| 1. |
- Fischer, Christian E., et al.
(författare)
-
Vibrational spectroscopic study of SiO2-based nanotubes
- 2013
-
Ingår i: Vibrational Spectroscopy. - : Elsevier BV. - 0924-2031 .- 1873-3697. ; 66, s. 104-118
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 2. |
- Mink, Janos, et al.
(författare)
-
Vibrational properties and bonding analysis of copper hexacyanoferrate complexes in solid state
- 2019
-
Ingår i: Applied spectroscopy reviews (Softcover ed.). - : Informa UK Limited. - 0570-4928 .- 1520-569X. ; 54:5, s. 369-424
-
Forskningsöversikt (refereegranskat)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.
|
|
| 3. |
- Mink, Janos, et al.
(författare)
-
Vibrational Spectroscopic Studies of Molecules with Biochemical Interest : The Cysteine Zwitterion
- 2012
-
Ingår i: Applied spectroscopy reviews (Softcover ed.). - : Informa UK Limited. - 0570-4928 .- 1520-569X. ; 47:6, s. 415-483
-
Forskningsöversikt (refereegranskat)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.
|
|
| 4. |
- Sandström, Magnus, 1945-, et al.
(författare)
-
Vibrational spectroscopic and theoretical studies of urea derivatives with biochemical interest: N,N’-dimethylurea, N,N,N’,N’-tetramethylurea and N,N’-dimethylpropyleneurea
- 2010
-
Ingår i: Applied spectroscopy reviews (Softcover ed.). - : Taylor and Francis. - 0570-4928 .- 1520-569X. ; 45, s. 274-326
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 5. |
- Szigyártó, Imola Cs, et al.
(författare)
-
Flow Alignment of Extracellular Vesicles: Structure and Orientation of Membrane-Associated Bio-macromolecules Studied with Polarized Light
- 2018
-
Ingår i: ChemBioChem. - : Wiley. - 1439-7633 .- 1439-4227. ; 19:6, s. 545-551
-
Tidskriftsartikel (refereegranskat)abstract
- Extracellular vesicles (EVs) are currently in scientific focus, as they have great potential to revolutionize the diagnosis and therapy of various diseases. However, numerous aspects of these species are still poorly understood, and thus, additional insight into their molecular-level properties, membrane–protein interactions, and membrane rigidity is still needed. We here demonstrate the use of red-blood-cell-derived EVs (REVs) that polarized light spectroscopy techniques, linear and circular dichroism, can provide molecular-level structural information on these systems. Flow-linear dichroism (flow-LD) measurements show that EVs can be oriented by shear force and indicate that hemoglobin molecules are associated to the lipid bilayer in freshly released REVs. During storage, this interaction ceases; this is coupled to major protein conformational changes relative to the initial state. Further on, the degree of orientation gives insight into vesicle rigidity, which decreases in time parallel to changes in protein conformation. Overall, we propose that both linear dichroism and circular dichroism spectroscopy can provide simple, rapid, yet efficient ways to track changes in the membrane–protein interactions of EV components at the molecular level, which may also give insight into processes occurring during vesiculation.
|
|
| 6. |
- Szigyártó, Imola Cs, et al.
(författare)
-
Membrane active Janus-oligomers of β 3 -peptides
- 2020
-
Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6539 .- 2041-6520. ; 11:26, s. 6868-6881
-
Tidskriftsartikel (refereegranskat)abstract
- Self-assembling peptides offer a versatile set of tools for bottom-up construction of supramolecular biomaterials. Among these compounds, non-natural peptidic foldamers experience increased focus due to their structural variability and lower sensitivity to enzymatic degradation. However, very little is known about their membrane properties and complex oligomeric assemblies-key areas for biomedical and technological applications. Here we designed short, acyclic β3-peptide sequences with alternating amino acid stereoisomers to obtain non-helical molecules having hydrophilic charged residues on one side, and hydrophobic residues on the other side, with the N-terminus preventing formation of infinite fibrils. Our results indicate that these β-peptides form small oligomers both in water and in lipid bilayers and are stabilized by intermolecular hydrogen bonds. In the presence of model membranes, they either prefer the headgroup regions or they insert between the lipid chains. Molecular dynamics (MD) simulations suggest the formation of two-layered bundles with their side chains facing opposite directions when compared in water and in model membranes. Analysis of the MD calculations showed hydrogen bonds inside each layer, however, not between the layers, indicating a dynamic assembly. Moreover, the aqueous form of these oligomers can host fluorescent probes as well as a hydrophobic molecule similarly to e.g. lipid transfer proteins. For the tested, peptides the mixed chirality pattern resulted in similar assemblies despite sequential differences. Based on this, it is hoped that the presented molecular framework will inspire similar oligomers with diverse functionality.
|
|
| 7. |
- Udyavara Nagaraj, Vignesh, et al.
(författare)
-
Stimuli-Responsive Membrane Anchor Peptide Nanofoils for Tunable Membrane Association and Lipid Bilayer Fusion
- 2022
-
Ingår i: ACS Applied Materials & Interfaces. - : American Chemical Society (ACS). - 1944-8252 .- 1944-8244. ; 14:50, s. 55320-55331
-
Tidskriftsartikel (refereegranskat)abstract
- Self-assembled peptide nanostructures with stimuli-responsive features are promising as functional materials. Despite extensive research efforts, water-soluble supramolecular constructs that can interact with lipid membranes in a controllable way are still challenging to achieve. Here, we have employed a short membrane anchor protein motif (GLFD) and coupled it to a spiropyran photoswitch. Under physiological conditions, these conjugates assemble into ∼3.5 nm thick, foil-like peptide bilayer morphologies. Photoisomerization from the closed spiro (SP) form to the open merocyanine (MC) form of the photoswitch triggers rearrangements within the foils. This results in substantial changes in their membrane-binding properties, which also varies sensitively to lipid composition, ranging from reversible nanofoil reformation to stepwise membrane adsorption. The formed peptide layers in the assembly are also able to attach to various liposomes with different surface charges, enabling the fusion of their lipid bilayers. Here, SP-to-MC conversion can be used both to trigger and to modulate the liposome fusion efficiency.
|
|
