Inelastic neutron scattering (INS) study of low frequency vibrations and hydrogen bonding of (E)-2-hydroxyimino-2-cyanoacetic acid ethyl ester

Article abstract of DOI:10.1524/zpch.2011.0054

The title unsubstituted (normal) (E)-2-hydroxyimino-2-cyanoacetic acid ethyl ester (the abbreviated name: (E)-2-cyanoethyl ester-2-oxime or 2-oxime) and its 2-deuterated analogue have been prepared and characterized using infrared, Raman and inelastic, incoherent neutron scattering (IINS) spectroscopy. Molecular structures (molecular conformations) of the compounds are proposed for the vapour state. Four molecular conformers, namely two pairs of the s-cis, s-trans rotational isomers (rotamers) from six lower energetic conformations of E-2-hydroxyimino-2-cyanoacetic ethyl ester, are predominating for the single molecule of the compound. They amount together to almost 100% of the conformational populations of both rotational isomers as it was theoretically calculated using DFT (B3LYP) method with 6-311G++(d,p) basis set. Additionally dimers of 2-oxime were considered using B3LYP/6-31G* method in order to improve the results obtained for single molecule. In both parent (=N-OH) and deuterated (=N-O-D) molecules of the (E)-2-ethylcyano ester-2-oxime respectively, extra bands corresponding primarily to hydrogen (deuterium) bond vibrations (γ -bending out of plane of hydrogen bond, σ-stretching of hydrogen bond bridge, δ-bending in plane of hydrogen bond, λ-bending of hydrogen bond bridge have been identified, namely σ (N-O-H?O) at 132.8, 212.5, 279, 358.7, 424, 448, 523.6, 872, γ (N-O-H?O) at 334, 564, 592, 745, 820, δ (N-OH?O) at 1461, 1600, 1862 cm^-1 in the low temperature IINS spectrum, whereas the frequency at 365 cm^-1 has been assigned as the out of plane (o.o.p.) (γO-D?O) vibrational mode. Formation of the O-H?O hydrogen bridge is reflected in shifting of the bands of the stretching and bending vibrations of OH group as well as arising of the bridge vibrations in the low frequency range. Moreover, equilibrium geometries and all harmonic vibrational frequencies of the (E)-2-cyano ethyl ester-2-oxime molecules with potential energy distribution (PED) were also calculated by means of the above mentioned theoretical programs. by Oldenbourg Wissenschaftsverlag, Mu?nchen.

Full text of DOI:10.1524/zpch.2011.0054

Z. Phys. Chem. 225 (2011) 183–216 / DOI 10.1524/zpch.2011.0054
© by Oldenbourg Wissenschaftsverlag, München
Inelastic Neutron Scattering (INS) Study of Low
Frequency Vibrations and Hydrogen Bonding of
(E)-2-Hydroxyimino-2-Cyanoacetic Acid Ethyl Ester
By M. Rachwalska1 ∗, I. Natkaniec2 3, K. Hołderna-Natkaniec4 , Z. H. Urbanek1, and
K. K. Zborowski1
,
,
1
Faculty of Chemistry, Jagiellonian University, 30-060 Krako´w, Poland
H. Niewodniczanski Institute of Nuclear Physics, PAS, 31-342 Krako´w, Poland
Frank Laboratory of Neutron Physics, JINR, 141980 Dubna, Russia
Faculty of Physics, A. Mickiewicz University, 61-614 Poznan´, Poland
2
3
4
(Received September 19, 2010; accepted September 28, 2010)
(E)-Cyano-Oxime / (E)-Configuration / S-Cis,S-Trans Rotational Isomerism /
Conformer (Rotamer) / Infrared (IR) / Raman Spectroscopy / IINS / Density
Functional Theory (DFT)
The title unsubstituted (normal) (E)-2-hydroxyimino-2-cyanoacetic acid ethyl ester (the abbreviated
name: (E)-2-cyanoethyl ester-2-oxime or 2-oxime) and its 2-deuterated analogue have been
prepared and characterized using infrared, Raman and inelastic, incoherent neutron scattering (IINS)
spectroscopy. Molecular structures (molecular conformations) of the compounds are proposed for
the vapour state. Four molecular conformers, namely two pairs of the s-cis, s-trans rotational
isomers (rotamers) from six lower energetic conformations of E-2-hydroxyimino-2-cyanoacetic
ethyl ester, are predominating for the single molecule of the compound. They amount together to
almost 100% of the conformational populations of both rotational isomers as it was theoretically
calculated using DFT (B3LYP) method with 6-311G++(d,p) basis set. Additionally dimers of
2-oxime were considered using B3LYP/6-31G∗ method in order to improve the results obtained
for single molecule. In both parent (=N−OH) and deuterated (=N−O−D) molecules of the (E)-2-
ethylcyano ester-2-oxime respectively, extra bands corresponding primarily to hydrogen (deuterium)
bond vibrations (γ–bending out of plane of hydrogen bond, σ–stretching of hydrogen bond bridge,
δ–bending in plane of hydrogen bond, λ–bending of hydrogen bond bridge have been identified,
namely σ (N−O−H···O) at 132.8, 212.5, 279, 358.7, 424, 448, 523.6, 872, γ (N−O−H···O)
at 334, 564, 592, 745, 820, δ (N−OH···O) at 1461, 1600, 1862 cm−1 in the low temperature
IINS spectrum, whereas the frequency at 365 cm−1 has been assigned as the out of plane (o.o.p.)
(γO−D···O) vibrational mode. Formation of the O−H···O hydrogen bridge is reflected in shifting
of the bands of the stretching and bending vibrations of OH group as well as arising of the
bridge vibrations in the low frequency range. Moreover, equilibrium geometries and all harmonic
vibrational frequencies of the (E)-2-cyano ethyl ester-2-oxime molecules with potential energy
distribution (PED) were also calculated by means of the above mentioned theoretical programs.
* Corresponding author. E-mail: rachwals@chemia.uj.edu.pl
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1. Introduction
Among the non-covalent interactions hydrogen bond (H-bond) is the most common and
important in biologically active compounds and processes. Hydrogen bonds determine
the molecular packing of the molecules in crystals and interactions in liquids and gas
phase [1]. The O−H···O hydrogen bond is the strongest among others and OH group
which forms the most common hydrogen bonds and can react as a proton donor (O−H)
as well as a proton acceptor (···O) so the hydrogen bonds are usually arranged in a com-
plicated hydrogen bond patterns. Among organic compounds alcohols and phenols have
been intensively investigated but the other families of compounds i.e. oximes, have not
been intensively investigated till now.
Formation of the hydrogen bond changes the structures of compounds with an OH
group and a consequence of this change is reflected in the vibrational spectra. The in-
plane OH (δ) and out-of-plane OH (γ) deformation bands shift to higher frequencies
(so called blue shift), while the stretching band OH shifts to a lower frequency range
(red shift) with an increase of O−H···O hydrogen bond strength [2]. The high frequency
υ[OH] band is the most convenient for studies of hydrogen bond formation and of hy-
drogen bond strength, because it has got a high intensity in IR spectra. Investigations
of changes in the deformation vibrations of the OH group with varying hydrogen bond
strength are more difficult because of their coupling with other molecular vibrations.
The INS method used in this work is especially useful in investigation of the proton vi-
brations in low energy transfer. It is well known that cross-section for inelastic neutron
scattering takes the values: 82, 5.55, 11.51, 4.23 barns for hydrogen, carbon, nitrogen
and oxygen, respectively [3]. Therefore in the IINS spectra the bands assigned to proton
vibration are dominant.
The crystal structure of 2-oxime [4] confirms that this compound in solid state is
engaged in complicated O−H···O hydrogen bond patterns although the precise pro-
ton location has not been determined in this X-ray structure [4] and is determined
in neutron powder diffraction (NPD) spectra [5]. In this paper we decided to com-
pare the structure (conformations) and vibrational spectra of monomer and dimer to
investigate the influence of O−H···O hydrogen bond formation on the vibrational
spectra. Because of the OH vibrations in 2-oxime with other molecular vibrations’
coupling, it can be expected that the formation of the O−H··· hydrogen bond will
strongly influence the vibrational spectrum of the proton donor and proton accep-
tor. Additionally, formation of the hydrogen bond changes the geometry of proton
donor and proton acceptor and these changes are reflected in the vibrational spec-
tra. The method used in this study is optimization of 2-oxime monomer and dimer
structure and comparison of the theoretical vibrational spectra with experimental
INS spectra to find changes caused by the formation of O−H···O hydrogen bond
bridges.
(E)-2-hydroxyimino-2-cyanoacetic acid ethyl ester (abbreviated name: (E)-2-
cyanoethyl ester-2-oxime or 2-oxime) which is the subject of the paper, belongs to the
family of bioactive organic substances. There are many publications dealing the prob-
lem. As some examples presenting the bioactive properties of some oximes we give
the following [33–36]. Many of them have been investigated for many years by IINS
as for example [6–9]. About physical and chemical properties of the substance we
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Fig. 1. (E)-2-hydroxyimino-2-cyanoacetic acid ethyl ester molecules in its crystal lattice showing the most
“comfortable” hydrogen bond between hydrogen atom of hydroxyimino group and the oxygen atom of car-
bonyl group in the nearest molecule. Such the dimer has been considered in the theoretical calculations of
the paper. The picture was drawn by using the crystallographic data [4].
have said in our publication [5] dealing the problem of structure of (E)-2-cyanoethyl
ester-2-oxime, estimated at various temperatures.
This knowledge [4,5] appeared to be very important for the present theoretical cal-
culations of the dynamics’ properties of the 2-oxime molecules (see later). It is known
as we said in [11] that oximes, previously investigated by Jackson [12] by using only
medium IR spectroscopy, can form intermolecular hydrogen bond in the solid state in
four different ways, namely:
O(1)−H1···N(2)=C(2) (I) , O(1)−H1···N(1)≡C(1) (II) ,
O(1)−H1···O(2)=C(3) (III) and O(1)−H1···O(1)−N(2) (IV) .
Numbering of all atoms of the (E)-2-cyanoethyl ester-2-oxime molecule is presented in
Fig. 1.
As to the first mode of the formation of H-bonds (i.e.) O(1)−H···N(2)= C(2) (I) in
the case of (E)-2-cyanoethyl ester-2-oxime, a reduction of the π-charge at the oxime’s
nitrogen atom is the effect of π conjugation between an oxime group =N(2)-O(1)-H(1)
and an π electron – withdrawing substituent in the oxime moiety. Therefore Jack-
son [12] suggested that as a result of such a conjugation, those oximes do not form H-
bonds of the O−H···N=C type. On the other hand, oximes possessing keto-substituents
(oximes of medium strength) may form intramolecular H-bonds O(1)−H···O(2)=C,
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186
M. Rachwalska et al.
but this kind of association is without any effect on the ν
vibrational frequency [12].
[C=N]
Therefore, on the basis of those considerations, 2-oxime molecule is unlikely to form
intermolecular H-bonds of the O(1)−H(1)···N(2)=C(2) type (I) but can form intermo-
lecular H-bonds of the O(1)−H···O(1)−N(2) type (IV).
Generally speaking, the phenomenon of inter molecular hydrogen bonded associ-
ation is the most characteristic feature for the oximes’ family. This phenomenon is
demonstrated in the case of oximes of weak acidity (pKa 10–12.5), oximes of medium
acidity (pKa 7–10) and acidic (or very acidic) oximes of pKa 4.5–6 [13]. We mean here
simple weakly conjugated oximes, also conjugated ones with one substituent electron
– withdrawing at C(2) as well as oximes possessing two conjugated electron-acceptor
substituent groups at C(2) and C(3) in the molecule. On intermolecular strong H-
bonding one may conclude from the IR spectrum of 2-oxime in its solid state [11].
Taking into consideration the two last ways of hydrogen bond formation as the most
probable in the case of the 2-oxime molecules [12], a detailed analysis of their funda-
mental vibrational modes, viz. stretching (ν), bending in plane (δ), bending out of plane
(γ) and σ (connected with displacement of oxygen atoms – stretching of the hydrogen
bond bridge) deformations of the oximino-group has been done and it is the essential
aim of this work. Particularly in this paper an experimental evidence of out of plane γ,
σ, δ deformations (in plane) of the OH in oximino-group (which may be observed in the
50–1700 cm−1 range) as well as ρ – out of plane internal modes and χ – torsional out
of plane modes is presented.
According to the X-ray [4] and NPD results [5] the 2-oxime molecules are linked
together by hydrogen bonds between the terminal O−H groups and the oxygen atoms
of carbonyl of the ester groups to form zigzag chains (Fig. 1).
Some spectroscopic studies have been performed until now [9,11,12] on various
kinds of C-mono-or disubstituted oximes having (E) or (Z) molecular configuration by
using optical (i.e. IR and Raman scattering) spectroscopy, but there is still lacking anal-
ogous work using inelastic incoherent neutron scattering (IINS) as a complementary
spectroscopic technique in comparison to the optical one. The last investigations allow
to describe protons’ dynamic at small energy transfers especially the protons’ dynamic
in the hydrogen bond.
Therefore we have undertaken such the investigations for (E)-2-cyanoethyl ester-2-
oxime. As compared with optical spectroscopic methods, incoherent neutron scattering
(IINS) presents a number of advantages in studying molecular vibrations in solids:
1. no selection rules are obvious in neutron spectroscopy,
2. low-wave number vibrations are the source of more intense bands than do high-
wave number ones,
3. the proton incoherent cross-section is much higher than that of other nuclei (as we
have already mentioned).
Consequently, the vibrational modes in which hydrogen atoms participate give rise to
IINS bands with much higher intensities than the bands due to other atoms. Therefore
the replacement of the hydrogen atom by deuterium, whose incoherent scattering cross
section for thermal neutrons is almost ten times smaller (equal to 7.64 barn [3], while
the oscillator mass is twice as large) makes it possible to identify uniquely the modes
due to hydrogen vibrations of the molecules of 2-oxime. IINS spectroscopy therefore
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may provide the important information about dynamic properties of organic hydrogen
bonded molecules in the energy range below 900 cm−1. On the other hand, Raman scat-
tering as well as IR spectroscopy make it possible to analyze the wave-number modes
located above 50 cm−1, in the region 50–4000 cm−1.
Finally it should be stressed here that the low-frequency vibrations of investigated
compounds in the range between 50–800 cm−1 are easily measurable by the method
of the inelastic incoherent neutron scattering (IINS), whereas the optical spectroscopy
(e.g. infrared and Raman scattering) may not be useful sometimes for that purpose.
Such a situation may happen when some fundamental vibrations (as for example, the
out of plane (o.o.p.) hydrogen-bonded γN−H···O ones in the case of certain amino-acids)
are inactive in infrared as well as Raman spectroscopy [14–16] e.g. when the double
exclusion rule does not work.
2. Experimental
2.1 Synthesis of the oximino-compounds
The (E)-2 cyanoethylester-2-oxime needed for the present work has been synthe-
sized with high yield by nitrosation reaction of the very reactive methylene group
of ethyl cyanoacetate according to Conrad’s procedure [17] by slowly dropping of
a saturated solution of NaNO2 into the reaction mixture of the cyanoester and glacial
acetic acid. The temperature of the reaction had to be kept all times between −5
and 0 ◦C. An orange solid being the crude product obtained in the reaction was fil-
tered off next day, made acidic to pH = 2 and after refrigeration it was filtered again.
The (E)-2 cyanoethylester-2 oxime was then recrystallized from aqueous ethanol and
when dry, it was again recrystallized twice from dichloromethane. Thus obtained (E)-
2 cyanoethylester-2-oxime is very pure for spectroscopic measurements. 2-deuterated
analogue of the 2-oxime was obtained after several crystallizations of 2-oxime in D2O.
2.2 IINS measurements and computational details
The IINS spectra and simultaneously neutron powder diffraction (NPD) were measured
at the inverted geometry time-of-flight spectrometer NERA [18,19] at the high-flux
pulsed reactor IBR-2 in the Joint Institute for Nuclear Research in Dubna. The sample
was mounted into a thin walled aluminum container (165×65 ×1 mm3) at room tem-
perature. The sample holder was then placed in the top-loaded neutron cryostat cooled
with a helium refrigerator. Sample temperature could be changed within the range
20–300 K and stabilized with 0.5 K accuracy at any chosen value. Within the energy
transfer 5–100 meV the resolution of the NERA spectrometer is about 2–3% [20]. More
details connected with neutron experiments, one can find in Supplement.
The neutron scattering intensities of 2-oxime were calculated by the α-CLIMAX
program [21], using output values of atomic displacements and normal modes frequen-
cies from the Gaussian 03 [22]. The IINS spectra of investigated molecular clusters
(dimers) were calculated as a convolution of calculated neutron scattering intensities
with the resolution function of the NERA-PR spectrometer [20]. Finally, the experi-
mental and calculated time – of-flight IINS spectra were transformed in one-phonon
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188
M. Rachwalska et al.
scattering approximation to the amplitude weighted density of vibrational states –
G(υ). Such procedure allows us to compare the experimental and calculated INS vibra-
tional spectra in a convenient energy transfer scale.
All calculations were carried out using the Gaussian’03 program [22]. Monomeric
and dimeric structures of the studied compound were calculated using the DFT (density
functional theory) approach. A series of geometry optimizations and vibrational fre-
quency calculations were performed to characterize the key stationary points on the
potential energy surface (PES) for the monomer. Geometry and frequency calcula-
tions were also executed for the dimer, starting from available crystallographic data [4].
Standard B3LYP functional (connection of Becke and Lee–Yang–Parr functionals) was
used [28]. For results accuracy comparison, the PM3 semiempirical method [22] was
employed for dimer calculations. Two basis sets were chosen for calculations, the 6-
311++G(d,p) basis set [29] was used for the (E)-2-hydroxyimino-2-cyanoacetic acid
ethyl ester monomer while calculations for the dimer (due to its size) were performed
with lower 6-31∗ basis set [30].
Semiempirical methods are based on the classical Hartree–Fock scheme in which
some integrals are parametrized, not calculated in a normal way [31]. In contrary the
DFT theory is based on the Hohenberg–Kohn theorem and Kohn–Sham equations [32].
In the last two decades DFT has emerged as a practical and versatile tool to obtain ac-
curate information about chemical systems. The popularity of DFT methods is based
on the fact that they include a big part of electron correlation effects. That’s why DFT
methods achieve significantly greater accuracy that Hartree–Fock theory with more or
less the same time of computations.
3. Results
The experimental IINS spectra of 2-oxime, obtained at different temperatures in this
work, are presented in Figs. 2 and 3, respectively.
In the IINS spectra at the incident neutrons wave length of 0.4 nm one can see an
elastic peak. Below 0.4 nm, i.e. in the region 0.05–0.4 nm there is an inelastic part of
the spectra. One can distinguish here the acoustic branch and optical one. An energy
gap is seen at 0.188 nm. An intensive band is seen at 0.15 nm in the low temperature
IINS spectra.
Sharp peaks observed on the IINS spectrum obtained at T = 20 K suggest that vi-
brations in crystals can be treated as harmonic.
Thus the function G(υ) may be calculated assuming a one phonon mechanism [23]
for the scattering process according to the formula:
ꢀ
ꢁ
d2σ
k1 hk2
k0 8π2 Mυ
exp(−2W(k))
ꢀ
−1
(binc)2
G(υ)
ꢂ
ꢃ
=
hυ
dΩ dυ
inc
exp
k
T
B
2
d σ
ꢀ ꢀ ꢀ
is the cross-section for incoherent neutron scattering, k = k0 −k1 the mo-
2 2 2
where
ꢁ
dΩ dE
ꢀ
mentum transfer, hω = (h /2M)(k0 −k1) the energy transfer, W(k) – the Debye–Waller
factor, and G(υ) – the phonon density of states function.
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Fig. 2. The IINS spectrum of the (E)-2-cyanoethylesters-2-oxime in the temperature region from 20 K to
290 K For changing x-axis units into energy one must use the well-known dependence: λ = 9.05 E−0.5 (Å),
where λ means the neutron wavelength and E the neutron energy (meV) corresponding to λ.
The IINS bands are getting broader when increasing temperature, they are getting
smeared. This behavior is typical for IINS of crystals and it corresponds to increase of
unharmonic character of vibrational modes with increasing temperature. At the room
temperature one can not see even any energy gap between the lattice mode and internal
ones. Figure 3 shows how temperature influences on the phonon density of state spectra
G(ν) of 2-oxime obtained from IINS in one phonon scattering approximation. In order
to assign reliable all experimental frequencies (vide Table 3) (20 K) of the G(υ) spec-
trum (Fig. 3) of the 2-oxime, the structure of isolated molecule and for dimer bonded
by hydrogen bridge bond [4,10,24–27] was optimized. Then the frequencies of normal
modes were calculated using methods described in the chapter Computational details.
The frequencies of internal modes were calculated for (E)-2-cyanoethyl ester-2-
oxime molecule and the same molecule but with OH group isotope substituted by the
OD group.
It is known that isolated 2-oxime molecule may obtain different conformations cis
or trans as shown Fig. 4. The Table 1 collect their energies of formation. The low-
est energy one is conformation 1. The low energetic conformations are presented on
Fig. 4a–f.
From Table 1 we can readily see that conformation 1 of the (E)-2-cyanoethylester
2-oxime molecule is predominant. In Table 2 we can see a comparison between calcu-
lated data of bond length and angles for the conformation 1 and structural X-ray data. It
should be noted that conformations 1, 2, 9 correspond to the S-cis conformations men-
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190
M. Rachwalska et al.
Fig. 3. Phonon density of states G(ν) for of the (E)-2-cyanoethylesters-2-oxime at variable temperatures.
Table 1. The most probable conformations of the (E)-2-cyanoethylesters-2-oxime molecule obtained by
theoretical calculations (B3LYP/6-311++G(d,p)), their energies [kJ/mol] and populations [%].
Energy
Relative
energy
Free
energy
Population
Conf1
Conf2
Conf3
Conf4
Conf5
Conf6
Conf7
Conf8
Conf9
Conf10
Conf11
Conf12
−529.39881171
−529.39233147
−529.39282101
−529.39843915
−529.38817324
−529.38186644
−529.38212772
−529.38756703
−529.39812401
−529.39812460
−529.39777421
−529.39777397
0.00000
17.01388
15.72860
0.97815
27.93130
44.48980
43.80383
29.52291
1.80555
1.80402
2.72396
2.72458
−529.32128
−529.31519
−529.31594
−529.32124
35.21
0.56
0.12
33.85
−529.32071
−529.32023
19.15
11.62
tioned at the beginning of the article, whereas 3, 4, 11 correspond to the S-trans forms
but all of them concern the configuration E (entgegen – from German) of the molecule.
In Fig. 5 we compare the Gexp(υ) spectrum at 20 K for normal (hydrogenous i.e.
undeuterated) and deuterated 2-oxime as well as for dimer-OH and for the single
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Fig. 4. (a) The molecule has the conformation 1 (S-cis) characterized by the lowest energy. In its deuterated
form used in the present work, there is a deuterium atom instead of hydrogen atom in =N−O−H group
of of the molecule. (b) Conformation 2 of (E)-2-cyanoethylester 2-oxime molecule (S-cis). (c) Conforma-
tion 3 of (E)-2-cyanoethylester 2-oxime molecule (S-trans). (d) Conformation 4 of 2(E)-2-cyanoethylester-
oxime molecule (S-trans). (e) Conformation 9 of (E)-2-cyanoethylester 2-oxime molecule (S-cis). Atomic
marking in the (E)-2-hydroxyimino-2-cyanoacetic acid ethyl ester molecule is presented. (f) Conformation
11 of (E)-2-cyanoethylester 2-oxime molecule (S-trans).
molecule. The spectra were calculated after transformation of theoretical frequencies
received for the conformation 1 and for higher energetical conformations from Table 1
to the IINS spectrum and for the conformation of dimer (shown also in inserts of Fig. 5
and in Table 3).
In Fig. 5a experimental phonon density of state Gexp(υ) in the frequency region
from very low till ca 1000 cm−1 can be observed, the resolution comparable with
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Fig. 5. (a) Experimental and calculated G(ν) for monomer and dimer O−H···O=C of (E)-2-cyanoethyl
ester-2-oxime.
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Fig. 5. (b) Experimental and calculated G(ν) for monomer and dimer O−D···O=C of (E)-2-cyanoethyl
ester-2-oxime (deuterated).
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Fig. 5. (c) Experimental and calculated G(ν) for dimer ···O−H···O=C of (E)-2-cyanoethyl ester-2-oxime
and dimer O−D···O=C of (E)-2-cyanoethyl ester-2-oxime.
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Fig. 5. (d) INS spectra for undeuterated and deuterated substance in the upper part of the diagram. In the
lower part there is the simulated IINS by using of the theoretical frequencies for dimers in the frequency
range up to 2000 cm−1
.
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that obtained by optical spectroscopy techniques. For energy transfers greater than
1000 cm−1 the intensity of scattered neutrons decreased, therefore our assignment in
Table 3 is mostly performed for frequencies up to ca. 1000 cm−1 and these results are
trustworthy. Some peaks seen in the higher frequency region on the picture of phonon
density function (Fig. 3) can be a result of scattered experimental points. In Table 3 the
wave numbers of subsequent normal modes from optical spectroscopy are collected as
well.
4. Discussion of results
4.1 Geometry of monomer and dimer of 2-oxime
The optimized molecular structure of 2-oxime dimer is the simplest step in reproduc-
tion of the real structure of this compound. Comparison of the geometric parameters of
monomer and proton donor and proton acceptor in the 2-oxime dimer (Table 2) shows
how formation of the hydrogen bond changes the geometry of proton donor and proton
acceptor. The O−H···O hydrogen bond in the lowest energetically structure obtained in
optimization is molecular one with the proton located at the proton donor. The O···O,
OH and H···O bonds length equals to 2.802, 0.987, 1.815 Å respectively. The O−H···O
angle is 176.6◦.
Comparison of the geometric parameters from Table 2 shows shortening of the OH
bond length if this group is used as a proton donor. The C=O bond length is also sensi-
tive to the formation of the hydrogen bond and decreases in the proton donor molecule
and elongates in proton acceptor. Other geometric parameters listed in Table 2 also un-
dergo changes under the hydrogen bond formation. The C−C bond lengths are slightly
elongated in proton donor (in the ethyl-group) and shortened in proton acceptor. Anal-
ogous changes are seen for the O−C−C angles which increase in the proton donor and
decrease in proton acceptor.
The X-ray data taken at room temperature given the O(1)···O(2) distance are 2.690
and 2.701 Å, while calculated for dimer is 2.802 Å. The hydrogen bond is nearly lin-
ear, i.e the angle O(1)−H···O(2) is 179◦ for optimized structure, while 169 and 174◦
in the X-ray data [4]. The root mean square deviation (RMS) between the experimental
bond length or angles Xi and the calculated ones Xi,cal by different quantum chemistry
methods (QC), (DFT or PM3) was calculated according to the formula:
ꢄ
ꢅ
1/2
2
Σ(Xi − Xi,cal
)
RMS =
.
n
The RMS factors calculated for the structures optimized by different QC method of
isolated molecule and for dimer are collected in Table 2. It takes the following values,
which are close to each others: for isolated molecule 0.0314, 0.0415, 0.0357 Å; 4.0937,
4.987, 3.7458◦ and for dimer 0.0341, 0.0346 Å and 3.7443, 3.9979◦, respectively.
4.2 Vibrational modes of 2-oxime monomer
The first step concerning the analysis of the experimental spectra of 2-oxime is inves-
tigation of the theoretical spectrum of its monomer and to make an assignment of the
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most characteristic vibrations. The υ(OH) stretching vibration of free (hydroxylic) OH
group in 2-oxime was located at 3725 cm−1. δ(O1−H1) was assigned to the band at
1660.48 cm−1 but it participated also in the other bands at 1451.7, 1428, 1411.1, 1303.0,
1200.2, 1081.6 cm−1. It was impossible to find a band assigned only to σ(O1−H1),
γ(O1−H1) vibrations which participated in the bands at 164.8, 247.6, 345.3, 418.2,
521.2 σ(O1−H1), 236.3, 293.8, 518, 642, 769.2 cm−1 γ(O1−H1). For monomer of 2-
oxime coupling of the proton vibrations with other molecular vibrations is well seen
in the results of calculations showing frequencies of vibrations and kinds of vibrations
contributing. We do not present an assignment for monomer in Table 3, but in Table 4.
It is characteristic that both deformation vibrations do not appear as separate bands but
are always coupled with other bonds. For example band at 164.8 cm−1 is coupled with
torsion vibration out of plane of ethyl group and with bending vibration of C−C≡N
group. Band at 247.6 cm−1 is coupled with bending vibration of ethyl and ethyl−O−C
group, with deformation in plane of C−C≡N group. Also the stretching vibration of
carbonyl group does not exist as separate band but is coupled with torsion vibration of
ethyl group.
4.3 Vibrations of 2-oxime dimer
To analyze the vibrations of the 2-oxime dimer the theoretical spectrum of the dimer has
been compared with the spectra of analogues deuterated in the −OH group.
Formation of the O−H···O hydrogen bond is reflected in the stretching vibration
of the proton donor OH group which shifts from 3725.9 to 3469.6 cm−1. The bands
with participation of the in-plane bending vibrations δ for donor are shifted to higher
frequencies from 1145.6, 1200.2, 1303.0, 1428, 1451.7 and 1660.5 cm−1 to 1218.2,
1340, 1416.6, 1472.7, 1544.8, 1661.9 cm−1, respectively. Analogous vibrational modes
with participation δ OH for proton acceptor are also different than those of monomer
and shifted to 1209, 1309.3, 1415.4, 1454.4, 1540.5, 1648.2 cm−1. σ(OH) for donor
are shifted to higher frequencies from 164.8, 247.9, 345.3, 418.2, 521.1 cm−1 to 189.6,
271.0, 352.4, 420.4, 525.4 cm−1, γ(OH) for donor are shifted to higher frequencies from
293.8, 518, 642, 769.2 cm−1 to 315.2, 615.1, 756.2, 832.6 cm−1.
4.4 Experimental spectra
According to the formula for the G(ν) function, the intensity of neutron scattering is
proportional to the square of atom displacement. The phonon density of states func-
tion of parent undeuterated oxime (Fig. 3) at various temperatures and undeuterated and
deuterated ones (at 20 K) are shown in Fig. 5. The frequencies of the observed INS
bands are collected in Table 3. Nine vibrational modes at 212.5, 448, 564, 592, 867.2,
937.5, 1461, 1600, 1862 cm−1 observed in undeuterated oxime were found to be ab-
sent for the deuterated sample of 2-oxime. Their predominant assignment we can find
in Table 3. The mentioned modes observed in our IINS experiment are related to the vi-
brations of hydrogen bonds between hydrogen atom of the N−O···H group and oxygen
atoms belonging to the ester carbonyl group of the neighboring molecule or to vibration
of N−O−H group (which is not bonded in the considered dimerical molecule). From
X-ray data of the (E)-2-cyanoethyl ester-2-oxime [4] we can see one single H-bond as
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Table 4. Frequencies calculated (by B3LYP/6-311++G(d,p) method) for conformation 1 and PEDS greater
than 10%.
Theor. freq.
Assignment
of G(υ)
3795.57
3122.09
3107.42
3095.62
ν O1H1 100
ν C(5)–H(5) 35% – ν C(5)–H(4) 35% – ν C(4)–H(3) 15% + νC(4)–H(2) 15%
ν C(5)–H(6) 60% – ν C(5)–H(4) 19% – ν C(5)–H(5) 19%
ν C(4)–H(2) 35% – ν C(4)– H(3) 35% – ν C(5)–H(5) 15%
+ ν C(5)–H(4) 15%
3057.96
3040.47
2337.99
1807.51
1645.99
1517.17
1498.27
1486.10
1429.52
1404.29
ν C(4)–H(3) 49% + ν C(4)–H(2) 49%
ν C(5)–C(4) 39% + ν C(5)–H(4) 30% + ν C(5)–H(5) 30%
ν C(1)–N(1) 89% – ν C(2)–C(1) 11%
ν C(3)–O(2) 79%
ν N(2)–C(2) 72% – δN(2)–H(1)–O(1) 10%
δ O(3)–C(5)–C(4) 72% δ H(5)–C(5) 14%
δ H(5)–C(5) 48% – δH(3)–H(2)–C(4), O(3)–C(5)–C(4) 26% δ H(5)–C(5) 16%
δC(5)–H(6) 68% – δ H(5)–C(5) 23%
δ C(5)–H(6), C(4)–C(5) 53% + δO(3)–C(4), C(4)–C(5) 24% + ν C(4)–C(5) 13%
δ C(5)–H(6), C(4)–C(5) 27% – δO(3)–C(4), C(4)C(5) 27%
+ δ N(2)–H(1)–O(1) 26%
1392.94
1299.0
1277.10
1185.55
δN(2)–H(1)–O(1) 45% + δ O(3)–C(4), C(4)C(5) 31%
δO(3)–C(4), C(4)–C(5) 88% + δ C(4)–C(5) 10%
ν C(3)–O(3) 32% – ν C(2)–C(3) 27% + δ C(2)–O(2)–C(3) 11%
ν C(2)–C(1) 20% – ν C(3)–O(3) 20% + δ N(2)–C(3)–O(2) 16%
+ δ C(2)–O(1)–N(2) 10%
1175.97
1133.12
1059.93
1024.57
881.34
850.42
816.09
792.01
751.43
639.06
522.37
513.98
421.08
δ O(3)–C(4), C(4)–C(5) 50% – δ C(4)–C(5) 36%
δ C(4)–C(5) 40% + ν C(4)–C(5) 22% + δO(3)–C(4)C(5) 13%
ν C(1)–N(2) 56% + ν O(3)–C(4) 19%
ν C(4)–C(5) 44% – ν O(3)–C(4) 20%
ν O(3)–C(4) 41% + δ C(4)–C(5)–H(6) 21%
δ O(2)–C(3)–O(3) 29% – δ C(3)–O(3)–C(4) 15% + ν C(2)–C(1) 12%
δ O(3)–H(3)–C(4) 39% + δ H(4)–C(4)–C(5) 35% – δ O(3)–H(3)–C(4) 13%
γ C(2)–C(3)–O(2) 59% + γ C(2)–C(1) 20%
δ O(1)–N(2)–C(3) 27% – δ C(3)–C(4) 23% – δ N(2)–C(3)–C(4) 21%
γ C(3)–C(2)–C(1) 23% – χ O(1)–N(2) 22% + χ N(2)–C(3) 20%
δ C(2)–C(1)–N(1) 16% – δ N(2)–C(2)–C(1) 16% + ν C(2)–C(1) 13%
χ O(1)–N(2) 77%
δ C(2)–C(3)–O(3) 23% + δ C(2)–C(1)–N(1) 22% – δ O(3)–C(4)–C(5) 22%
– δ O(1)–N(2)–C(2) 18%
412.06
342.57
293.43
279.97
247.57
233.60
166.47
113.23
98.90
ν C(2)–C(3) 30% + δ O(1)–N(2)–C(2) 23% + δ C(2)–C(3)–O(2) 22%
δ C(4)–O(3)–C(5) 24% + δ C(3)–C(4)–O(3) 22% – δ C(2)–O(2)–C(3) 13%
χ C(2)–N(3) 49% – γ C(2)–C(1)–N(1) 42%
χ C(4)–C(5) 37% – χ C(3)–O(3) 26%
δ N(2)–C(3)–C(2) 38% – δ C(3)–O(3)–C(4) 22%
χ C(4)–C(5) 56%
δ C(2)–C(1)–N(1) 38% + δ N(2)–C(1)–C(2) 30%
χ C(3)–O(3) 62%
δ C(2)–C(3)–O(3) 28% – δ C(3)–O(3)–C(4) 24%
χ O(3)–C(4) 83% – χ C(2)–C(3) 13%
67.27
33.01
χ C(2)–C(3) 88%
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hydrogen bridge between OH and oxygen atom of carbonyl group of neighboring. The
length of the hydrogen bond O1−H1···O2 is equal 2.701 Å based on crystallographic
data [4] whereas the corresponding length but of the distance O1−H1···N2 is equal to
3.236 Å in the same molecule of (E)-2 cyanoethylester-2-oxime. The angle between
atoms: OHO = 174.86◦ in the first case and 114.23◦ in the second case (here between
atoms: OHN).
Additionally, as we can see in Table 3 that nearly all vibrations associated with hy-
drogen bond bridge appear not as pure modes but they are accompanied by another
vibrations. Typical vibrations related to the vibrations of hydrogen bonds between hy-
drogen atom of the hydroxyimino (N)−O···H group and oxygen atoms belonging to
the ester carbonyl group C=O of the neighboring molecule are: σ(O−H···O): 132.8,
212.5, 279, 358.7, 424, 448, 522.6, 872, γ(O−H···O)-out-of-plane: 334, 564, 592, 745,
820 cm−1, δ(N−OH···): 1461, 1600, 1862 cm−1. The frequency at 405 cm−1 has been
assigned as the out of plane (o.o.p.) (γO−D···O) vibrational modes. It is present in the D
sample and absent in the H-sample. The 937.5 cm−1 frequency could be responsible for
torsion O−H (no peak in the D spectrum).
On the basis of [14,15] we can assign the modes at 150.9, 250, 293.8 cm−1 as as-
cribed to the libration of CH3 group, out of plane vibrations of hydrogen of CH2 group
and of torsion of CH3 respectively. It is in agreement with our assignment shown in
Table 3 where at such the frequencies we observe out of plane torsion motions of the
ethyl group.
The corresponding vibrations were observed in IINS spectra at 309 cm−1 (torsion of
CH3) in [15] for L and DL-valine, 228, 281 cm−1 [14] for L-isolueucine. A high intensity
peak at 250 cm−1 suggests a large proton displacement in the CH2 group. According to
our assignment at the frequency we observe torsional motions of ethyl group.
The frequency 293.8 cm−1 describes out of plane skeletal motions and its result is
a displacement of all protons. In methyl group there are 3 protons, in the methylene
group there are 2 protons, hence the torsional motion of ethyl group is responsible for
such a great intensity of the corresponding peaks.
Observed in the region 390–430 cm−1 changes in the G(ν) spectra i.e. the shift in
peak position at 424 cm−1 in undeuterated to 419 cm−1 in deuterated sample of (E)-
2-cyanoethyl ester-2-oxime is a result of substitution of H by deuterium in the O−H
group.
The intensity of the G(ν) bands also decreased after deuterization. The IINS peaks
with rather great intensity are connected with modes of groups with hydrogen atoms
in the (E)-2-cyanoethyl ester-2-oxime molecule, although also the other parts of the
molecules take part in those vibrations. It is also a case for example for peaks at 358.7
and 424 cm−1 where bending (deformational in plane) of the bond between oxime and
etoxy (C−CO−) group takes place causing some replacement of H atoms.
A comparison of experimental G(ν) frequencies with theoretical ones (calculated
for the most probable conformations from Table 1) in the frequency region up to
1700 cm−1 shows that the best agreement between the experimental result and the-
oretical one is for conformation 1 of a isolated molecule and for the dimer with
O(1)−H(1)···O(2) HB shown in Fig. 5.
One can see a lack of theoretical frequencies in the corresponding spectrum of
dimer in regions: ca. 450–500, 580–600 and 920–1000 cm−1 which one can see when
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Fig. 6. Comparison of the experimental IR spectra of 2-oxime in KBr taken at 100 K with the calculated
ones for dimer by the DFT method with B3LYP/6-31G∗ basis set.
comparing those regions with the corresponding ones in the experimental IINS ex-
periment. The reason of the event is obvious, namely our theoretical calculations are
connected with a dimeric molecule. It is an assumption because in reality there are not
only two molecules linked by hydrogen bond but all molecules are bound in such the
way.
In the first step of our calculations we obtained the theoretical frequencies also for
a single molecule. Generally speaking the theoretical spectrum for dimer is similar to
the theoretical spectrum for the single molecule. In spectrum for dimer we can see ad-
ditional frequencies at ca. 20, 50, 190, 300, 420, 560, 660 cm−1 which are absent in
spectrum for single molecule and present in the INS spectra. We can admit that also
dimer molecule model is a simplification of the real situation of molecules in the crystal
lattice, which is known from X-ray diffraction and from NPD methods [5].
An inspection of Table 3 reveals that in the energy transfer range from 100 to
1000 cm−1 all modes observed by using of optical spectroscopy methods, presented in
our previous paper [11] can be also identified by the IINS spectroscopy, with the ex-
ception of the γ O−H hydrogen bond modes, which are only observable in the IINS
spectra. We mean here the frequencies 335 and 590 cm−1. The other are observed in
IINS and in the optical spectroscopy, because not only O−H vibrations appear at certain
frequency and the last ones are seen in the optical spectroscopy. If only the correspond-
ing O−H γ vibration had appeared at the frequency it would not have been seen in the
optical spectroscopy.
Figure 6 shows a comparison of IR spectra taken at 293 K and calculated frequen-
cies and intensities of modes active in IR spectra for dimer forming O(1)−H(1)···O(2)
hydrogen bridge bond. The calculated scaling factor is 0.97 (Fig. 7), what means that
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Fig. 7. Scaling procedure between IR frequencies and those obtained from calculations.
Fig. 8. Scaling procedure between Ra frequencies and those obtained from calculations.
the harmonic approximation seems to be good. The calculated scaling factor has been
calculated also for the comparison between experimental Ra frequencies and those cal-
culated (Fig. 8) and it shows also that the harmonic approximation seems to be good as
it was a case in Fig. 7.
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