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1
Content available remote

Thermodynamic and kinetic properties of scandium (I) ion reacting with SCO in gas phase

100%
Yin P., Qu R., Chen H., Tian Y., Yin G., Bao C.
Open Chemistry
|
2008
|
vol. 6
|
issue 3
438-442
EN
Theoretical studies on the thermodynamic and kinetic properties of the reactions of scandium (I) ion with the sulfur-transfer reagent SCO via the C-O bond activation pathway have been carried out over the temperature range of 200-1200 K using the DFT/B3LYP method, general statistical thermodynamics, and Eyring transition state theory with Wigner correction. The relevant reactions include reaction 1 1Sc+ + SCO → 1IM1 → 1TS1 → 1IM2 (Step 1) → 1TS2 → 1IM3 → 1ScO+ + 1CS (Step 2), and reaction 2 3Sc+ + SCO → 3IM1 → CP → 1IM2 → 1TS2 → 1IM3 → 1ScO+ +1CS in which the spin multiplicity changes from the triplet state to the singlet state in the crossing region. It was concluded that the order of the equilibrium constants (K) and the reaction rate constants (k) are consistent with that of their corresponding exoergic energies, ΔE, and reaction barriers, respectively. Step 2 of reaction 1 is both thermodynamically and kinetically favored over the whole temperature range. Moreover, both Reaction 1 and reaction 2 are exothermic and spontaneous processes in which their entropy increases, and the magnitudes of their thermodynamic values all decrease with increasing temperature. [...]
2
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Hyperpolarizability of 6-vertex carboranes quantum chemical study

100%
Suponitsky K., Timofeeva T.
Open Chemistry
|
2003
|
vol. 1
|
issue 1
1-9
EN
Structure and molecular first hyperpolarizability (β) of nitro-amino-substituted 6-vertex 1,6-carboranes are investigated by means of DFT calculations. The results obtained have revealed that the relative orientation of substituents with respect to the carborane cage influences bond lengths distribution in the cage, which leads to significant changes in the values of hyperpolarizabilities. Calculations with different basis sets have demonstrated that the value of β is not significantly affected by the choice of basis set. The calculated data shows that hyperpolarizability of carborane molecules substituted for carbon atoms is lower than when substituted for boron atoms. For latter molecule, the value of β is of the same order as that of para-nitroaniline molecule.
3
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A DFT study on the interaction between europium, uranium and SWCNT

100%
Xie J.-C., Yong-Jian-Tang, Zhang H.
Open Physics
|
2011
|
vol. 9
|
issue 3
716-721
EN
We investigate the electronic and band structure for the (8; 0) single-wall carbon nanotube (SWCNT) with a europium (Eu) and a uranium (U) atom outside by using the first-principles method with the density functional theory (DFT). The calculated band structure (BS), total density of state (TDOS), and projected density of state (PDOS) can elucidate the differences between the pure (8; 0) SWCNT and the nuclei outside the SWCNT. The indirect band gaps are obtained when Eu and U atom are put outside the (8; 0) CNT; they are 0.037 eV and 0.036 eV, respectively, which is much smaller than 0.851 eV for pure CNT. Compared with pure (8; 0) SWCNT, the bottom of the conduction band moves down by 0.383 eV and 0.451 eV with the Eu and U outside, and the top of valence band moves up by 0.127 eV and 0.162 eV, respectively. More significantly, the top of the valence band has exceeded the fermi-level. So, a single nucleus changes the semiconductor character of pure nanotube to semi-metal.
4
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Exploring the possibility of high-valent copper in models of copper proteins with a three-histidine copper-binding motif

100%
Anamaria I., Mot A., Silaghi-Dumitrescu R.
Open Chemistry
|
2012
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vol. 10
|
issue 5
1527-1533
EN
An important function of many copper-containing proteins is activation of O2 and subsequent substrate oxidation. The Cu (III) oxidation state is generally considered to be less accessible because of the highly positive Cu (III)/Cu (II) redox potentials with typical amino acid ligands. Here, we employ density functional (DFT) calculations to explore to what extent copper (III) may be accessed in a biologically-relevant coordination environment around a mononuclear copper center, by breaking the oxygen-oxygen bond in a copper-(hydro) peroxide complex. In agreement with previous findings by Solomon and co-workers on copper models with related coordination patterns, the formally high-valent copper complex produced by O-O bond cleavage appears to harbor both oxidizing equivalents on the ligands. The potential energy surface for such a reaction reveals that with the three-histidine binding motif at the copper, O-O bond cleavage is not impossible, but rather disfavored thermodynamically. [...]
5
Content available remote

The effect of alloying on the H-atom adsorption on the (100) surfaces of Pd-Ag, Pd-Pt, Pd-Au, Pt-Ag, and Pt-Au. A theoretical study

100%
Matczak P., Romanowski S.
Open Chemistry
|
2011
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vol. 9
|
issue 3
474-480
EN
The effect of alloying on the adsorption of atomic hydrogen was studied using density functional theory (DFT). In the study the (100) surfaces of Pd-Ag, Pd-Pt, Pd-Au, Pt-Ag, and Pt-Au alloys were considered by means of a cluster model. The structural and energetic properties of the H atom adsorbed on the Pd4Me (Me = Ag, Pt, Au) and Pt4Me (Me = Pd, Ag, Au) clusters were calculated and compared with the H-atom adsorption on monometallic clusters. The effect of alloying on the H-atom adsorption is evident for all the investigated bimetallic systems. However, it strongly depends on the second metal atom, Me, is placed in the surface layer or in the subsurface one. In general, the H atom adsorbed in a site containing the second metal exhibits different properties from those characteristic of its adsorption on Pd(100) and Pt(100). Hence, the modified interaction between atomic hydrogen and the alloyed surfaces may increase the selectivity of the catalytic hydrogenation reactions on such surfaces.
6
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Synthesis and pharmacological properties of 3-(2-methyl-furan-3-yl)-4-substituted-Δ2-1,2,4-triazoline-5-thiones

100%
Siwek A., Wujec M., Dobosz M., Jagiełło-Wójtowicz E., Chodkowska A., Kleinrok A., Paneth P.
Open Chemistry
|
2008
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vol. 6
|
issue 1
47-53
EN
By the reaction of 2-methyl-furan-3-carboxylic acid hydrazide with isothiocyanates, 1-[(2-methyl-furan-3-yl)carbonyl]-4-substituted thiosemicarbazides 1 were obtained. Further cyclization with 2% NaOH led to the formation of 3-(2-methyl-furan-3-yl)-4-substituted-Δ2-1,2,4-triazoline-5-thiones 2. The pharmacological effects of 2 on the central nervous system in mice were investigated. Strong antinociceptive properties of the investigated derivatives were observed in a wide range of doses. [...]
7
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The influence of (5′R) and (5′S)-5′,8-cyclo-2′-deoxyadenosine for the electronic properties of nucleosides pairs. The theoretical quantum mechanics studies

88%
Karwowski B.
Open Chemistry
|
2013
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vol. 11
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issue 7
1079-1090
EN
Oxidatively generated damage to DNA frequently appears in the human genome as the effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents such as ionization radiation. In this paper, for the first time, the electronic properties of nucleoside pairs containing 5′,8-cyclo-2′-deoxyadenosine (cdA) in their 5′R and 5′S diastereomeric forms (cdA(R)::T and cdA(S)::T) as the simplest model of ds-DNA have been discussed. The following values of the selected electronic parameters, measured in eV, were found for cdA(R)::T, cdA(S)::T, and dA::T, respectively, adiabatic/vertical electron affinity: 0.39/0.24, 0.35/0.18, 0.33/0.21; and adiabatic/vertical ionization potential: 7.27/7.50, 7.7.25/7.49, 7.03/7.27. Moreover, based on the results of the relaxation energy, the presence of cdA(S)::T should provide the highest barrier for electron transfer in ds-DNA. Analyses of hydrogen bond length deviations reveal that the formation of cationic forms results in higher elongation than that of anionic forms. Moreover, during the electron attachment or detachment for the investigated cdA(R)::T, cdA(S)::T, and dA::T nucleoside pairs, the same scheme of changes in hydrogen bond length was noted. [...]
8
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Consequence of hydrogen atom abstraction from 5’-hydroxyl group of 2’-deoxyadenosine. Theoretical quantum mechanics study

88%
Karwowski B.
Open Chemistry
|
2008
|
vol. 6
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issue 3
450-455
EN
Reactive oxygen species (ROS) may generate different nucleoside/nucleotide radicals in a cell environment. In this study, the possibility of cyclic-2’-deoxyadenosines formation by a rearrangement of their free radicals was investigated. It seems that for cyclic-nucleosides formation, adoption of an O4’-exo conformation by the sugar moiety is necessary. However, this is the energetically unfavoured form of the 2-deoxyribose ring. Moreover, the creation of a O5’, C8 bond in purine deoxy-nucleosides/nucleotides leads to the termination of the DNA elongation process. [...]
9
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A first-principles study of π-conjugated thiol phenothiazine derivatives adsorbed on Au(111) surface

88%
Morari C., Bogdan D., Turcu I.
Open Physics
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2009
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vol. 7
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issue 2
332-339
EN
We present an extensive theoretical study of a series of phenothiazine derivatives adsorbed on Au(111). A series of experimentally accessible quantities are calculated (ultra-violet photoemission spectra, scanning tunneling microscopy images). All simulations were performed by using DFT techniques and LCAO expansion of the molecular orbitals. The microscopic picture established in this work provides a deeper understanding of the interfacial processes that govern the working principle of single-molecule electronics and organic electronic devices.
10
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Oxygen decorating at the one ring and at the N-mouth of (10, 0) aluminum nitride nanotube: A DFT investigation

88%
Seif A., Torkashavand L., Mohammadi F.
|
|
issue 2
131-139
EN
We have investigated oxygen decorating in the (10, 0) aluminum nitride nanotube (AlNNT) by density functional theory. Band gaps, total (TDOS) and partial (PDOS) densities of state and chemical-shielding isotropic (CSI) and chemical-shielding anisotropic (CSA) have been calculated or determined in three models of the investigated (10, 0) AlNNT: pristine (model.0), O-decorating at the one ring in the middle of AlNNT (Model.1) and O-decorating at the nitrogen mouth of AlNNT (Model.2). The results indicated that the dipole moment does not detect the significant effects of dopant whereas TDOS, PDOS and band gap energies detect notable effects. The CSI and CSA values for the Al and N atoms-contributed to the Al-O bonds or those atoms close to the decorated region, in both models of O-decorated AlNNTs are changed.
11
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Bonding xenon and krypton on the surface of uranium dioxide single crystal

88%
Dąbrowski L., Szuta M.
Nukleonika
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2014
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vol. 59
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issue 3
83-89
EN
We present density functional theory (DFT) calculation results of krypton and xenon atoms interaction on the surface of uranium dioxide single crystal. A pseudo-potential approach in the generalised gradient approximation (GGA) was applied using the ABINIT program package. To compute the unit cell parameters, the 25 atom super-cell was chosen. It has been revealed that close to the surface of a potential well is formed for xenon and krypton atom due to its interaction with the atoms of oxygen and uranium. Depth and shape of the well is the subject of ab initio calculations in adiabatic approximation. The calculations were performed both for the case of oxygenic and metallic surfaces. It has been shown that the potential well for the oxygenic surface is deeper than for the metallic surface. The thermal stability of immobilising the atoms of krypton and xenon in the potential wells were evaluated. The results are shown in graphs.
12
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Scaled quantum chemical studies of the structural and vibrational spectra of acetyl coumarin

88%
Bahgat K.
Open Chemistry
|
2006
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vol. 4
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issue 4
773-785
EN
The solid phase FT-IR and FR-Raman spectra of acetyl coumarin have been recorded in the regions 4000–50 cm−1. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on density functional theory (DFT) and Hartree-Fock (HF) at 6–31G* and 6–311++G** basis sets. The resulting force fields were transformed to internal coordinates, the calculated vibrational frequencies and normal modes were utilized in the assignment of the observed vibrational fundamentals. The measured spectral data were used to refine the vibrational force constants by means of a small number of scaling factors.
13
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Theoretical studies on the electronic structures and spectra of single silicon-doped SWCNTs

88%
Gao P., Yu Y., Ni Z., Teng Q.
Open Chemistry
|
2010
|
vol. 8
|
issue 3
587-593
EN
The equilibrium geometries and electronic structures of a series of SWCNTs doped with a silicon atom were studied by using density function theory (DFT). The most stable doping site of silicon predicted at B3LYP/6-31G(d,p) level was located near the boundary of the SWCNTs. The energy gaps of (3,3) C48, (3,3) C60 and (3,3) C72 were respectively decreased by 0.43, 0.25 and 0.14 eV after doping. Based on the B3LYP/6-31G(d) optimized geometries, the electronic spectra of the doped SWCNTs were computed using the INDO/CIS method. The first UV absorption at 973.9 nm of (5,5)-Si(L) (C59Si) compared with that at 937.5 nm of (5,5) (C60) was red-shifted. The 13C NMR spectra and nuclear independent chemical shifts (NICS) of the doped SWCNTs were investigated at B3LYP/6-31G(d) level. The chemical shift at 119.4 of the carbon atom bonded with the silicon atom in (3,3)-Si(L) (C59Si) in comparison with that at 144.1 of the same carbon atom in (3,3) (C60) moved upfield. The tendency of the aromaticity (NICS = −0.1) for (3,3)-Si(H) (C47Si) with respect to that of the anti-aromaticity (NICS = 6.0) for (3,3) (C48) was predicted. [...]
14
Content available remote

Ionisation potential and electron affinity of free 5′,8-cyclopurine-2′-deoxynucleosides. DFT study in gaseous and aqueous phase

88%
Karwowski B.
Open Chemistry
|
2010
|
vol. 8
|
issue 1
70-76
EN
Oxidatively generated damage to DNA frequently appears in the human genome as an effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents. Due to these facts it was decided to present, for the first time, the electron affinity, ionization potential of 5′,8-cyclo-2′-deoxyadenosine/guanosine (cdA, cdG) in their 5′R and 5′S diastereomeric forms. For all points of quantum mechanics studies presented, the density functional theory (DFT) with B3LYP parameters on 6-311++G** basis set level was used. The zero-point vibrational corrected adiabatic electron affinity (AEA) and adiabatic ionization potential (AIP) were calculated. Additionally the vertical electron affinity (VEA), vertical detachment energy (VDE) and vertical ionization potential were taken into consideration. AEA in eV (gaseous/aqueous phase) are as follows: 0.3/1.81 (5′R)cdA, 0.13/1.76 (5′S)cdA, 0.17/1.49 (5′R)cdG, 0.14/1.53 (5′S)cdG and AIP followed the order 7.43/5.59(5′S)cdG, 7.49/5.60(5′R)cdG, 7.77/5.97(5′R)cdA, 7.84/5.93(5′S)cdA. The obtained AIPs were found to be lower than that for corresponding natural nucleosides. Therefore, even though the 5′,8-cyclopurine-2′-deoxynucleoside level in a cell was judged as low, they can play an important role in the stability, replication and transcription of genes. [...]
15
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The difference in stability between 5′R and 5′S diastereomers of 5′,8-cyclopurine-2′-deoxynucleosides. DFT study in gaseous and aqueous phase

88%
Karwowski B.
Open Chemistry
|
2010
|
vol. 8
|
issue 1
134-141
EN
Oxidatively generated damage to DNA frequently appears in the human genome as an effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents. Due to these facts it has been decided to calculate the stability of 5′,8-cyclo-2′-deoxyadenosine/guanosine (cdA, cdG) in their 5′R and 5′S diastereomeric forms. For all points of quantum mechanics studies presented, the density functional theory (DFT) with B3LYP parameters on 6-311++G** basis set level was used. The calculations showed a significant negative enthalpy for glycosidic bond cleavage reaction for cationic forms and slightly negative for neutral ones. The preliminary study of the discussed process has shown the nature of stepwise nucleophilic substitution DN*AD type mechanism. Surprisingly, the different values in free energy, between short-lived oxacarbenium ion intermediates, have been found to lie over a relatively small range, around 1 and 2.8 kcal mol−1. For anions, the decomposition enthalpies were found as positive in aqueous phases. These theoretical results are supported by the formic acid hydrolysis experiments of both diastereomers of cdA, for the first time. (5′S)cdA exhibited higher stability than (5′R)cdA. [...]
16
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New 5-bromo-2-hydroxybenzaldehyde S-ethylisothiosemicarbazone and its mixed-ligand Cu(II) complex with imidazole: synthesis, characterization and DFT calculation

88%
Takjoo R., Akbari A., Ahmadi M., Rudbari H., Bruno G.
Open Chemistry
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2013
|
vol. 11
|
issue 11
1844-1851
EN
A new Schiff base ligand of 5-bromo-2-hydroxybenzaldehyde S-ethyl-isothiosemicarbazone (H2L) was synthesized and its mixed-ligand Cu(II) complex was also prepared by reaction of Cu(NO3)2·3H2O with H2L and imidazole. Their structures were fully characterized by elemental analysis, FT-IR, molar conductivity and UV-Vis methods. The analytical data suggest that the metal, H2L and imidazole ratios in the Schiff base complex are 1:1:1. Single crystal diffraction was also used to better understand the molecular structure of the Cu(II) complex. The results of physico-chemical analyses of the Schiff base complex reveal the coordination geometry around the central atom is square planar. The H2L ligand (NNO donor) is coordinated to the metal center as a tridentate bionegatively agent. Another position of the square planar geometry is occupied by the imidazole ligand. Furthermore, computational studies of the new complex were performed by carrying out DFT calculations. Geometry optimization and natural band analysis of the complex is discussed in further detail. [...]
17
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NBO and NICS analysis of the allylic rearrangements (the Cope and 3-aza-Cope rearrangements) of hexa-1,5-diene and N-vinylprop-2-en-1-amine: A DFT study

88%
Zahedi E., Ali-Asgari S., Keley V.
Open Chemistry
|
2010
|
vol. 8
|
issue 5
1097-1104
EN
In this work, ab initio density functional theory (DFT) calculations have been performed on the 3,3-sigmatropic rearrangements of hexa-1,5-diene (Cope) and N-vinylprop-2-en-1-amine (3-aza-Cope) in the gas phase. The barrier heights and heats of reactions calculated at the B3LYP/6-311G** level of theory were in good agreement with experimental data. Transition states optimized with B3LYP/6-311G** theory were used for calculating the nucleus independent chemical shift (NICS) and, a natural bond orbital (NBO) analysis was also performed at the same level of theory. Our results indicate that the aromaticities of the transition states are controlled by the out-of-plane component and that the chair-like transition state of the Cope rearrangement exhibits the strongest aromatic character. Analysis of donor-acceptor (bonding and anti-bonding) interactions of σ3–4 → π*1–2 suggests that the TS structure in the hexa-1,5-diene reaction (the Cope rearrangement) has more aromatic character than the N-vinylprop-2-en-1-amine reaction (the 3-aza-Cope rearrangement). The NBO results show that in the hexa-1,5-diene and N-vinylprop-2-en-1-amine rearrangements, activation energies are controlled by σ3–4 → π*1–2 and σ3–4 → π*1–2 resonance energies. [...]
18
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Theoretical investigation of the Anti-Parkinson drug rasagiline and its salts: conformations and infrared spectra

88%
Başköse U., Bayarı S., Sağlam S., Özışık H.
Open Chemistry
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2012
|
vol. 10
|
issue 2
395-406
EN
The conformational analysis of rasagiline [N-propargyl-1(R)-aminoindan] was performed by the density functional theory (DFT) B3LYP method using the 6–31++G (d,p) basis set. A single point energy calculations based on the B3LYP optimized geometries were also performed at MP2/6-31++G (d, p) level. The vibrational frequencies of the most stable conformer of rasagiline was calculated at the B3LYP level and vibrational assignments were made for normal modes on the basis of scaled quantum mechanical force field (SQM) method. The influence of mesylate and ethanedisulfonate salts on the geometry of rasagiline free base and its normal modes are also discussed. [...]
19
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Vibrational Spectroscopic and Computational Studies on Bis(2-aminopyridinium)fumarate - Fumaric Acid (1:1) Complex

88%
Kanagathara N., Pawlus K., Marchewka M.
Acta Physica Polonica A
|
2018
|
vol. 133
|
issue 1
45-56
EN
The new vibrational and computational studies on bis(2-aminopiridinium) fumarate - fumaric acid (1:1) complex have been made. The molecular geometry, vibrational frequencies and intensities of vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (B3LYP) method with 6-311++G(d,p) basis set. The highly occupied-lowly unoccupied molecular orbital energies and chemical reactivity of the molecule have been calculated with time-dependent density functional theory approach. Stability energies of the molecule have been studied using natural bond orbital analysis. The predicted nonlinear optical properties of the title compound are much greater that those of urea. In addition, the molecular electrostatic potential surfaces and thermodynamic properties were calculated.
20
Content available remote

The first transition metal iodato peroxido complex: the synthesis, vibrational spectra and crystal structure from powder diffraction data of K3[V2O2(O2)4(IO3)]·H2O

88%
Šimuneková M., Schwendt P., Chrappová J., Smrčok Ľ., Černý R., Beek W.
Open Chemistry
|
2013
|
vol. 11
|
issue 8
1352-1359
EN
The first transition metal iodato peroxido complex, K3[V2O2(O2)4(IO3)]·H2O (I), was prepared by crystallization from the KVO3 - KIO3 - H2O2 - H2O - ethanol (HNO3) solution. The dinuclear anion is immediately decomposed in aqueous solution; the 51V NMR spectrum exhibits signals corresponding to [VO(O2)2(H2O)]−, [V2O2(OH)(O2)4]3− and H2VO4− species only. The IR and Raman spectra contain all characteristic bands of the VO(O2)2 group and the coordinated IO3− ligand. Based on the positions of bands assigned to the vibrations of the VO(O2)2 groups a pentagonal pyramidal arrangement around the vanadium atoms can be supposed. The crystal structure was solved from X-ray synchrotron powder data by direct space method and refined by energy minimization in the solid state employing a hybrid PBE0 functional. This crystal and molecular structure, has confirmed the presence of hexacoordinated vanadium atoms and revealed asymmetric dinuclear structure of the [V2O2(O2)4(IO3)]3− ion. The coordination spheres of vanadium atoms are different - the IO3− anion is coordinated only to one vanadium center. A thermal analysis of the complex confirmed the presence of water molecules in the crystal structure and revealed a considerable stability of the dehydrated complex. [...]
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