Vlasta Mohaček Grošev | Ruder Boskovic Institute (original) (raw)

Papers by Vlasta Mohaček Grošev

MATERIALS, 2021

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2022

New Raman data are presented concerning H2O and D2O water aggregation in argon matrix having the ... more New Raman data are presented concerning H2O and D2O water aggregation in argon matrix having the ratio of number of argon atoms to water molecules close to 40:1. Experiments were conducted at temperatures from 8 K to 34 K allowing observation of OH and OD stretching vibrations of water monomers, dimers, trimers and higher multimers, as well as broad bands corresponding to solid amorphous water. Molecular dynamics simulations were performed for thirteen or sometimes fourteen water molecules dispersed among 500 argon atoms. Resulting final configurations included dimers, trimers, tetramers and pentamers, all in open chain configurations which upon optimization resulted in mostly cyclic conformations. Observed OH stretching vibrations were assigned by comparing calculated normal modes in harmonic approximation at the B3LYP/aug-cc-pVDZ and PBEPBE1/aug-cc-pVDZ level of theory with our data and previously observed bands from infrared matrix isolation studies and Raman jet cooled experiments. Raman bands assigned to water multimers in argon matrix are shifted 20 to 25 cm-1 towards lower wavenumbers with respect to the positions of OH stretching vibrations of almost free water clusters.

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2022

The binding of glucosamine to gold in water solutions of glucosamine hydrochloride mixed with cle... more The binding of glucosamine to gold in water solutions of glucosamine hydrochloride mixed with clean colloidal gold nanoparticles obtained by laser ablation in liquid was studied using surface-enhanced Raman scattering (SERS), dynamic light scattering (DLS) and UV-VIS spectroscopy. The purpose of this study was to establish whether the binding of charged aminogroup to gold nanoparticles (AuNPs) is taking place, and if it does, how can it be identified by means of SERS. The average size of dried gold nanoparticles was (20 ± 4) nm determined by averaging the sizes observed in transmission electron microscopy micrographs, which is smaller than the average size of gold nanoparticles in water solution as determined by DLS: (52 ± 2) nm. Upon adding the glucosamine solutions to gold colloid, average hydrodynamic diameter of ions was slightly larger for 0.1 mM glucosamine solution (55 ± 2 nm), while it increased to (105 ± 22) nm in the case of 1 mM solution, and was (398 ± 54) nm when 10 mM glucosamine solution was added. Most prominent Raman bands observed both for 0.1 mM and 1 mM glucosamine solutions were located at 1165 cm-1, 1532 and 1586 cm-1 and assigned to C-N coupled with C-C stretching, and C-NH3+ deformation angles bending. In SERS spectrum of 1 mM GlcN+ solution, two strong bands at 999 and 1075 cm-1 were found and attributed to C-Oring stretching coupled with C-NH3+ bending (999 cm-1) and to dominantly C-O stretching vibration. The differences in SERS spectra are attributed to different number of glucosamine molecules that attach to gold nanoparticles and their orientation with respect to the metal particle surface, partly due to presence of beta anomers protonated at anomeric oxygen position. The assignment of glucosamine bands was further corroborated by comparison with vibrational spectra of alpha and beta glucose and of polycrystalline powder of glucosamine hydrochloride. For all three substances comprehensive calculation of vibrational density of states was conducted using density functional theory. Benchmark bands for polycrystalline glucose anomers distinction are 846 and 915 cm-1 for alpha glucose, and 902 cm-1 for beta glucose. However, the bands observed in SERS spectra of 0.1 mM glucosamine solution at 831, 899, and 946 cm-1 or in 1 mM solution at 934 cm-1 cannot be easily identified as belonging either to alpha or beta glucosamine anomer, due to complexity of atomic motions involved. The identification of vibrational bands associated with -CNH3+ group will aid SERS studies on amino acids, especially in cases when several atomic groups could possibly bind to AuNPs.

Croatica chemica acta, 2020

Structural characterization of the β-polymorph of glycolaldehyde dimer by powder X-ray diffractio... more Structural characterization of the β-polymorph of glycolaldehyde dimer by powder X-ray diffraction, Raman and infrared spectroscopies is described. The previously described α-polymorph and the β-polymorph both crystallize in the monoclinic crystal system, space group P21/c, but with different cell parameters. There are no significant differences in the glycolaldehyde dimer molecular structure, the molecules in both polymorphs are trans-isomers with the hydroxyl groups in axial positions. The two polymorphs have a different arrangement of the glycolaldehyde dimer molecules. In the previously reported α-polymorph the molecules are arranged in hydrogen bonded layers parallel to (100) while in the β-polymorph the hydrogen bonded molecules are arranged in a three-dimensional network. Theoretically calculated Gibbs free energy as well as differential scanning calorimetry indicate β-polymorph to be the stable crystal phase of glycolaldehyde.

Radiation Physics and Chemistry, 2019

Four structurally different amines: 1,3-diamino-2-propanol (DAP), diethylenetriamine (DETA), tris... more Four structurally different amines: 1,3-diamino-2-propanol (DAP), diethylenetriamine (DETA), tris(2aminoethyl)amine (TAEA) and triethylenetetramine (TETA) were reacted with diglycidyl ether terminated poly(dimethylsiloxane), PDMS-DGE at relatively low temperature of 50 ºC. Stable transparent networks with gel-like properties but without a liquid component, "gel networks" were obtained. Raman spectra revealed presence of residual epoxy-group absorptions in cured gel-networks but secondary amine absorption intensities in FTIR spectra were used for monitoring of the curing reaction extent. To assess their radiation stability gel-networks were gamma-irradiated to absorbed dose of 50 kGy. Even though contribution of amine segments to PDMS-based gel-networks is relatively small their structure significantly influenced the properties of studied PDMS-based gel-networks. The most important property of an amine was the ability to either form hydrogen bonds, or produce denser network like a triamine. However there were also significant differences in properties of gel-networks prepared with mutually similar diamines DETA and TETA that can be considered a dimer and a trimer of ethylenediamine. In the studied gel-networks there is a complex interaction of extent of initial curing that depended on the amine used and the resulting (dis)order that strongly influenced the outcome of irradiation. The temperature of an endothermic transition presumably caused by reversible gel-network collapse was observed in DSC thermograms of all the gelnetworks. The temperature depended on the amine type and shifted to higher values on irradiation. Changes in most properties like residual gel content on extraction or AC electrical conductivity and its frequency dependence were more pronounced in gel-networks prepared with diamines DETA and TETA than in those prepared with amines capable of significant secondary valent interactions (DAP and TAEA). Radiation curing and/or crosslinking seem to have occurred only in TETA-cured gel-network and it was mostly due to lower extent of initial reaction. Since swelling of gel-networks increased it may be concluded that irradiation improved their properties.

Materials Research Express, 2018

The main purpose of this paper is to focus on details of the fabrication process of horizontally ... more The main purpose of this paper is to focus on details of the fabrication process of horizontally and vertically oriented silicon nanowires (SiNWs) substrates for the application of surface-enhanced Raman spectroscopy (SERS). The fabrication process is based on the vapor–liquid–solid method and electroless-assisted chemical etching, which, as the major benefit, resulting in the development of economical, easy-to-prepare SERS substrates. Furthermore, we examined the fabrication of Au coated Ag nanoparticles (NPs) on the SiNWs substrates in such a way as to diminish the influence of silver NPs corrosion, which, in turn, enhanced the SERS time stability, thus allowing for wider commercial applications. The substances on which high SERS sensitivity was proved are rhodamine (R6G) and 4-mercaptobenzoic acid (MBA), with the detection limits of 10−8Mand 10−6 M, respectively

Silicon, 2018

This paper shows steps for silicon nanowires substrates synthesis in detail. The research is focu... more This paper shows steps for silicon nanowires substrates synthesis in detail. The research is focused on experimental techniques optimization while the targeted application was a fabrication of highly sensitive substrates for surface-enhanced Raman spectroscopy (SERS). Horizontal silicon nanowires on top of two-inch wafers were obtained by vapour-liquid-solid growth inside the low-pressure chemical vapour deposition reaction tube. The silicon nanowires morphology was monitored by scanning electron microscope after a short and long growth period which defined an adequate deposition time for SERS applications. Surface-enhanced Raman spectroscopy features were tested on silver nanoparticles decorated substrates and the detection concentration limit of 10 −9 M of rhodamine 6G molecules was reached. Raman spectroscopy showed that the 532 nm laser excitation powers of less than 4 mW (∼0.57 kW/cm 2) do not widen the phonon peak or shift its frequency and the nanostructure distribution parameter of 3.7 nm was calculated. The horizontally placed Ag decorated nanowires are proved to be sensitive substrates for surface-enhanced Raman spectroscopy only if the silicon nanowires thickness, length, volume density as well as metal nanoparticle size and distribution are carefully designed.

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2018

Modern diagnostic tools ever aim to reduce the amount of analyte and the time needed for obtainin... more Modern diagnostic tools ever aim to reduce the amount of analyte and the time needed for obtaining the result. Surface-enhanced Raman spectroscopy is a method that could satisfy both of these requirements, provided that for each analyte an adequate substrate is found. Here we demonstrate the ability of gold-sputtered silicon nanowires (SiNW) to bind p-mercaptobenzoic acid in 10 −3 , 10 −4 and 10 −5 M and adenine in 30 and 100 μM concentrations. Based on the normal mode analysis, presented here for the first time, the binding of p-mercaptobenzoic acid is deduced. The intensity enhancement of the 1106 cm −1 band is explained by involvement of the C-S stretching deformation, and the appearance of the broad 300 cm −1 band attributed to S-Au stretching mode. Adenine SERS spectra demonstrate the existence of the 7H tautomer since the strongest band observed is at 736 cm −1. The adenine binding is likely to occur in several ways, because the number of observed bands in the 1200-1600 cm −1 interval exceeds the number of observed bands in the normal Raman spectrum of the free molecule.

Croatica Chemica Acta, 2017

The silicon based substrates for surface enhanced Raman spectroscopy (SERS) have been synthesized... more The silicon based substrates for surface enhanced Raman spectroscopy (SERS) have been synthesized and tested. The silver-assisted electroless wet chemical etching method has been utilized for silicon nanowires production which has been proved as the promising SERS substrate. The morphology of the silicon nanowires coated with silver nanoparticles has been examined by scanning electron microscopy. The SERS measurements tested on rhodamine 6G molecules indicated the optimal silicon nanowire substrate production obtained for 5 M hydrofluoric acid and 30 mM silver nitrate etching solution. The results show SERS detection limit of 10-8 M rhodamine in aqueous solution.

Monthly Notices of the Royal Astronomical Society: Letters, 2016

Although it was found that the FeH lines exist in the spectra of some stars, none of the spectral... more Although it was found that the FeH lines exist in the spectra of some stars, none of the spectral features in the ISM have been assigned to this molecule. We suggest that iron atoms interact with hydrogen and produce Fe-H nanoparticles which sometimes contain many H atoms. We calculate infrared spectra of hydrogenated iron nanoparticles using density functional theory methods and find broad, overlapping bands. Desorption of H 2 could induce spinning of these small Fe-H dust grains. Some of hydrogenated iron nanoparticles posses magnetic and electric moments and should interact with electromagnetic fields in the ISM. Fe n H m nanoparticles could contribute to the polarization of the ISM and the anomalous microwave emission. We discuss the conditions required to form FeH and Fe n H m in the ISM.

Journal of Alloys and Compounds, 2017

The local structural changes within the normal spinel structure of a ZnAl 2 O 4 host caused by th... more The local structural changes within the normal spinel structure of a ZnAl 2 O 4 host caused by the titanium incorporation as studied by the Raman spectroscopy and computationally using the density functional theory have been analyzed. The lattice dynamics calculation of the ZnAl 2 O 4 phonons were performed within the density functional theory for the 3D periodic crystal structures. Band structure calculations by the grid-based PAW method predicted a direct band gap in the pure ZnAl 2 O 4 sample to be 4.732 eV, while doping with Ti 4þ produced a density of states in the middle of the gap. The lattice dynamics calculations using Gaussian-type wavefunctions as basis set and a local density approximation gave a good agreement between observed and predicted Raman bands. Doping with Ti 4þ causes the infrared active T 1u phonons as well as the inactive phonons (T 1g , A 2u , E u and T 2u symmetries) to appear in the Raman spectra and breaking of the symmetry selection rules.

Journal of Molecular Structure, 2017

Crystals of (HGua)2[Cu2Cl6]•2H2O (HGua = protonated guanine) were prepared and analysed by spectr... more Crystals of (HGua)2[Cu2Cl6]•2H2O (HGua = protonated guanine) were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis have given us new insight into the vibrational states of the (HGua)2[Cu2Cl6]•2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer (HGua)2[Cu2Cl6]•2H2O with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained form periodic DFT calculations gave us an insight into the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

The Journal of Physical Chemistry A, 2016

Low temperature Raman spectra of oxalic acid dihydrate (8K-300 K) both for polycrystalline and si... more Low temperature Raman spectra of oxalic acid dihydrate (8K-300 K) both for polycrystalline and single crystal phase show strong variation with temperature in the interval from 1200 to 2000 cm-1. Previous low temperature diffraction studies all confirmed the stability of the crystal P21/n phase with no indications of any phase transition, reporting the existence of a strong hydrogen bond between the oxalic acid and a water molecule. A new group of Raman bands in the 1200-1300 cm-1 interval below 90 K is observed, caused by possible loss of the centre of inversion. This in turn could originate either due to disorder in hydroxyl proton positions, or due to proton transfer from carboxylic group to water molecule. The hypothesis of proton transfer is further supported by the emergence of new bands centered at 1600 cm-1 and 1813 cm-1 , which can be explained with vibrations of H3O + ions. The broad band at 1600 cm-1 looses intensity, while the band at 1813 cm-1 gains intensity on cooling. The agreement between quantum calculations of vibrational spectra and experimentally observed Raman bands of hydronium ions in oxalic acid sesquihydrate crystal corroborate this hypothesis.

Monthly Notices of the Royal Astronomical Society, 2014

Calcium silicate hydrate is used to model the properties of cement on Earth. We study cementitiou... more Calcium silicate hydrate is used to model the properties of cement on Earth. We study cementitious nanoparticles and propose these structures as components of cosmic dust grains. Quantum density functional theory methods are applied for the calculation of infrared spectra of Ca 4 Si 4 O 14 H 4 , Ca 6 Si 3 O 13 H 2 and Ca 12 Si 6 O 26 H 4 clusters. We find bands distributed over the near-, mid-and far-infrared regions. A specific calcium silicate hydrate spectral feature at 14 μm, together with bands at 10 and 18 μm, which exist for other silicates as well, could be used for the detection of cosmic cement. We compare the calculated bands with the 14-μm features in the spectra of HD 45677, HD 44179 and IRC+10420, which were observed by the Infrared Space Observatory and classified as remaining. A high abundance of oxygen atoms in cementitious nanoparticles could partially explain the observed depletion of this element from the interstellar medium on to dust grains.

The asymmetric band profile of the triple C=C stretching Raman band in bis(trimethylsilyl)acetyle... more The asymmetric band profile of the triple C=C stretching Raman band in bis(trimethylsilyl)acetylene was decomposed into a higher and a lower wavenumber part, each described as one half of a Lorentzian bandshape with its own halfwidth (Ghigh and Glow), but with common band centre and maximum point. Ghigh and Glow were fitted at seventeen different temperatures ranging from 110 K

Vibrational Spectroscopy, 2013

We present a Raman study of liquid and polycrystalline dioxolane, together with data for a solid ... more We present a Raman study of liquid and polycrystalline dioxolane, together with data for a solid dioxolane/argon film. Observed bands are assigned to the bent conformer on the basis of ab initio calculated vibrations, accompanied with potential energy distribution. Two internal modes were calculated at 658 and 720 cm −1 for the bent form. These were observed at 665 and 722 cm −1 in liquid, and split into four bands (at 694, 697, 725, and 728 cm −1) in the crystal at 10 K. In the solid dioxolane/argon film an additional band appears at 705 cm −1 (between the bands at 675 and 726 cm −1). A search for an additional dioxolane conformer trapped in argon was undertaken by performing molecular dynamics simulations of dioxolane/argon solid film and averaging overall molecular conformations. The resulting conformation did not correspond to an energy minimum, but indicated that changes of only a few degrees in dihedral angles could shift ring deformation and O C O bending modes for more than 10 cm −1. Differential scanning calorimetric measurements gave evidence of solidification upon cooling at 146 K, and two phase changes on heating (one at 158.3 K, and a melting transition at 180.3 K). Further study is required on the hysteresis effect in the temperature behavior of dioxolane, and on the nature of the intermediate solid phase.

The Journal of Physical Chemistry A, 2007

Raman spectra of acetylacetone were recorded for molecules isolated in an argon matrix at 10 K an... more Raman spectra of acetylacetone were recorded for molecules isolated in an argon matrix at 10 K and for a polycrystalline sample. In the solid sample, broad bands appear superimposed on a much weaker Raman spectrum corresponding mainly to the stable enol form. The position of these bands depends on the excitation wavelength (514.5 and 488.8 nm argon ion laser lines were used), sample temperature, and cooling history. They are attributed to transitions from an excited electronic state to various isomer states in the ground electronic state. Laser photons have energies comparable to energies of a number of excited triplet states predicted for a free acetylacetone molecule (Chen, X.-B.; Fang, W.-H.; Phillips, D. L. J. Phys. Chem. A 2006, 110, 4434). Since singlet-to-triplet photon absorption transitions are forbidden, states existing in the solid have mixed singlet/triplet character. Their decay results in population of different isomer states, which except for the lowest isomers SYN enol, TS2 enol (described in Matanović I.; Došlić, N. J. Phys. Chem. A 2005, 109, 4185), and the keto form, which can be detected in the Raman spectra of the solid, are not vibrationally resolved. Differential scanning calorimetry detected two signals upon cooling of acetylacetone, one at 229 K and one at 217 K, while upon heating, they appear at 254 and 225 K. The phase change at higher temperature is attributed to a freezing/melting transition, while the one at lower temperature seems to correspond to freezing/melting of keto domains, as suggested by Johnson et al.

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2005

In order to be able to fully understand the vibrational dynamics of monosaccharide sugars, we sta... more In order to be able to fully understand the vibrational dynamics of monosaccharide sugars, we started with hydroxyacetone CH 2 OHCOCH 3, and glycolaldehyde CH 2 OHCOH, which are among the smallest molecules that contain hydroxyl and carbonyl group on neighboring carbon atoms. This sterical configuration is characteristic for saccharides and determines their biochemical activity. In this work vibrational analysis of hydroxyacetone was undertaken by performing the normal coordinate analysis for glycolaldehyde first, and transferring these force constants to hydroxyacetone. The observed Raman and infrared bands for 90 wt.% solution of hydroxyacetone in water (acetol) were used as a first approximation for the bands of free hydroxyacetone. The number of observed Raman and infrared bands for acetol exceeds the number of calculated values for the most stable hydroxyacetone conformer with C s symmetry, which suggests more than one conformer of hydroxyacetone in water solution. In particular, there are two bands both in infrared (1083 and 1057 cm −1) and in Raman spectrum (1086.5 and 1053 cm −1) that are assigned to the CO stretching mode and this is one of the indicators of several hydroxyacetone conformers in the solution. Additional information was obtained from low temperature Raman spectra: at 240 K a broad assymmetric band centered around 280 cm −1 appears, suggesting a disorder in the orientation of hydroxyl groups. Glassy state forms at ∼150 K. The broad band at 80 cm −1 is assigned to frozen torsions of hydroxymethyl groups.

Proceedings of the National Academy of Sciences, 2011

The amide III region of the peptide infrared and Raman spectra has been used to determine the rel... more The amide III region of the peptide infrared and Raman spectra has been used to determine the relative populations of the three major backbone conformations ( P II , β, and α R ) in 19 amino acid dipeptides. The results provide a benchmark for force field or other methods of predicting backbone conformations in flexible peptides. There are three resolvable backbone bands in the amide III region. The major population is either P II or β for all dipeptides except Gly, whereas the α R population is measurable but always minor (≤ 10%) for 18 dipeptides. (The Gly φ,ψ map is complex and so is the interpretation of the amide III bands of Gly.) There are substantial differences in the relative β and P II populations among the 19 dipeptides. The band frequencies have been assigned as P II , 1,317–1,306 cm -1 ; α R , 1,304–1,294 cm -1 ; and β, 1,294–1,270 cm -1 . The three bands were measured by both attenuated total reflection spectroscopy and by Raman spectroscopy. Consistent results, both ...

Phys. Chem. Chem. Phys., 2014

Supplementary Information Contents: S1 Crystal structures S2 Details on theoretical calculations ... more Supplementary Information Contents: S1 Crystal structures S2 Details on theoretical calculations S2.1 Optimization of crystalline ZNATH by various programs S2.2 Optimization of substituted analogs of ZNATH in the solid state S2.3 Structure, NBO analysis and proton affinity of NA analogs (dianions) in the gas phase S2.4 First-principle calculations of isotropic chemical shifts S3 Spectroscopic characteristics of the nitranilate anion S3.1 Infrared spectroscopy S3.2 Raman spectroscopy

MATERIALS, 2021

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2022

New Raman data are presented concerning H2O and D2O water aggregation in argon matrix having the ... more New Raman data are presented concerning H2O and D2O water aggregation in argon matrix having the ratio of number of argon atoms to water molecules close to 40:1. Experiments were conducted at temperatures from 8 K to 34 K allowing observation of OH and OD stretching vibrations of water monomers, dimers, trimers and higher multimers, as well as broad bands corresponding to solid amorphous water. Molecular dynamics simulations were performed for thirteen or sometimes fourteen water molecules dispersed among 500 argon atoms. Resulting final configurations included dimers, trimers, tetramers and pentamers, all in open chain configurations which upon optimization resulted in mostly cyclic conformations. Observed OH stretching vibrations were assigned by comparing calculated normal modes in harmonic approximation at the B3LYP/aug-cc-pVDZ and PBEPBE1/aug-cc-pVDZ level of theory with our data and previously observed bands from infrared matrix isolation studies and Raman jet cooled experiments. Raman bands assigned to water multimers in argon matrix are shifted 20 to 25 cm-1 towards lower wavenumbers with respect to the positions of OH stretching vibrations of almost free water clusters.

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2022

The binding of glucosamine to gold in water solutions of glucosamine hydrochloride mixed with cle... more The binding of glucosamine to gold in water solutions of glucosamine hydrochloride mixed with clean colloidal gold nanoparticles obtained by laser ablation in liquid was studied using surface-enhanced Raman scattering (SERS), dynamic light scattering (DLS) and UV-VIS spectroscopy. The purpose of this study was to establish whether the binding of charged aminogroup to gold nanoparticles (AuNPs) is taking place, and if it does, how can it be identified by means of SERS. The average size of dried gold nanoparticles was (20 ± 4) nm determined by averaging the sizes observed in transmission electron microscopy micrographs, which is smaller than the average size of gold nanoparticles in water solution as determined by DLS: (52 ± 2) nm. Upon adding the glucosamine solutions to gold colloid, average hydrodynamic diameter of ions was slightly larger for 0.1 mM glucosamine solution (55 ± 2 nm), while it increased to (105 ± 22) nm in the case of 1 mM solution, and was (398 ± 54) nm when 10 mM glucosamine solution was added. Most prominent Raman bands observed both for 0.1 mM and 1 mM glucosamine solutions were located at 1165 cm-1, 1532 and 1586 cm-1 and assigned to C-N coupled with C-C stretching, and C-NH3+ deformation angles bending. In SERS spectrum of 1 mM GlcN+ solution, two strong bands at 999 and 1075 cm-1 were found and attributed to C-Oring stretching coupled with C-NH3+ bending (999 cm-1) and to dominantly C-O stretching vibration. The differences in SERS spectra are attributed to different number of glucosamine molecules that attach to gold nanoparticles and their orientation with respect to the metal particle surface, partly due to presence of beta anomers protonated at anomeric oxygen position. The assignment of glucosamine bands was further corroborated by comparison with vibrational spectra of alpha and beta glucose and of polycrystalline powder of glucosamine hydrochloride. For all three substances comprehensive calculation of vibrational density of states was conducted using density functional theory. Benchmark bands for polycrystalline glucose anomers distinction are 846 and 915 cm-1 for alpha glucose, and 902 cm-1 for beta glucose. However, the bands observed in SERS spectra of 0.1 mM glucosamine solution at 831, 899, and 946 cm-1 or in 1 mM solution at 934 cm-1 cannot be easily identified as belonging either to alpha or beta glucosamine anomer, due to complexity of atomic motions involved. The identification of vibrational bands associated with -CNH3+ group will aid SERS studies on amino acids, especially in cases when several atomic groups could possibly bind to AuNPs.

Croatica chemica acta, 2020

Structural characterization of the β-polymorph of glycolaldehyde dimer by powder X-ray diffractio... more Structural characterization of the β-polymorph of glycolaldehyde dimer by powder X-ray diffraction, Raman and infrared spectroscopies is described. The previously described α-polymorph and the β-polymorph both crystallize in the monoclinic crystal system, space group P21/c, but with different cell parameters. There are no significant differences in the glycolaldehyde dimer molecular structure, the molecules in both polymorphs are trans-isomers with the hydroxyl groups in axial positions. The two polymorphs have a different arrangement of the glycolaldehyde dimer molecules. In the previously reported α-polymorph the molecules are arranged in hydrogen bonded layers parallel to (100) while in the β-polymorph the hydrogen bonded molecules are arranged in a three-dimensional network. Theoretically calculated Gibbs free energy as well as differential scanning calorimetry indicate β-polymorph to be the stable crystal phase of glycolaldehyde.

Radiation Physics and Chemistry, 2019

Four structurally different amines: 1,3-diamino-2-propanol (DAP), diethylenetriamine (DETA), tris... more Four structurally different amines: 1,3-diamino-2-propanol (DAP), diethylenetriamine (DETA), tris(2aminoethyl)amine (TAEA) and triethylenetetramine (TETA) were reacted with diglycidyl ether terminated poly(dimethylsiloxane), PDMS-DGE at relatively low temperature of 50 ºC. Stable transparent networks with gel-like properties but without a liquid component, "gel networks" were obtained. Raman spectra revealed presence of residual epoxy-group absorptions in cured gel-networks but secondary amine absorption intensities in FTIR spectra were used for monitoring of the curing reaction extent. To assess their radiation stability gel-networks were gamma-irradiated to absorbed dose of 50 kGy. Even though contribution of amine segments to PDMS-based gel-networks is relatively small their structure significantly influenced the properties of studied PDMS-based gel-networks. The most important property of an amine was the ability to either form hydrogen bonds, or produce denser network like a triamine. However there were also significant differences in properties of gel-networks prepared with mutually similar diamines DETA and TETA that can be considered a dimer and a trimer of ethylenediamine. In the studied gel-networks there is a complex interaction of extent of initial curing that depended on the amine used and the resulting (dis)order that strongly influenced the outcome of irradiation. The temperature of an endothermic transition presumably caused by reversible gel-network collapse was observed in DSC thermograms of all the gelnetworks. The temperature depended on the amine type and shifted to higher values on irradiation. Changes in most properties like residual gel content on extraction or AC electrical conductivity and its frequency dependence were more pronounced in gel-networks prepared with diamines DETA and TETA than in those prepared with amines capable of significant secondary valent interactions (DAP and TAEA). Radiation curing and/or crosslinking seem to have occurred only in TETA-cured gel-network and it was mostly due to lower extent of initial reaction. Since swelling of gel-networks increased it may be concluded that irradiation improved their properties.

Materials Research Express, 2018

The main purpose of this paper is to focus on details of the fabrication process of horizontally ... more The main purpose of this paper is to focus on details of the fabrication process of horizontally and vertically oriented silicon nanowires (SiNWs) substrates for the application of surface-enhanced Raman spectroscopy (SERS). The fabrication process is based on the vapor–liquid–solid method and electroless-assisted chemical etching, which, as the major benefit, resulting in the development of economical, easy-to-prepare SERS substrates. Furthermore, we examined the fabrication of Au coated Ag nanoparticles (NPs) on the SiNWs substrates in such a way as to diminish the influence of silver NPs corrosion, which, in turn, enhanced the SERS time stability, thus allowing for wider commercial applications. The substances on which high SERS sensitivity was proved are rhodamine (R6G) and 4-mercaptobenzoic acid (MBA), with the detection limits of 10−8Mand 10−6 M, respectively

Silicon, 2018

This paper shows steps for silicon nanowires substrates synthesis in detail. The research is focu... more This paper shows steps for silicon nanowires substrates synthesis in detail. The research is focused on experimental techniques optimization while the targeted application was a fabrication of highly sensitive substrates for surface-enhanced Raman spectroscopy (SERS). Horizontal silicon nanowires on top of two-inch wafers were obtained by vapour-liquid-solid growth inside the low-pressure chemical vapour deposition reaction tube. The silicon nanowires morphology was monitored by scanning electron microscope after a short and long growth period which defined an adequate deposition time for SERS applications. Surface-enhanced Raman spectroscopy features were tested on silver nanoparticles decorated substrates and the detection concentration limit of 10 −9 M of rhodamine 6G molecules was reached. Raman spectroscopy showed that the 532 nm laser excitation powers of less than 4 mW (∼0.57 kW/cm 2) do not widen the phonon peak or shift its frequency and the nanostructure distribution parameter of 3.7 nm was calculated. The horizontally placed Ag decorated nanowires are proved to be sensitive substrates for surface-enhanced Raman spectroscopy only if the silicon nanowires thickness, length, volume density as well as metal nanoparticle size and distribution are carefully designed.

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2018

Modern diagnostic tools ever aim to reduce the amount of analyte and the time needed for obtainin... more Modern diagnostic tools ever aim to reduce the amount of analyte and the time needed for obtaining the result. Surface-enhanced Raman spectroscopy is a method that could satisfy both of these requirements, provided that for each analyte an adequate substrate is found. Here we demonstrate the ability of gold-sputtered silicon nanowires (SiNW) to bind p-mercaptobenzoic acid in 10 −3 , 10 −4 and 10 −5 M and adenine in 30 and 100 μM concentrations. Based on the normal mode analysis, presented here for the first time, the binding of p-mercaptobenzoic acid is deduced. The intensity enhancement of the 1106 cm −1 band is explained by involvement of the C-S stretching deformation, and the appearance of the broad 300 cm −1 band attributed to S-Au stretching mode. Adenine SERS spectra demonstrate the existence of the 7H tautomer since the strongest band observed is at 736 cm −1. The adenine binding is likely to occur in several ways, because the number of observed bands in the 1200-1600 cm −1 interval exceeds the number of observed bands in the normal Raman spectrum of the free molecule.

Croatica Chemica Acta, 2017

The silicon based substrates for surface enhanced Raman spectroscopy (SERS) have been synthesized... more The silicon based substrates for surface enhanced Raman spectroscopy (SERS) have been synthesized and tested. The silver-assisted electroless wet chemical etching method has been utilized for silicon nanowires production which has been proved as the promising SERS substrate. The morphology of the silicon nanowires coated with silver nanoparticles has been examined by scanning electron microscopy. The SERS measurements tested on rhodamine 6G molecules indicated the optimal silicon nanowire substrate production obtained for 5 M hydrofluoric acid and 30 mM silver nitrate etching solution. The results show SERS detection limit of 10-8 M rhodamine in aqueous solution.

Monthly Notices of the Royal Astronomical Society: Letters, 2016

Although it was found that the FeH lines exist in the spectra of some stars, none of the spectral... more Although it was found that the FeH lines exist in the spectra of some stars, none of the spectral features in the ISM have been assigned to this molecule. We suggest that iron atoms interact with hydrogen and produce Fe-H nanoparticles which sometimes contain many H atoms. We calculate infrared spectra of hydrogenated iron nanoparticles using density functional theory methods and find broad, overlapping bands. Desorption of H 2 could induce spinning of these small Fe-H dust grains. Some of hydrogenated iron nanoparticles posses magnetic and electric moments and should interact with electromagnetic fields in the ISM. Fe n H m nanoparticles could contribute to the polarization of the ISM and the anomalous microwave emission. We discuss the conditions required to form FeH and Fe n H m in the ISM.

Journal of Alloys and Compounds, 2017

The local structural changes within the normal spinel structure of a ZnAl 2 O 4 host caused by th... more The local structural changes within the normal spinel structure of a ZnAl 2 O 4 host caused by the titanium incorporation as studied by the Raman spectroscopy and computationally using the density functional theory have been analyzed. The lattice dynamics calculation of the ZnAl 2 O 4 phonons were performed within the density functional theory for the 3D periodic crystal structures. Band structure calculations by the grid-based PAW method predicted a direct band gap in the pure ZnAl 2 O 4 sample to be 4.732 eV, while doping with Ti 4þ produced a density of states in the middle of the gap. The lattice dynamics calculations using Gaussian-type wavefunctions as basis set and a local density approximation gave a good agreement between observed and predicted Raman bands. Doping with Ti 4þ causes the infrared active T 1u phonons as well as the inactive phonons (T 1g , A 2u , E u and T 2u symmetries) to appear in the Raman spectra and breaking of the symmetry selection rules.

Journal of Molecular Structure, 2017

Crystals of (HGua)2[Cu2Cl6]•2H2O (HGua = protonated guanine) were prepared and analysed by spectr... more Crystals of (HGua)2[Cu2Cl6]•2H2O (HGua = protonated guanine) were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis have given us new insight into the vibrational states of the (HGua)2[Cu2Cl6]•2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer (HGua)2[Cu2Cl6]•2H2O with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained form periodic DFT calculations gave us an insight into the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

The Journal of Physical Chemistry A, 2016

Low temperature Raman spectra of oxalic acid dihydrate (8K-300 K) both for polycrystalline and si... more Low temperature Raman spectra of oxalic acid dihydrate (8K-300 K) both for polycrystalline and single crystal phase show strong variation with temperature in the interval from 1200 to 2000 cm-1. Previous low temperature diffraction studies all confirmed the stability of the crystal P21/n phase with no indications of any phase transition, reporting the existence of a strong hydrogen bond between the oxalic acid and a water molecule. A new group of Raman bands in the 1200-1300 cm-1 interval below 90 K is observed, caused by possible loss of the centre of inversion. This in turn could originate either due to disorder in hydroxyl proton positions, or due to proton transfer from carboxylic group to water molecule. The hypothesis of proton transfer is further supported by the emergence of new bands centered at 1600 cm-1 and 1813 cm-1 , which can be explained with vibrations of H3O + ions. The broad band at 1600 cm-1 looses intensity, while the band at 1813 cm-1 gains intensity on cooling. The agreement between quantum calculations of vibrational spectra and experimentally observed Raman bands of hydronium ions in oxalic acid sesquihydrate crystal corroborate this hypothesis.

Monthly Notices of the Royal Astronomical Society, 2014

Calcium silicate hydrate is used to model the properties of cement on Earth. We study cementitiou... more Calcium silicate hydrate is used to model the properties of cement on Earth. We study cementitious nanoparticles and propose these structures as components of cosmic dust grains. Quantum density functional theory methods are applied for the calculation of infrared spectra of Ca 4 Si 4 O 14 H 4 , Ca 6 Si 3 O 13 H 2 and Ca 12 Si 6 O 26 H 4 clusters. We find bands distributed over the near-, mid-and far-infrared regions. A specific calcium silicate hydrate spectral feature at 14 μm, together with bands at 10 and 18 μm, which exist for other silicates as well, could be used for the detection of cosmic cement. We compare the calculated bands with the 14-μm features in the spectra of HD 45677, HD 44179 and IRC+10420, which were observed by the Infrared Space Observatory and classified as remaining. A high abundance of oxygen atoms in cementitious nanoparticles could partially explain the observed depletion of this element from the interstellar medium on to dust grains.

The asymmetric band profile of the triple C=C stretching Raman band in bis(trimethylsilyl)acetyle... more The asymmetric band profile of the triple C=C stretching Raman band in bis(trimethylsilyl)acetylene was decomposed into a higher and a lower wavenumber part, each described as one half of a Lorentzian bandshape with its own halfwidth (Ghigh and Glow), but with common band centre and maximum point. Ghigh and Glow were fitted at seventeen different temperatures ranging from 110 K

Vibrational Spectroscopy, 2013

We present a Raman study of liquid and polycrystalline dioxolane, together with data for a solid ... more We present a Raman study of liquid and polycrystalline dioxolane, together with data for a solid dioxolane/argon film. Observed bands are assigned to the bent conformer on the basis of ab initio calculated vibrations, accompanied with potential energy distribution. Two internal modes were calculated at 658 and 720 cm −1 for the bent form. These were observed at 665 and 722 cm −1 in liquid, and split into four bands (at 694, 697, 725, and 728 cm −1) in the crystal at 10 K. In the solid dioxolane/argon film an additional band appears at 705 cm −1 (between the bands at 675 and 726 cm −1). A search for an additional dioxolane conformer trapped in argon was undertaken by performing molecular dynamics simulations of dioxolane/argon solid film and averaging overall molecular conformations. The resulting conformation did not correspond to an energy minimum, but indicated that changes of only a few degrees in dihedral angles could shift ring deformation and O C O bending modes for more than 10 cm −1. Differential scanning calorimetric measurements gave evidence of solidification upon cooling at 146 K, and two phase changes on heating (one at 158.3 K, and a melting transition at 180.3 K). Further study is required on the hysteresis effect in the temperature behavior of dioxolane, and on the nature of the intermediate solid phase.

The Journal of Physical Chemistry A, 2007

Raman spectra of acetylacetone were recorded for molecules isolated in an argon matrix at 10 K an... more Raman spectra of acetylacetone were recorded for molecules isolated in an argon matrix at 10 K and for a polycrystalline sample. In the solid sample, broad bands appear superimposed on a much weaker Raman spectrum corresponding mainly to the stable enol form. The position of these bands depends on the excitation wavelength (514.5 and 488.8 nm argon ion laser lines were used), sample temperature, and cooling history. They are attributed to transitions from an excited electronic state to various isomer states in the ground electronic state. Laser photons have energies comparable to energies of a number of excited triplet states predicted for a free acetylacetone molecule (Chen, X.-B.; Fang, W.-H.; Phillips, D. L. J. Phys. Chem. A 2006, 110, 4434). Since singlet-to-triplet photon absorption transitions are forbidden, states existing in the solid have mixed singlet/triplet character. Their decay results in population of different isomer states, which except for the lowest isomers SYN enol, TS2 enol (described in Matanović I.; Došlić, N. J. Phys. Chem. A 2005, 109, 4185), and the keto form, which can be detected in the Raman spectra of the solid, are not vibrationally resolved. Differential scanning calorimetry detected two signals upon cooling of acetylacetone, one at 229 K and one at 217 K, while upon heating, they appear at 254 and 225 K. The phase change at higher temperature is attributed to a freezing/melting transition, while the one at lower temperature seems to correspond to freezing/melting of keto domains, as suggested by Johnson et al.

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2005

In order to be able to fully understand the vibrational dynamics of monosaccharide sugars, we sta... more In order to be able to fully understand the vibrational dynamics of monosaccharide sugars, we started with hydroxyacetone CH 2 OHCOCH 3, and glycolaldehyde CH 2 OHCOH, which are among the smallest molecules that contain hydroxyl and carbonyl group on neighboring carbon atoms. This sterical configuration is characteristic for saccharides and determines their biochemical activity. In this work vibrational analysis of hydroxyacetone was undertaken by performing the normal coordinate analysis for glycolaldehyde first, and transferring these force constants to hydroxyacetone. The observed Raman and infrared bands for 90 wt.% solution of hydroxyacetone in water (acetol) were used as a first approximation for the bands of free hydroxyacetone. The number of observed Raman and infrared bands for acetol exceeds the number of calculated values for the most stable hydroxyacetone conformer with C s symmetry, which suggests more than one conformer of hydroxyacetone in water solution. In particular, there are two bands both in infrared (1083 and 1057 cm −1) and in Raman spectrum (1086.5 and 1053 cm −1) that are assigned to the CO stretching mode and this is one of the indicators of several hydroxyacetone conformers in the solution. Additional information was obtained from low temperature Raman spectra: at 240 K a broad assymmetric band centered around 280 cm −1 appears, suggesting a disorder in the orientation of hydroxyl groups. Glassy state forms at ∼150 K. The broad band at 80 cm −1 is assigned to frozen torsions of hydroxymethyl groups.

Proceedings of the National Academy of Sciences, 2011

The amide III region of the peptide infrared and Raman spectra has been used to determine the rel... more The amide III region of the peptide infrared and Raman spectra has been used to determine the relative populations of the three major backbone conformations ( P II , β, and α R ) in 19 amino acid dipeptides. The results provide a benchmark for force field or other methods of predicting backbone conformations in flexible peptides. There are three resolvable backbone bands in the amide III region. The major population is either P II or β for all dipeptides except Gly, whereas the α R population is measurable but always minor (≤ 10%) for 18 dipeptides. (The Gly φ,ψ map is complex and so is the interpretation of the amide III bands of Gly.) There are substantial differences in the relative β and P II populations among the 19 dipeptides. The band frequencies have been assigned as P II , 1,317–1,306 cm -1 ; α R , 1,304–1,294 cm -1 ; and β, 1,294–1,270 cm -1 . The three bands were measured by both attenuated total reflection spectroscopy and by Raman spectroscopy. Consistent results, both ...

Phys. Chem. Chem. Phys., 2014

Supplementary Information Contents: S1 Crystal structures S2 Details on theoretical calculations ... more Supplementary Information Contents: S1 Crystal structures S2 Details on theoretical calculations S2.1 Optimization of crystalline ZNATH by various programs S2.2 Optimization of substituted analogs of ZNATH in the solid state S2.3 Structure, NBO analysis and proton affinity of NA analogs (dianions) in the gas phase S2.4 First-principle calculations of isotropic chemical shifts S3 Spectroscopic characteristics of the nitranilate anion S3.1 Infrared spectroscopy S3.2 Raman spectroscopy