| 1. |
- Damian Risberg, Emiliana, et al.
(author)
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Ambidentate dimethyl sulfoxide coordination in protonated dimethyl sulfoxide, (CH3)2SO-H+, and in dichlorobis(dimethyl sulfoxide) palladium(II) and platinum(II) solid solvates, by vibrational and sulfur K-edge X-ray absorption spectroscopy
- 2008
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In: Dalton Transactions.
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Journal article (peer-reviewed)abstract
- The protonated dimethyl sulfoxide cation (CH3)2SO-H+ formed in concentrated hydrochloric acid displays a new low energy feature in its sulfur K-edge X-ray absorption near edge structure (XANES) spectrum. Density Functional Theory – Transition Potential (DFT-TP) calculations reveal that the energy of the transition S(1s) LUMO, which has antibonding *(S-O) character, has decreased about 0.8 eV. Normal coordinate force field analyses of the vibrational spectra show that the SO stretching force constant of the oxygen-coordinated (CH3)2SO-H+ species has decreased to 3.73 N cm-1 from 4.72 N cm-1 in neat liquid dimethyl sulfoxide. The effects of sulfur coordination on the ambidentate dimethyl sulfoxide molecule were investigated for the trans-Pd((CH3)2SO)2Cl2 and cis-Pt((CH3)2SO)2Cl2 complexes with square planar coordination of the chlorine and sulfur atoms. The XANES spectra again showed shifts toward low energy of the transition S(1s) LUMO, now with antibonding *(M-Cl, M-S) character, with a larger shift for M = Pt than Pd. DFT-TP calculations indicated that the differences between the XANES spectra of the geometrical isomers of the M((CH3)2SO)2Cl2 complexes are expected to be too small to allow experimental distinction. The vibrational spectra of the palladium(II) and platinum(II) complexes were recorded and complete assignments of the fundamentals were achieved. Even though the M-S bond distances are quite similar the high covalency especially of the Pt-S bonds induces significant increases in the S-O stretching force constants, 6.79 and 7.18 N cm-1, respectively.
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| 2. |
- Fischer, Christian E., et al.
(author)
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Vibrational spectroscopic study of SiO2-based nanotubes
- 2013
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In: Vibrational Spectroscopy. - : Elsevier BV. - 0924-2031 .- 1873-3697. ; 66, s. 104-118
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Journal article (peer-reviewed)abstract
- Novel organic-inorganic hybrid nanotubes containing silica and ethane (EtSNT), ethylene (ESNT) and acetylene (ASNT) units, as well as brominated ESNT (Br-ESNT) and glycine-modified Br-ESNT (Gly-ESNT) have been studied by IR and Raman spectroscopy. The results are compared with the spectral features for conventional silica nanotubes (SNT) and amorphous silica. Bands peculiar to organic moieties have been detected and assigned. Assignment of the silicate backbone vibrations was based on the results of normal coordinate calculations. Furthermore, characteristic silicate, so-called 'nanotube' vibrations have been identified and their band positions have been summarized to serve as a future reference for such compounds. SiOSi antisymmetric stretchings were observed in the range 1000-1110 cm(-1), while the symmetric stretchings appeared between 760 and 960 cm(-1) for EtSNT, ESNT and Br-ESNT. Force constants have been refined for models of the repeating structure units: O3SiOSi(OSi)(3) for SNT and SiCHnCHnSi(OSi)(3) for organosilica nanotubes (n = 2, EtSNT: n = 1, ESNT and n = 0, ASNT). The calculated SiO stretching force constants were increased from 4.79 to 4.88 and 5.11 N cm(-1) for EtSNT, ESNT and ASNT, respectively. The force constants have been compared with those for several silicates and SiO bond length are predicted and discussed.
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| 3. |
- Mink, Janos, et al.
(author)
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Vibrational properties and bonding analysis of copper hexacyanoferrate complexes in solid state
- 2019
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In: Applied spectroscopy reviews (Softcover ed.). - : Informa UK Limited. - 0570-4928 .- 1520-569X. ; 54:5, s. 369-424
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Research review (peer-reviewed)abstract
- Vibrational spectroscopic study of crystalline copper hexacyanoferrate complexes of composition K4Cu6II [Fe-II(CN)(6)](4)nH(2)O (1) and Cu-6(II)[Fe-III(CN)(6)](4)nH(2)O (2) with -Cu-N equivalent to C-Fe- bridging structures have been performed. The cubic Fmm (O-h(5)) unit-cells contain ideally 4 Fe and 4 Cu ions which were calculated by periodic density functional theory (DFT) (using the Gaussian09 C.01 software package) for ideal lattice compositions of K8Cu4II[Fe-II(CN)(6)](4) (1a), K4Cu4II[Fe-III(CN)(6)](4) (2a) and with lattice water molecules KCu4II[Fe-III(CN)(6)](3)6H(2)O (3a). Systematically, non-linear Cu-N equivalent to C structure was fitted with Cu-N equivalent to C bond angles about 155 degrees for complexes 1a, 2a, and 3a. Practically, all optically active internal modes of Fe(CN6)(n-) moieties resulted from factor group analysis as 4A(1g) + 6E(g) + 4F(1g) + 10F(1u) were experimentally observed and assigned. Some low-frequency translatory and librational modes were also interpreted. Vibrational bands were assigned to cis- and trans-Cu(NC)(4)(OH2) complexes which are formed in the lattice holes of both complexes. Vibrational spectra and force constants of a great number of transition metal hexacyano complexes of compositions K-4[M-II(CN)(6)], K-3[M-III(CN)(6)], CsLi2[M-III(CN)(6)] and Prussian blue analogues have been reexamined and recalculated. Internal and external modes of 6 different lattice water species (coordinated, hydrogen bonded, or zeolitic type) have been interpreted for complex 2 using results of periodic DFT calculation of model complex 3a.
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| 4. |
- Mink, Janos, et al.
(author)
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Vibrational Spectroscopic Studies of Molecules with Biochemical Interest : The Cysteine Zwitterion
- 2012
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In: Applied spectroscopy reviews (Softcover ed.). - : Informa UK Limited. - 0570-4928 .- 1520-569X. ; 47:6, s. 415-483
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Research review (peer-reviewed)abstract
- The L-cysteine zwitterions in the orthorhombic crystal structure and in aqueous solution, including the deuterated isotopologues HSCD2CH(NH3+)COO-, DSCH2CH(ND3+)COO-, and DSCD2CH(ND3+)COO-, have been studied by midinfrared, far-infrared, and Raman spectroscopy. Density functional theory (DFT) calculations were performed for an equilibrium molecular geometry of the cysteine zwitterion to obtain vibrational frequencies of fundamental modes, infrared (IR) and Raman intensities, and the depolarization ratio of the Raman bands and combined with normal coordinate force field analyses. The force field obtained for dissolved (in H2O and D2O) cysteine, based on the 4 x 36 experimental fundamental modes of the four isotopologues, was successfully transferred to the two conformers in the solid state. The experimentally observed multiple bands (generally doublets) of L-cysteine and its deuterated isotopologues in the solid state were interpreted based on the coexistence of two conformers in the unit cell. The calculated frequencies were used for full assignments of the fundamental IR and Raman vibrational transitions, including an attempt to interpret all low-frequency vibrations (below 400 cm(-1)) of the zwitterion also in the solid state. In particular, the hydrogen bonding effects on conformation, bond lengths, and force constants were studied, including those of the distorted NH3+ amino group. The -S-H and -S-D stretching vibrations were found to be local modes, not sensitive to deuterium substitution of the -CH2 and -NH3+ groups in the molecule or to the H(D)-S-C-C torsional angle. The two major -S-H or -S-D stretching bands observed in the solid state correspond to different S-H/D bond lengths and resulted in the force constants K-SH = 3.618 N.cm(-1) and 3.657 N.cm(-1) for the SH center dot center dot center dot S and SH center dot center dot center dot O hydrogen-bonded interactions. A remarkable result was that the S(H)center dot center dot center dot O interaction was weaker than the S(H)center dot center dot center dot S interaction in the solid state and even weaker in aqueous solution, K-SH = 3.715 N.cm(-1), possibly due to intramolecular interactions between the thiol and amino groups. A general correlation between the S-H/D bond length and vibrational frequency was developed, allowing the bond length to be estimated for sulfhydryl groups in, for example, proteins. The C-S stretching modes were fitted with different C-S stretching force constants, K-CS = 3.213 and 2.713 N.cm(-1), consistent with the different CS bond lengths for the two solid-state conformers.
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| 5. |
- Risberg, Emiliana Damian, et al.
(author)
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Ambidentate coordination in hydrogen bonded dimethyl sulfoxide, (CH3)2SO H3O+, and in dichlorobis(dimethyl sulfoxide) palladium(II) and platinum(II) solid solvates, by vibrational and sulfur K-edge X-ray absorption spectroscopy
- 2009
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In: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; , s. 1328-1339
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Journal article (peer-reviewed)abstract
- The strongly hydrogen bonded species (CH3)2SOH3O+ formed in concentrated hydrochloric acid displays a new low energy feature in its sulfur K-edge X-ray absorption near edge structure (XANES) spectrum. Density Functional Theory-Transition Potential (DFT-TP) calculations reveal that the strong hydrogen bonding decreases the energy of the transition S(1s) → LUMO, which has antibonding σ*(S–O) character, with about 0.8 eV. Normal coordinate force field analyses of the vibrational spectra show that the SO stretching force constant decreases from 4.72 N cm−1 in neat liquid dimethyl sulfoxide to 3.73 N cm−1 for the hydrogen bonded (CH3)2SOH3O+ species. The effects of sulfur coordination on the ambidentate dimethyl sulfoxide molecule were investigated for the trans-Pd((CH3)2SO)2Cl2, trans-Pd((CD3)2SO)2Cl2 and cis-Pt((CH3)2SO)2Cl2 complexes with square planar coordination of the chlorine and sulfur atoms. The XANES spectra again showed shifts toward low energy for the transition S(1 s) → LUMO, now with antibonding σ*(M–Cl, M–S) character, with a larger shift for M = Pt than Pd. DFT-TP calculations indicated that the differences between the XANES spectra of the geometrical cis and trans isomers of the M((CH3)2SO)2Cl2 complexes are expected to be too small to allow experimental distinction. The vibrational spectra of the palladium(II) and platinum(II) complexes were recorded and complete assignments of the fundamentals were achieved. Even though the M–S bond distances are quite similar the high covalency especially of the Pt–S bonds induces significant increases in the S–O stretching force constants, 6.79 and 7.18 N cm−1, respectively.
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| 6. |
- Sandström, Magnus, 1945-, et al.
(author)
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Vibrational spectroscopic and theoretical studies of urea derivatives with biochemical interest: N,N’-dimethylurea, N,N,N’,N’-tetramethylurea and N,N’-dimethylpropyleneurea
- 2010
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In: Applied spectroscopy reviews (Softcover ed.). - : Taylor and Francis. - 0570-4928 .- 1520-569X. ; 45, s. 274-326
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Journal article (peer-reviewed)abstract
- Mid-infrared, far-infrared and Raman vibrational spectroscopic studies were combined with DFT calculations and normal coordinate force field analyses for N,N’-dimethylurea (DMU), N,N,N’,N’-tetramethylurea (TMU) and N,N'-dimethylpropyleneurea (DMPU, IUPAC name 1,3-dimethyltetrahydropyrimidin-2(1H)-one). The equilibrium molecular geometry of DMU (all three conformers), TMU and DMPU, and the frequencies, intensities and depolarization ratios of their fundamental IR and Raman vibrational transitions were obtained by DFT calculations. The vibrational spectra were fully analysed by normal coordinate methods as well. A starting force field for DMPU was obtained by adapting corresponding force constants for DMU and TMU, resulting after refinements in the stretching force constants: C=O (7.69, 7.30, 7.68 N×cm -1), C-N (5.16, 5.55, 5.05 N×cm -1) and C-Me (5.93, 4.00, 4.22 N×cm-1) for DMU, TMU and DMPU, respectively. The dominating conformer of liquid DMU was identified as trans-trans, strong intermolecular hydrogen bonding was verified in solid DMU, and weak dipole-dipole association was found in liquid TMU and in DMPU. Special attention was paid to analysing the methyl group frequencies, which revealed deviations from local C3v symmetry. A linear correlation was found between the CH stretching force constants and the inverse of the CH bond lengths (1/r2). The averaged NH stretching frequencies of gaseous, dissolved and solid urea and of DMU, with variations for hydrogen bonding of different strength, are linearly correlated to the NH stretching force constants. Characteristic skeletal vibrations were assigned for a broad variety of urea derivatives and also for pyrimidine derivatives, which all contain the N2C=O entity. The very strong IR bands of C=O stretching (1676 ± 40 cm-1) and asymmetric CN2 stretching (1478 ± 60 cm-1), and the very intense Raman feature of symmetric CN2 stretching or ring breathing (757 ± 80 cm-1), can be recognized as fingerprint bands also for the pyrimidine derivatives cytosine, thymine and uracil, which all are nucleobases in DNA and RNA nucleotides.
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| 7. |
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