basis sets (the latter denotes the augcc-pVTZ basis set for all nonmetal atoms and LanL2DZ for
Cu). However, calculations of the spectra at the B3LYP/III level
are computationally very expensive, whereas the results are very
similar to those obtained with the II basis set. The performance
of the unrestricted M05-2X functional in calculations of the
vibrational frequencies is very disappointing. All the calculated
frequencies are seriously overestimated in comparison with
experiment. For example, the predicted ν(C7dO3) carboxyl and
ν(C4dO4) carbonyl stretching vibrations are larger than experiment by about 200 cm-1 (see the Supporting Information).
Recently, Riley and co-workers52 performed a critical assessment of the performance of 37 DFT methods for their ability
to accurately calculate molecular properties. These authors have
concluded that B3LYP is the most accurate functional for
calculating vibrational frequencies. Our conclusions from this
work support their findings and show that the B3LYP/II level
of theory is more reliable than the M05-2X/II method for
predicting vibrational spectra of the Cu(II) complex.
Therefore, in this paper, the theoretical frequencies, infrared
intensities, Raman scattering activities, and PED calculated at
the B3LYP/II level of theory are shown in Tables 3 and 4,
whereas all other theoretical results are compared in the
Supporting Information (Tables 1S and 2S).
Orotate Ligand Vibrations. Figure 3 illustrates the experimental FT-IR and Raman spectra of cis-[Cu(oro)(NH3)2] in the
range from 3500 to 600 cm-1. Table 3 lists the observed bands
and the theoretical results obtained for this region.
As is seen in Figure 3, the Raman spectrum of cis[Cu(oro)(NH3)2] is dominated by an extremely intense band at
1210 cm-1. According to PED, this band corresponds to mode
23, which is generated by the uracilate ring stretching vibration
(69%) coupled with the in-plane δ(C5-H) bending vibration
(17%), as shown in Table 3. A similar strong band has been
observed in the FT-Raman spectra of cis-[Pt(oro)(NH3)2]10 and
[Ni(oro)(H2O)4],11 at 1217 and 1215 cm-1, respectively. In all
these complexes, the metal ion binds to the deprotonated N1
nitrogen atom of the uracilate ring. In the FT-Raman spectrum
of anhydrous orotic acid, the corresponding very strong band
occurs at 1251 cm-1.9 Thus, it can be concluded that the shift
of this intense Raman band to the range 1220-1210 cm-1 is
diagnostic for the N1 deprotonation of the uracil ring and
formation of the N1-metal bond in these complexes.
Cu(II)-cis-[Cu(oro)(NH3)2] Noncovalent Interaction
J. Phys. Chem. B, Vol. 113, No. 23, 2009 8163
TABLE 3: Experimental IR and Raman Bands and Theoretical Frequencies (cm-1), Infrared Intensities (IIR, km mol-1), and
Raman Scattering Activities (SR Å4 amu-1) for cis-[Cu(oro)(NH3)2] Calculated at the B3LYP Level of Theory
theora
exptl
no.
IR
Raman
1
2
3
4
5
6
7
8
3339
3317
3264
ov
3181
3135
3105
2980
2872
2812
9
10
11
12
13
14
15
16
17
18
19
20
21
22
1661 vs
1639 vs
ov
1614 s
ov
1580 sh
ov
1548 w
1479 m
1412 m
1374 s
1315 m
1292 s
1268 s
1240 sh
ov
1141 w
1050 w
1021 m
944 m
894 br
ov
843f w
802 m
ov
773 m
715 w
668 w
619 w
ov
607 w
ov
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
m
m
br
m
sh
sh
br
w
w
3339
3319
ov
3257
3184
ov
3104
w
w
w
m
m
1674 w
1643e sh
1631
1615
1605
1576
ov
ov
1470
1420
1364
1315
ov
1266
s
sh
sh
m
m
m
w
m
w
1210 vs
1050 w
950 w
ov
844 w
800 m
775 br
668 w
ov
ov
ov
602 s
ωb
IIR
SR
band assignment, PED (%)c
3328
3319
3298
3247
3182
3334
3002
2942d
32
19
54
36
13
68
9
777
72
71
55
160
117
106
66
55
1701
1631
1699
1615
1605
1578
1574
1550
1470
1395
1372
1288
1315
1198
644
32
385
545
21
25
2
141
158
204
40
76
489
260
73
1
173
17
5
56
19
15
33
30
13
3
4
16
1216
1157
1043
1028
935
866
807
676
796
772
773
732
673
640
636
596
582
12
3
18
18
17
18
135
64
26
16
36
0
15
47
43
4
12
24
3
<1
14
10
3
2
2
<1
52
<1
1
3
1
4
5
16
νa NH3 (N4) (100)
νa NH2° (N5) (100)
νa NH3 (N4) (100)
νs NH2° (N5) (100)
νs NH3 (N4) (100)
ν N3H (100)
ν C5H (100)
ν NHi (N5) (100)
ν17 + ν18 (1479 + 1412)2891)
2ν18 (2 × 1412)2824)
ν25 + ν39 (1050 + 602)1652)
ν C4O (80)
δa NH3 (N5) (98)
ν C7O3 (91)
ν C2O (+54), δ (U ring) (27)
δa NH3 (N4) (98)
ν C5C6 (-58), ν C4O (+10)
δa NH3 (N4) (92)
δa NH3 (N5) (76), ν C2O (-11)
ν (U ring) (75)
ν N3C2 (-36), ν N1C2 (+26), ν C6N1 (+19)
δ N3H (62), ν C2O (-22)
ν C7O1 (-66), δs NH3 (N5) (30)
δs NH3 (N5) (78), ν C7O1 (+12)
δs NH3 (N4) (97)
ν35 + ν40 (668 + 590 ) 1258)
ν (U ring) (69), δ C5H (17)
δ C5H (35), ν (U ring) (35), ν C7O1 (-12)
ν (U ring) (77)
δ (U ring) (52), ν C6C7 (+26)
ν (U ring) (60), ν C6C7 (-21)
γ C5H (+61), τ (U ring) (21), γ C7O3 (-10)
Fr NH3 (N5) (89)
γ N3H (85), τ (U ring) (15)
γ C7O3 (-53), γ C4O (+14), γ C5H (-13)
δ C7O3 (-67), ν C4C5 (+10)
γ C2O (+80), γ C4O (+20)
γ C4O (-59), τ (U ring) (25), γ C2O (+16)
δ C2O (-25), δ chel (23), δ C4O (-18)
Fr ΝΗ3 (Ν5) (77), Fr ΝΗ3 (Ν4) (16)
Fr ΝΗ3 (Ν4) (74), Fr ΝΗ3 (Ν5) (10)
δ (U ring) (64), δ chel (14)
δ (U ring) (67), δ C2O (14)
a
Calculations performed with the D95V(d,p) basis set for all nonmetal atoms and LanL2DZ for Cu atom. b Two scaling factors for the
calculated harmonic frequencies have been used: 0.920 for modes 1-7 and 0.957 for modes 9-16. Other calculated frequencies are left
unscaled; see text. c The predominant components of the PED matrix or their linear combination (e.g., stretching or bending of the ring).
Abbreviations: ν, stretching; δ, in-plane bending or deformation; Fr, rocking; γ, out-of-plane bending; τ, torsion; br, broad; m, medium; ov,
overlapped; s, strong; sh, shoulder; w, weak; v, very; chel, chelating ring; U, uracilate ring. Subscripts: a, asymmetric; s, symmetric. The +
sign corresponds to a simultaneous elongation (or contraction) of the bonds or to the in-phase bending motion of the A-B bonds. The - sign
has the opposite meaning. d Downward shift of ν(NHi) frequency due to the intramolecular N-Hi · · · O2 hydrogen bond. e Crystal field effect;
see text. f An upward shift of γNH frequency due to an intermolecular hydrogen bonding in crystal.
The medium intensity bands at 1479, 1412, 1021, and 944
cm-1 in the FT-IR spectrum of cis-[Cu(oro)(NH3)2] have been
assigned to the uracilate ring vibrations (modes 17, 18, 26, and
27, respectively) on the basis of the calculated PED. It should
be noted that the B3LYP-calculated (unscaled) frequencies of
these modes are in very good agreement with experiment.
Both the Raman and infrared spectra of cis-[Cu(oro)(NH3)2]
exhibit a very complex pattern in the range 1700-1500 cm-1,
where several modes should be observed: three CdO stretching
vibrations; ν(C5dC6) stretching; and four asymmetric bending
vibrations, δa(NH3), of two ammonia groups. The theoretically
predicted intensity pattern of the IR and Raman bands can be
of great help in making assignment. However, overlapping
fundamental transitions, Fermi resonance effects, and crystal
field splitting of some modes cause difficulties in making the
definite assignment in this range. As revealed by our X-ray
study,9 in the crystal of cis-[Cu(oro)(NH3)2], each two complex
molecules are linked by a pair of linear N3-H3 · · · O4a hydrogen
bonds (see Figure 1). A very similar pattern of intermolecular
hydrogen bonding was reported for dimers of 1-methyluracil
(1-MeU) in crystal.53
Thus, in the vibrational spectra of these molecules, we may
expect a splitting of the ν(C4dO4) stretching vibrations into
two modes, one symmetric and one antisymmetric, with respect
to the center of symmetry in the dimer. Therefore, the infrared
and Raman frequencies of ν(C4dO4) should be different. In
8164
J. Phys. Chem. B, Vol. 113, No. 23, 2009
Helios et al.
TABLE 4: Experimental IR and Raman Bands; the 63Cu/65Cu Isotope Shift Effect; and the Theoretical Frequencies (cm-1),
Infrared Intensities (IIR, km mol-1), and Raman Scattering Activities (SR, Å4 amu-1) for cis-[Cu(oro)(NH3)2] Calculated by the
B3LYP Method
theora
exptl
no.
IR
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
589 m
529 m
492 m
453 s
435 sh
406 m
370 sh
296 m
279 m
258 m
250 sh
ov
213 m
ov
162 m
152 sh
128 br
118 sh
80 w
62 w
a
b
∆ν
2
4
1
3
2
1
1
2
Raman
585
529
492
450
435
395
w
w
m
sh
m
br
295
279
258
248
sh
m
m
sh
205 br
180 w
ω
IIR
SR
PED (%)
545
514
491
425
441
380
350
289
274
261
249
214
203
177
162
158
136
99
86
52
30
10
11
4
35
26
1
15
<1
12
36
1
2
10
1
6
4
5
<1
2
8
<1
1
2
5
3
10
17
2
1
19
7
6
1
1
<1
2
0
<1
0
<1
1
0
Fr ΝΗ3 (N4) (78), Fr ΝΗ3 (N5) (17)
τ (U ring) (61), γ C7O3 (-24), τ chel (10)
δ (U ring) (36), δ chel (25), δ C7O3 (20)
δ C4O (-40), δ (U ring) (29), ν CuN5 (+15)
ν CuN5 (-30), δ chel (30), ν CuO1 (+24)
ν CuN5 (+45), ν CuN4 (+25), δ chel (17)
ν CuN4 (+49), δ chel (36), ν CuN5 (-15)
τ NH3 (N5) (97)
ν CuO1 (+41), δ chel (31),ν CuN5 (+13)
δ N4CuN5 (+50), ν CuN1 (-26)
δ chel (74), ν CuN4 (+18)
τ (U ring) (54), τ chel (27), γ Ν4 (+12)
δ O1CuN4 (+45), ν CuN1 (+28), δ chel (19)
τ (U ring) (78), τ chel (22)
δ N4CuN5(+42), δO1CuN4(-35), νCuN1(+13)
τ (U ring) (39), γ N5 (-33), γ Ν4 (-24)
τ (U ring) (57), τ chel (37)
τ NH3 (N4) (94)
τ chel (92)
τ chel (60), τ (U ring) (40)
γ N5 (-47), γ Ν4 (+38)
Abbreviations as in Table 3. b Isotope shift of the bands (in cm-1) due to the 63Cu/65Cu substitution.
the IR spectrum of cis-[Cu(oro)(NH3)2], the very strong band
at 1661 cm-1 is assigned to the antisymmetric ν(C4dO4)
stretching in crystal. The corresponding symmetric counterpart
is assigned to the shoulder at 1643 cm-1 in the Raman spectrum
(mode 9). For solid 1-MeU, the ν(C4dO4) stretching vibrations
were assigned at very similar frequencies, 1660 (IR) and 1649
cm-1 (Raman).54
The largest Raman intensity has been calculated for the
ν(C7dO3) stretching vibration (mode 11); therefore, the very
strong Raman band at 1631 cm-1 is attributed to this mode.
This assignment is confirmed by the vibrational spectra of
copper(II) complexes with amino acids, where Cu is bonded to
one carboxylate oxygen atom. For the second carboxylate
oxygen atom, the CdO stretching vibration (the so-called
asymmetric COO stretching vibration) has been reported in the
range 1590-1640 cm-1.55,56
According to the theoretical results, the ν(C2dO2) carbonyl
stretching vibration is strongly coupled with the uracilate ring
bending vibration, and it should be assigned to the strong band
at 1614 cm-1 in infrared (mode 12). A strong interligand
N5-Hi · · · O2 hydrogen bond involves the O2 oxygen atom of
the uracil ring and the neighboring ammonia group (see
Figure 2).
The nature of a narrow band at 1576 cm-1 in the Raman
spectrum (Figure 3) was puzzling. In our previous study,9 this
band was tentatively assigned to the ν (C2dO2) stretching
vibration. However, in this work, on the basis of the theoretical
results, we have reassigned this band to mode 14 involving the
predominant contribution from the ν (C5dC6) stretching
vibration. This assignment is supported by the results from NBO
analysis (Section 3.2), which have shown that the C5dC6
double bond is considerably weakened by an extensive delocalization of π electron density within the pseudoaromatic uracil
ring.
According to the calculated PED, the ν (C7-O1) carboxylate
stretching vibration is strongly coupled with the bending
vibration of the ammonia group, δsNH3, and is assigned at 1315
cm-1 in the IR and Raman spectra (mode 20). The large
frequency difference (316 cm-1) between the ν(C7dO3) and ν
(C7-O1) carboxylate stretching frequencies gives additional
evidence for the unidentate coordination of the carboxylate
group to the copper(II) ion.
The out-of-plane γ(N3H) vibration is very sensitive to the
strength of intermolecular N3-H3 · · · O4a hydrogen bonding.
In the IR spectra of uracil derivatives in the solid state, this
vibration occurs in the range 850-880 cm-1,54 whereas for
1-MeU isolated in a low-temperature argon matrix, it is observed
at 659 cm-1.44 Therefore, the calculated frequency of γ(N3H)
vibration in cis-[Cu(oro)(NH3)2] is 676 cm-1 (mode 30), whereas
in the IR spectrum of the crystalline complex, this mode is
assigned to a weak band at 843 cm-1 (Table 3).
According to PED, the strong band at 1374 cm-1 in the IR
spectrum should be assigned to mode 19, which involves
predominant contribution from the in-plane δ(N3H) bending
vibration. The calculated frequency of this mode (1372 cm-1)
is in excellent agreement with experiment.
In the IR spectrum of the copper(II) complex, the two bands
of medium intensity at 802 and 773 cm-1 are due to the outof-plane vibrations of the CdO groups (modes 31 and 33). The
calculated frequencies of these modes (796 and 773 cm-1,
respectively) nearly reproduce the experiment. The calculated
relatively large Raman intensity for mode 32 (the in-plane
C7dO3 bending vibration) indicates that it should be assigned
to the prominent band at 800 cm-1 in the Raman spectrum. The
strong Raman band at 602 cm-1 arises from the in-plane bending
vibration of the uracilate ring (mode 39).
Ammonia Vibrations. Vibrations of the NH3 groups are
strongly anharmonic; therefore, the double harmonic approximation (being inherent in the calculations of the force constants
and dipole moment derivatives) may not be adequate for
accurate description of these modes. However, scaling of the
calculated N-H stretching frequencies by a factor of 0.920 leads
to good agreement with experiment. As shown in Table 3, the
bands at 3339, 3317, 3264, and 3181 cm-1 in the FT-IR
spectrum and the corresponding bands in the Raman spectrum
are assigned to the N-H stretching vibrations of two ammonia
Cu(II)-cis-[Cu(oro)(NH3)2] Noncovalent Interaction
J. Phys. Chem. B, Vol. 113, No. 23, 2009 8165
Figure 3. Comparison of the experimental FT-IR and Raman spectra of cis-[Cu(oro)(NH3)2], in the region 3500-600 cm-1.
groups. It is worth noting that in the IR spectrum of
[Cu(NH3)4]SO4, the ν(NH3) stretching vibrations were assigned
at very similar frequencies: 3327, 3253, and 3169 cm-1.55
However, in the title complex, a strong hydrogen bond (N5Hi · · · O2) should decrease the frequency of the ν(N5-Hi)
stretching vibration. Therefore, in our normal coordinate
analysis, we have used different internal coordinates for the inplane N-Hi and out-of-plane N-Ho bonds in the N5-ammonia
group. According to calculations, the broad band at 2980 cm-1
in the FT-IR spectrum should be assigned to the ν(N5-Hi)
stretching vibration (mode 8). The other weak bands at 2872
and 2812 cm-1 are generated most probably by the combination
(ν17 + ν18) and overtone (2ν18) transitions, respectively. These
bands gain their infrared intensity through Fermi resonance with
the ν(N-H) fundamentals.
The bands arising from asymmetric deformation vibrations,
δa(NH3), probably overlap with the CdO stretching vibrations.
All these vibrations contribute to the very strong IR bands at
1661 and 1639 cm-1. Interestingly, for [Cu(NH3)4]SO4, the
corresponding δa(NH3) vibrations were reported at nearly the
same wavenumbers, 1669 and 1639 cm-1, in the IR spectrum.55
The symmetric deformation vibrations, δs(NH3), in cis[Cu(oro)(NH3)2] are attributed to the intense bands at 1292 and
1268 cm-1 in the IR spectrum (modes 21 and 22). However, it
should be noted that the calculated frequency of mode 22 is
underestimated by 70 cm-1 in comparison to experiment. Similar
results were obtained in our earlier calculations of the frequencies of δs(NH3) vibrations in cis-[PtCl2(NH3)2] (cisplatin).57 This
indicates that the harmonic approximation is unable to reproduce
the frequency of anharmonic “umbrella”-type vibration of the
NH3 group.
Copper-Ligand Vibrations. Figure 4 compares the experimental FT-IR and Raman spectra of cis-[Cu(oro)(NH3)2] in the
range 600-100 cm-1. Table 4 lists the corresponding experimental and theoretical frequencies and intensities and the
calculated PED. To provide the definite assignment of the
8166
J. Phys. Chem. B, Vol. 113, No. 23, 2009
Helios et al.
Figure 5. The optimized structure of the supramolecular system
containing three molecules: cis-[Cu(oro)(NH3)2], ethylene, and formaldehyde. Calculations performed by the M05-2X functional.
Figure 4. Comparison of the experimental FT-IR and Raman spectra
of cis-[Cu(oro)(NH3)2] in the region 600-100 cm-1.
copper-ligand vibrations, we have measured the 63Cu/65Cu
isotope shift effect and compared it with the theoretical results.
As is seen in Table 4, the IR bands at 589, 529, and 492
cm-1 are insensitive to the metal isotope substitution. According
to the calculated PED, these bands arise from the bending
vibrations of the NH3 and orotate ligands (modes 40-42). The
strong and broad band at 453 cm-1 and the shoulder at 435
cm-1 show the metal isotope shift of 2 and 4 cm-1, respectively.
The former band is assigned to mode 43, with the predominant
contribution from the in-plane bending vibration of the C4dO4
group (δC4O), as shown in Table 4. All calculations with
various basis sets consistently predicted a large infrared intensity
and small Raman intensity for this mode, which is supported
by experiment. However, the calculated frequency of this mode
(425 cm-1) is lower than experiment. It should be remembered
that the calculations refer to a molecule in the gas phase, whereas
in the solid state, the intermolecular N3-H3 · · · O4a hydrogen
bond should increase the frequency of the δ(C4dO4) bending
vibration. Therefore, the observed wavenumber of this band
should be higher than the theoretical. A small isotope shift of
this band (2 cm-1) is attributed to some contribution of
ν(Cu-N5) stretching vibration (15%) to this mode.
In the Raman spectrum (Figure 4), the prominent band at
435 cm-1 has been assigned to mode 44 on the basis of a
relatively large metal isotope shift (4 cm-1) and the theoretical
results (high Raman scattering activity). According to the
calculated PED, mode 44 can be described as a compression of
the Cu-N5 bond with the simultaneous stretch of the Cu-O1
bond (and vice versa). The in-plane deformation of the chelate
ring also contributes to this mode (25%).
The band at 406 cm-1 in the infrared spectrum and the broad
band at 395 cm-1 in the Raman spectrum are assigned to mode
45, which involves ν(Cu-N5), ν(Cu-N4), and bending vibrations of the chelate ring. The measured isotope effect for the
band at 406 cm-1 is very small (1 cm-1). Such a small metal
isotope shift is observed in the case when the metal-ligand
stretching vibration is coupled with chelate ring deformation
in such a way that the resulting displacement of the metal atom
is very small.55 It is worth noticing that in the spectra of
[Cu(NH3)4]SO4, the corresponding Cu-N stretching vibrations
were reported at similar frequencies: 426 cm-1 (IR); and 420,
375 cm-1 (Raman).55
The band at 279 cm-1 in the IR and Raman spectra of cis[Cu(oro)(NH3)2] is assigned to mode 48, with the predominant
contribution (41%) from the ν(Cu-O1) stretching vibration.
This assignment is supported by the observed metal isotopic
shift of 3 cm-1. The calculated frequency of this mode, 274
cm-1, is in very good agreement with experiment (Table 4).
According to the calculated PED, the ν(Cu-N1) stretching
vibration is strongly coupled with the N4CuN5 and O1CuN4
bending vibrations. The corresponding normal modes, 49 and
52, are observed in the IR spectrum at 258 and 213 cm-1,
respectively. In the Cu(II) complex with pyridine, the Cu-N
stretching vibration occurs at a similar frequency, 268 cm-1,55
which indicates that the strength of the Cu-N1 bond in the
title complex is comparable to that in copper(II) complexes with
N-aromatics.
3.4. Supramolecular System and the Role of Dispersion
Energy. Figure 5 illustrates the optimized structure of the
supramolecule consisting of the cis-[Cu(oro)(NH3)2] complex
(in the middle), ethylene (above), and formaldehyde (below the
complex). Such a model mimics very well the coordination
sphere around the copper atom in the crystal structure of the
title complex. Full geometry optimization performed by the
unrestricted MP2 and M05-2X methods predicted the stable
structure of this system. In contrast, the unrestricted B3LYP
method failed in geometry optimization. This indicates that
dispersion energy (which is neglected by the B3LYP functional)
is very important for the stability of this system.
Comparison of the bond lengths and bond angles in crystal
of cis-[Cu(oro)(NH3)2] with those calculated at the MP2/I, M052X/I, and M05-2X/II levels of theory has revealed that the M052X/I method predicts the most accurate copper-ligand distances
(all the calculated geometry parameters for supramolecule are
available in the Supporting Information, Table 4S). The
calculated Cu-x distance (where x denotes the midpoint of
the CdC bond) is equal to 3.000 Å, which is quite close to the
corresponding Cu-x (C5dC6) distance in the crystal of the title
complex, 3.293 Å.9 The theoretical axial distance between the
Cu(II)-cis-[Cu(oro)(NH3)2] Noncovalent Interaction
copper ion and the oxygen atom in formaldehyde varies from
2.391 Å (M05-2X/I) to 2.459 Å (M05-2X/II). The experimental
Cu-O4a distance in crystal of cis-[Cu(oro)(NH3)2] (Figure 1)
is somewhat longer, 2.927 Å, however, the calculated x-Cu-O
angle of 173.4° is very similar to that in the title complex,
169.6°.9
Calculations performed at the M05-2X/I level of theory
predicted the Cu-N1 and Cu-O1 bond lengths (1.992 and
1.956 Å), in excellent agreement with the experimental bond
lengths for crystal, 1.999 and 1.959 Å, respectively (see
Supporting Information, Table 4S). However, the calculated
atom distances between copper and the nitrogen atoms from
the ammonia groups (N4 and N5) are similar to those calculated
for an isolated copper complex (in both cases, they are
overestimated in comparison to experiment).
Nevertheless, it should be emphasized that according to
calculations for the supramolecule, the copper atom remains in
the plane formed by the O1, N1, N4, and N5 atoms, which is
confirmed by the X-ray data for cis-[Cu(oro)(NH3)2]. This
indicates that an axial interaction between the copper ion and
the CdC double bond is strong enough to counteract the
interaction between copper and the axial oxygen atom on the
opposite side of the coordination plane.
Calculations of the interaction energy between ethylene and
the copper complex (bonded with formaldehyde) have been
performed by the M05-2X functional with two basis sets, I and
II. The BSSE-corrected energies are -6.68 (1.84) kcal mol-1
and -7.33 (1.99) kcal mol-1 for I and II basis set, respectively
(the BSSE corrections are shown in parentheses). Zhao and
Truhlar33 in their theoretical study with the same functional,
M05-2X, reported a very similar interaction energy of -8.47
kcal mol-1 (with a CP correction for BSSE) for stacked uracil
dimer, which is a dispersion-dominated complex.
It should be emphasized that the interaction between the
chelated copper ion and the ethylene molecule in the investigated
supramolecule leads to a very small elongation of the calculated
CdC bond (by about 0.003 Å), in comparison to that in free
ethylene. This is reflected in a small red shift of the CdC
stretching frequency, only by 9 cm-1, as revealed by calculations
at the M05-2X/II level of theory. These results indicate a
noncovalent character of the copper-π interaction in this
complex. If appreciable π electron density had been transferred
from the CdC bond to a metal cation, this would lead to a
large red shift of the CdC stretching vibration. For example,
in Zeise’s salt, K[Pt(C2H4)Cl3]H2O, the formation of the
Pt(II)-π covalent bond causes a marked shift of the CdC
stretching frequency of ethylene from 1623 to 1526 cm-1.55
The comparison of our results obtained for the title complex
with those obtained for Cu+ complexes with π ligands (benzene
and its derivatives) indicates that the Cu+-ring distance is much
shorter and the bonding is stronger. Rodgers and co-workers25
employed threshold collision-induced dissociation techniques
and the B3LYP calculations to determine the bond dissociation
energies of a wide variety of Cu+-π complexes. In the Cu+
complex with C6H6 in the gas phase, the experimental binding
energy is equal to 51.88 kcal mol-1. According to B3LYP
calculations, Cu+ sits above the center of the aromatic ring with
a calculated Cu+-R⊥ distance of 1.73 Å (η6 mode of coordination), and the nature of this interaction is mainly electrostatic.25
However, in the condensed phase, the mode of Cu+ binding
with the aromatic compounds is different. Studies of the crystal
structures of benzene-CuAlCl458 and (benzene-CuCl3)2Zr59
complexes have revealed that the copper atom is located almost
directly above one CdC bond (η2 edge site) and the Cu-x
J. Phys. Chem. B, Vol. 113, No. 23, 2009 8167
distance is equal to about 2.2 Å (x is the midpoint of CdC
bond). Thus, it has been concluded that in the presence of a
counteranion, there is a covalent bonding between Cu+ and one
of the π bonds. Zhang et al.23 in their theoretical studies on the
η2 complexes between benzene and CuX (X ) F, Cl, Br, CN)
reported binding energies in the range from -25.6 to -21.4
kcal mol-1. According to the NBO analysis, a strong donation
from the π orbitals of benzene to the 4s orbital of Cu+, (π f
4sCu) is accompanied by the 3dCu f π* back-bonding interaction. A similar mode of orbital interactions has been found in
the complexes of 1-alkenes with Cu+. The result is a lengthening
of the CdC bond, which is reflected in a large red shift of the
CdC stretching frequency, by as much as 142 cm-1.26 Therefore,
it seems unreasonable to consider the Cu+-π interactions as
being dominated by noncovalent forces.
It is nowadays recognized that dispersion interactions are the
major source of stabilization energy between two aromatic
molecules.60 Recently, Hobza and co-workers61 convincingly
demonstrated that London dispersion energy plays a key role
for stacking of DNA bases. The authors nicely illustrated by
molecular dynamics simulations that the lack of the dispersion
term leads to an increase in the vertical separation of the bases
as well as a loss of helicity of β-DNA. Dispersion energy can
be expected whenever aromatic residues are present.
Single-crystal X-ray study of cis-[Cu(oro)(NH3)2] has shown
that the distance between the copper atom and the CdC bond
is very similar to that between stacking DNA bases.9 Our results
from NBO analysis for isolated cis-[Cu(oro)(NH3)2] have
revealed that the N1-deprotonated orotate ligand displays an
aromatic character. Vibrational spectroscopy has confirmed that
both the orotate ligand and the chelate ring with copper form a
strongly conjugated aromatic system. The calculated interaction
energy between the chelated Cu(II) complex and ethylene is
similar to that determined for stacked uracil dimer, which is a
dispersion-dominated complex. Additionally, and perhaps most
importantly, the stable structure of the supramolecular complex
can be obtained only in calculations by the M05-2X and MP2
methods, which include dispersion energy. The B3LYP method
(with an inherent lack of dispersion) fails in geometry optimization of this complex. Thus, the results obtained in this work
clearly indicate that the dispersion energy (the London force)
plays a significant role in the noncovalent interaction between
the chelated Cu(II) ion and the uracilate ring in the crystal of
cis-[Cu(oro)(NH3)2].
4. Conclusions
The crystal structure of the Cu(II) complex with Vitamin B13
(orotic acid), cis-[Cu(oro)(NH3)2] has revealed the presence of
unusual, noncovalent, π-type interaction between the chelated
Cu(II) ion and the CdC bond of the uracilate ring.9 It is
interesting to note that this axial Cu(II)-π interaction is strong
enough to counteract the Cu-O4a axial binding (to the carbonyl
oxygen atom) on the opposite side of the coordination plane.
The copper atom is coplanar with the N1 and O1 atoms of the
chelating orotate ligand and N4 and N5 atoms from two bonded
ammonia groups. The question arises: what is the origin of this
Cu(II)-π interaction?
In this work, comprehensive studies of the molecular and
electronic structures and vibrational spectra of the title complex
have been performed using the unrestricted density functional
theory methods, B3LYP, and the newly developed M05-2X
functional. Calculations at the UMP2 level were also carried
out for comparison. A variety of basis sets have been employed
in the DFT calculations, including aug-cc-pVTZ, D95V(d,p),
SDD, and LanL2DZ.
8168
J. Phys. Chem. B, Vol. 113, No. 23, 2009
The most important results and conclusions obtained in this
work can be summarized as follows:
(1) Geometry optimization of the isolated cis-[Cu(oro)(NH3)2]
complex, (Figure 2) has revealed that the Cu-O and Cu-N
(orotate) bond lengths calculated by the M05-2X functional are
slightly shorter (and in worse agreement with experiment) than
the bond lengths predicted by the B3LYP functional with the
same basis sets. On the other hand, full geometry optimization
of the supramolecular complex (Figure 5) performed by the
M05-2X functional yields the Cu-O and Cu-N atom distances
in excellent agreement with experiment. Both methods, however,
overestimate the copper-ammonia bond lengths, regardless of
the basis set used.
(2) The new M05-2X functional performs very well for
predicting the structure of the supramolecular complex, in which
the noncovalent interactions are important. In the optimized
structure, the CdC bond is located directly above the copper
atom with the Cu-x distance of 3.000 Å (x denotes midpoint
of the CdC bond). This result is in very good agreement with
the experimentally determined Cu-x distance of 3.293 Å in
the crystal structure of cis-[Cu(oro)(NH3)2]. Consistent results
are obtained in calculations by the MP2 and M05-2X methods.
In contrast, the B3LYP method (with the inherent lack of
dispersion energy) failed in geometry optimization of this
supramolecule.
(3) The natural bond orbital (NBO) analysis of cis-[Cu(oro)(NH3)2] has provided detailed insight into the bonding in this
complex. The results indicate that the N1-deprotonated uracilate
ring displays strong π-donating capability, and the strength of
the copper-N1 bond should be similar to that between Cu(II)
and pyridine. These theoretical predictions are supported by the
vibrational spectra of the complex.
(4) The 63Cu/65Cu isotope substitution technique was applied
to identify the copper-ligand vibrations in the infrared spectra.
The clear-cut assignment of all the bands in the FT-IR and
Raman spectra has been made on the basis of the calculated
potential energy distribution, PED. It is shown that the extremely
intense band at 1210 cm-1 in the Raman spectrum of cis[Cu(oro)(NH3)2] is diagnostic for the N-1 deprotonation of the
uracilate ring and coordination to the copper(II) ion. The
reported vibrational assignment will be very helpful for the
interpretation of the vibrational spectra of other transition metal
complexes with Vitamin B13 (orotic acid).
(5) The B3LYP functional performs better than M05-2X in
predicting vibrational frequencies of the title complex in the
solid state. Comparison of the results obtained with various basis
sets indicates that the accurate and the most economic level of
theory in calculation of the vibrational spectra is the B3LYP
method with the combined basis set: D95V(d,p) for nonmetal
atoms and LanL2DZ for Cu (denoted as II in this work).
(6) The M05-2X/II calculated interaction energy between the
chelated Cu(II) complex and ethylene amounts to -7.33 kcal
mol-1 (with CP correction for BSSE), which is similar to that
determined for stacked uracil dimer. It is concluded that the
London dispersion energy plays a significant role in the
noncovalent interaction between the chelated Cu(II) ion and the
uracilate ring in the crystal of cis-[Cu(oro)(NH3)2].
(7) Many copper enzymes in their active sites contain the
chelated Cu(II) ion and the aromatic groups (Phe, Tyr, and Trp)
as the potential binding sites; therefore, it is possible that the
noncovalent copper(II)-π interaction can be very important for
the structure and functioning of these enzymes.
Acknowledgment. This work was supported by Wrocław
University of Technology. The generous computer time from
Helios et al.
the Wrocław Supercomputer and Networking Center as well
as Poznan Supercomputer and Networking Center is acknowledged.
Supporting Information Available: Vibrational frequencies
and intensities calculated by the M05-2X and B3LYP density
functional methods with a variety of basis sets (Tables 1S and
2S), the results from NBO analysis (Table 3S), and the structure
parameters of supramolecule calculated by the MP2 and M052X methods (Table 4S) are available as Supporting Information.
This material is available free of charge via the Internet at http://
pubs.acs.org.
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