Search Results (297)

Vibrational analysis of peptides in solution and the theoretical determination of the effects of the microenvironment on infrared and Raman spectra are of key importance in many fields of chemical interest. In this work, we present a computational study combining static quantum mechanical calculations with ab initio molecular dynamics simulations to investigate the vibrational behavior of three peptide models in both the gas phase and in explicit water, under non-periodic boundary conditions. The vibrational spectra of the main amide bands, namely amide I-III and A, were analyzed using a time–frequency approach based on the wavelet transform, which allows the resolution of transient frequency shifts and mode couplings along the trajectories. This combined approach enabled us to perform a time-resolved vibrational analysis revealing how vibrational frequencies, especially of the C=O and N–H stretching modes, evolve over time due to dynamical microsolvation. These fluctuations modulate vibrational couplings and lead to spectral broadening and frequency shifts that correlate with the local structuring of the solvent. In conclusion, our results highlight how the proposed protocol allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, the peptide backbone, and its microenvironment. Full article

The defects in zinc oxide crystals are of crucial importance for their usability in many applications and are not yet fully understood. Here, we demonstrate that dioxygen species are present as defects in the grown ZnO, resulting in a bending of the atom layers that lie perpendicular to the c-axis. In the Raman spectra, these defects cause the appearance of bands different from the known bands of perfect ZnO crystals allowed by symmetry. These additional Raman bands, which have been frequently reported for ZnO in the past, can thus be fully explained by the presence of dioxygen species, and the widespread assumption of second-order modes for the assignments of these bands is not necessary. Furthermore, the Raman spectrum belonging to perfect zinc oxide in the ideal wurtzite structure is presented, obtained from small domains in ZnO(0001) crystals exposed to pressures up to 2 GPa. The dependence of the O-O stretching modes on the applied pressure proves the presence of dioxygen species in ZnO, which is also confirmed by phonon calculations of structure models with embedded dioxygen species. The surface quality of the ZnO crystals studied is also reflected in the Raman spectra and is included in the analysis. Full article

This study presents a detailed Raman spectroscopic investigation of hydrogels composed of sodium hyaluronate and two N-terminally blocked dipeptides: N-acetyl-L-alanine-methyl-amide (NAcAlaNHMA) and N-acetyl-L-tyrosine-methyl-amide (NAcTyrNHMA). Vibrational spectra of the dipeptides in both crystalline and aqueous forms were analyzed and supported by density functional theory (DFT) calculations. Spectral features of the hyaluronan component were elucidated by simulating the vibrational modes of its two principal disaccharide building blocks. Gels were prepared with varying dipeptide-to-hyaluronan ratios, and their structural characteristics were examined using Raman spectroscopy and atomic force microscopy. The results showed that while NAcAlaNHMA exhibited no significant interaction with the HA matrix, NAcTyrNHMA demonstrated specific binding behavior, as evidenced by notable shifts in its N–H and C–O–H vibrational bands. These findings indicate that NAcTyrNHMA binds to hyaluronic acid via hydrogen bonding, likely involving carboxyl and hydroxyl functional groups. This study highlights the potential for selective tuning of HA-based hydrogels using dipeptides, with implications for biomedical applications such as drug delivery, antimicrobial gels and biomaterial design. Full article

Spinel ferrites have emerged as fascinating materials, not just for their diverse functionalities, but for the dynamic structural transformations they undergo under varying conditions. These phase transitions, often subtle yet deeply influential, play a pivotal role in tuning their electronic, magnetic, and vibrational properties. At the heart of this complexity lies the versatile arrangement of divalent and trivalent cations between the tetrahedral (A) and octahedral (B) sites, giving rise to a rich spectrum of magnetic interactions, charge dynamics, and lattice responses. This intricate cation interplay makes spinel ferrites a playground for exploring structure–property relationships in advanced functional materials. In this study, we investigated the structural, vibrational, and magnetic properties of Cd ferrite using advanced hybrid functionals (B3LYP, HSE06, and PBE0). Our calculations reveal that the normal spinel phase is the most stable configuration, with minimal energy differences between spin arrangements (~0.005–0.008 eV) and slightly larger differences when including zero-point energy (~0.023 eV). All the investigated structures exhibit a semiconducting nature, with band gaps varying depending on the spin arrangements. The IR and Raman spectra highlight the influence of spin ordering on vibrational modes. The simulations of the Raman spectra demonstrate that both the frequencies and intensities of the Raman peaks strongly depend on the magnetic ordering. The present theoretical study offers a consistent framework for assigning vibrational modes, which may help resolve ambiguities and contribute to a deeper understanding of the vibrational properties of Cd ferrite. These findings provide a robust foundation for further experimental and computational exploration of this material. Full article

This work investigated the optical characteristics of BaWO₄ nanoparticles that were produced through direct mechanochemical synthesis at varying speeds and times. This research expands upon our previous study. We demonstrated that the mechanochemical activation of the precursor of BaCO₃ and WO₃, at elevated milling speeds (850 rpm), facilitates the formation of tetragonal BaWO₄ in a reduced reaction time. The final products were characterized by scanning electron microscopy (SEM), as well as Raman, infrared (IR), UV-Vis diffuse reflectance, and photoluminescence spectroscopies. The crystallite sizes and particles shapes were determined by X-ray diffraction and SEM analysis. Round particles with a size below 50 nm formed under different milling conditions. The Raman spectra of the synthesized samples confirmed the presence of a scheelite-type structure with the typical six distinct vibrational peaks. The symmetry of the structural WO₄ groups was determined by IR spectroscopy. The absorption spectra of both samples exhibited intensive peaks at 210 nm, and the calculated optical band gaps of BaWO₄ were 5.10 eV (3 h/500 rpm) and 5.24 eV (1 h/850 rpm). A strong (400 nm) and weak (465 nm) emission were observed for the BaWO₄ that was obtained at a higher milling speed, while wider emission at 410 nm was visible for the BaWO₄ that was prepared at a lower milling speed. The CIE coordinates of the mechanochemically synthesized BaWO₄ were located within the blue area, exhibiting various positions. Full article

Developing advanced materials with enhanced performance through the doping of nanoclusters is a promising strategy. However, there remains an insufficient understanding of the specific effects induced by such doped nanoclusters, particularly regarding the structural evolution pattern after doping with rare-earth elements and their impact on performance. To solve this problem, we used first-principles calculation to study the structural evolution pattern and spectroscopic properties of anionic TbGe_n (n = 6–17) nanoclusters through the ABCluster global search technique coupled with the mPW2PLYP double-hybrid density functional theory. The results revealed that the geometrical evolution pattern is from the typical Tb-linked structures (for n = 10–13, in which Tb acts as a linker connecting two germanium sub-clusters) to Tb-centered cage configurations (for n = 14–17). The simulated photoelectron spectroscopy of anionic TbGe₁₆ agrees well with its experimental counterpart. Furthermore, we calculated properties such as infrared spectroscopy, Raman spectroscopy, ultraviolet–visible (UV–vis) spectra, magnetism, charge transfer, the HOMO-LUMO gap, and relative stability. The results suggest that TbGe₁₂⁻ and TbGe₁₆⁻ clusters, with their remarkable stability and tunable photothermal properties, can serve as ideal building blocks for developing novel functional nanomaterials. These clusters demonstrate promising applications in solar photothermal conversion, photoelectric conversion, and infrared imaging technologies through their distinct one- and three-dimensional architectures, respectively. Full article

Chromium (Cr) is a vital metal utilized in materials physics, healthcare, and various other domains. In this study, we propose an eco-friendly method for separating Cr from potassium chromate (K₂CrO₄) based on photon–phonon resonance absorption theory. Using first-principles density functional theory calculations, we obtained the Raman and infrared spectra of K₂CrO₄ and assigned the vibrational modes to the peaks observed in the experimental spectra. We confirmed that the strongest infrared absorption peak corresponds to the Cr-O bond stretching vibration theoretically located at 931 cm⁻¹. We propose employing a high-power terahertz laser at this resonant frequency for photothermal energy transfer. This approach is expected to enhance the efficiency of separating Cr from K₂CrO₄. Experimental investigations are expected in the future. Full article

Cesium hexafluorosilicate (Cs₂SiF₆, CSF) and potassium hexafluorosilicate (K₂SiF₆, KSF) compounds are suitable hosts for luminescent impurities. In this work, the results of first-principle calculations of the basic properties of both these compounds are discussed and compared with the available experimental and theoretical data. The simulations were performed using the CRYSTAL23 computer code within the linear combination of atomic orbitals (LCAO) method of the density functional theory (DFT) and the advanced hybrid DFT-HF exchange-correlation B1WC functional. A comparative study of the structural, electronic, and elastic properties of the two materials is presented, along with a study of the dependence of properties on external pressure in the range of 0–20 GPa. In particular, the electronic properties with an emphasis on the effective atomic charges (by means of Mulliken analysis) and the chemical bonding properties (by means of crystal orbital overlap population (COOP) analysis) were addressed, with regards to the pressure effects. The structure of the valence bands at 0 and 20 GPa was compared. The vibrational properties of CSF and KSF were calculated, including the simulation of the one-phonon IR and Raman spectra. The calculated Raman spectra exhibit excellent agreement with the experimental ones. The pressure dependences of sound speeds and the Debye temperature are evaluated. Full article

Because of the involvement of π-electron cyclic constituents in their side chains, the so-called aromatic residues give rise to a number of strong, narrow, and well-resolved lines spread over the middle wavenumber (1800–600 cm⁻¹) region of the Raman spectra of peptides and proteins. The number of characteristic aromatic markers increases with the structural complexity (Phe → Tyr → Trp), herein referred to as (F_i = 1, …, 6) in Phe, (Y_i = 1, …, 7) in Tyr, and (W_i = 1, …, 8) in Trp. Herein, we undertake an overview of these markers through the analysis of a representative data base gathered from the most structurally simple tripeptides, Gly-Xxx-Gly (where Xxx = Phe, Tyr, Trp). In this framework, off-resonance Raman spectra obtained from the aqueous samples of these tripeptides were jointly used with the structural and vibrational data collected from the density functional theory (DFT) calculations using the M062X hybrid functional and 6-311++G(d,p) atomic basis set. The conformation dependence of aromatic Raman markers was explored upon a representative set of 75 conformers, having five different backbone secondary structures (i.e., β-strand, polyproline-II, helix, classic, and inverse γ-turn), and plausible side chain rotamers. The hydration effects were considered upon using both implicit (polarizable solvent continuum) and explicit (minimal number of 5–7 water molecules) models. Raman spectra were calculated through a multiconformational approach based on the thermal (Boltzmann) average of the spectra arising from all calculated conformers. A subsequent discussion highlights the conformational landscape of conformers and the wavenumber dispersion of aromatic Raman markers. In particular, a new interpretation was proposed for the characteristic Raman doublets arising from Tyr (~850–830 cm⁻¹) and Trp (~1360–1340 cm⁻¹), definitely excluding the previously suggested Fermi-resonance-based assignment of these markers through the consideration of the interactions between the aromatic side chain and its adjacent peptide bonds. Full article

Sulfamic acid (SA) is extensively utilised in industry as a component in the production of flameproof materials, a catalyst for swift and highly efficient synthesis, in dye and pigment manufacturing processes, or as herbicide. Under ambient conditions, this compound exists as a solid in zwitterionc form, undergoing pressure-induced isosymmetric polymorphic phase transition (IPT), starting at approximately 10.0 GPa. In this work, multiple computational approaches were used to predict and describe this transition. While geometry optimisation at an increased pressure using periodic DFT-level calculations have not resulted in the anticipated IPT, the comparison of the experimental and theoretical Raman spectra confirmed this transformation. Thermodynamic calculations enabled the comparison of the stability of the modelled phases and explained the experimental observations. Ab initio molecular dynamics simulations revealed the mechanisms behind the observed transition. This work presents a complex methodology that can be successfully used to predict the IPT of molecular crystals. Full article

The interaction between terahertz (THz) photons and phonons of materials is crucial for the development of THz photonics. In this work, typical two-dimensional (2D) van der Waals (vdW) transition metal chalcogenide (TMD) layers and heterostructures are used in THz time-domain spectroscopy (TDS) measurements, low-wavenumber Raman spectroscopy measurements, calculation of 2D materials’ phonon spectra, and theoretical analysis of thermal responses. The TDS results reveal strong absorption of THz photons in the frequency range of 2.5–10 THz. The low-wavenumber Raman spectra show the phonon vibration characteristics and are used to establish phonon energy bands. We also set up a computational simulation model for thermal responses. The temperature increases and distributions in the individual layers and their heterostructures are calculated, showing that THz photon absorption results in significant increases in temperature and differences in the heterostructures. These give rise to interesting photothermal effects, including the Seebeck effect, resulting in voltages across the heterostructures. These findings provide valuable guidance for the potential optoelectronic application of the 2D vdW heterostructures. Full article

Two new 2-N-phenylamino-(4 or 6)-methyl-3-nitropyridine derivatives were synthesized. Their structures were characterized on the basis of X-ray diffraction, IR, and Raman spectra as well as electron UV-Vis and emission spectra measurements. The experimental results were analyzed in terms of theoretical data in which the quantum chemical DFT and NBO calculations were applied. To elucidate the relaxation pathways of electronically excited states, multiple excitation wavelengths were employed to probe energy dissipation mechanisms in the studied compounds. A systematic analysis was conducted to evaluate how variations in methyl substituent positioning modulate both the structural architecture and photophysical behavior of the isomeric systems. The spectroscopic, structural and theoretical considerations allow us to propose the potential technological applications derived from the unique properties of these isomers. Full article

The narrow bandgap InN material, with exceptional physical properties, has recently gained considerable attention, encouraging many scientists/engineers to design infrared photodetectors, light-emitting diodes, laser diodes, solar cells, and high-power electronic devices. The InN/Sapphire samples of different film thicknesses that we have used in our methodical experimental and theoretical studies are grown by plasma-assisted molecular-beam epitaxy. Hall effect measurements on these samples have revealed high-electron-charge carrier concentration, η. The preparation of InN epifilms is quite sensitive to the growth temperature T, plasma power, N/In ratio, and pressure, P. Due to the reduced distance between N atoms at a higher P, one expects the N-flow kinetics, diffusion, surface components, and scattering rates to change in the growth chamber which might impact the quality of InN films. We believe that the ionized N, rather than molecular, or neutral species are responsible for controlling the growth of InN/Sapphire epifilms. Temperature- and power-dependent photoluminescence measurements are performed, validating the bandgap variation (~0.60–0.80 eV) of all the samples. High-resolution X-ray diffraction studies have indicated that the increase in growth temperature caused the perceived narrow peaks in the X-ray-rocking curves, leading to better-quality films with well-ordered crystalline structures. Careful simulations of the infrared reflectivity spectra provided values of η and mobility μ, in good accordance with the Hall measurements. Our first-order Raman scattering spectroscopy study has not only identified the accurate phonon values of InN samples but also revealed the low-frequency longitudinal optical phonon plasmon-coupled mode in excellent agreement with theoretical calculations. Full article

A surface-enhanced Raman scattering (SERS) study of diquat (DQ) on silver and copper electrodes is presented in this work in order to complete previous studies on the SERS of DQ on metal nanoparticles. We supported the experimental results with theoretical calculations of different species of DQ, analyzing the most important molecular differences and their corresponding Raman spectra. DQ SERS spectra on Ag and Cu electrodes were obtained at different excitation wavelengths. An analysis of the SERS spectra revealed that at more positive electrode potentials, the interaction of DQ with the metal formed a charge-transfer complex via the chloride anion previously adsorbed on the surface; additionally, at more negative potentials, other species of diquat, such as DQ²⁺, could be directly adsorbed on the metal’s surface. Finally, we detected new SERS bands corresponding to DQ at negative electrode potentials that were sensitive to the excitation wavelength, suggesting that lateral interactions between radical cation species on the electrode surface lead to intramolecular dimerization and a possible multilayer of the adsorbate. Full article

This study is focused on the effects of the sulphur atom in position 2 of the cytosine molecule, 2-thiocytosine (2TC), on the molecular structural parameters in the isolated state, as well as in the hydration, solid state arrangement, Watson–Crick pairs, and DNA–DNA microhelices, as compared to the canonical form. The main six tautomers were optimised at the MP2 and CCSD levels, and the sulphur atom does not show any effect on the stability trend of cytosine. The energy difference between T2b and T2a tautomers is twice as low in 2TC (1.15 kJ/mol) than in cytosine (2.69 kJ/mol). The IR and laser Raman spectra of 2TC were accurately assigned using DFT computations and solid-state simulations of the crystal unit cell through several tetramer forms. The results notably improve those previously published by other authors. The effect of explicit water molecules surrounding 2TC up to 30, corresponding to the first and second hydration shells, on geometries and tautomerism was analysed. The Watson–Crick base pairs’ stability (ΔE^CP = −97.458 kJ/mol) was found to be less than with cytosine (−105.930 kJ/mol). The calculated dipole moment was also lower (4.205 D) than with cytosine (5.793 D). The effect of 2TC on the 5′-dG-dC-dG-3′ and 5′-dA-dC-dA-3′ DNA–DNA optimised microhelices was evaluated through their calculated helical parameters, which indicates a clear deformation of the helix formation. The radius (R) with 2TC appears considerably shorter (6.200 Å) in the 5′-dA-dC-dA-3′ microhelix than that with cytosine (7.050 Å). Because of the special characteristics of the 2TC molecule, it can be used as an anticancer drug. Full article