Calculated Raman Spectra Research Articles

RASCBEC: RAman Spectroscopy Calculation via Born Effective Charge

We present a reformulated algorithm for ab initio calculations of Raman spectra for large systems by applying an external electric field, and complement it by a code implementation we name RASCBEC. With the RASCBEC code, we have successfully benchmark crystalline materials and compute Raman spectra of large molecules, and amorphous oxides. Our results demonstrate a remarkable level of agreement with the results from other commonly used codes as well as the experimental data. The electric field approach for Raman spectra calculation is designed to overcome the computational challenges associated with the conventional method, which requires calculating the macroscopic dielectric tensor at numerous molecular geometries. This approach is favored because it can significantly reduce computational time. We reformulated this method by obtaining the Raman intensity from the first-order derivative of the Born Effective Charge (BEC), which is computed directly from vasp (the Vienna Ab Initio Simulation Package). This differs from other electric field-based methods that calculate Raman intensities as the second-order derivative of force with respect to the electric field. By reducing the order of derivatives, we can avoid numerical noise and accuracy concerns. Additionally, since forces are often very small numbers, taking the derivative of BEC is numerically more stable, allowing our method to be applied to a broader range of material parameters. This advantage makes RASCBEC particularly beneficial for large molecules and extensive amorphous systems.

Ultrafast Time-Domain Spectroscopy Reveals Coherent Vibronic Couplings upon Electronic Excitation in Crystalline Organic Thin Films.

The coherent coupling between electronic excitations and vibrational modes of molecules largely affects the optical and charge transport properties of organic semiconductors and molecular solids. To analyze these couplings by means of ultrafast spectroscopy, highly ordered crystalline films with large domains are particularly suitable because the domains can be addressed individually, hence allowing azimuthal polarization-resolved measurements. Impressive examples of this are highly ordered crystalline thin films of perfluoropentacene (PFP) molecules, which adopt different molecular orientations on different alkali halide substrates. Here, we report polarization-resolved time-domain vibrational spectroscopy with 10 fs time resolution and Raman spectroscopy of crystalline PFP thin films grown on NaF(100) and KCl(100) substrates. Coherent oscillations in the time-resolved spectra reveal vibronic coupling to a high-frequency, 25 fs, in-plane deformation mode that is insensitive to the optical polarization, while the coupling to a lower-frequency, 85 fs, out-of-plane ring bending mode depends significantly on the crystalline and molecular orientation. Comparison with calculated Raman spectra of isolated PFP molecules in vacuo supports this interpretation and indicates a dominant role of solid-state effects in the vibronic properties of these materials. Our results represent a first step toward uncovering the role of anisotropic vibronic couplings for singlet fission processes in crystalline molecular thin films.

First-Principles Linear Combination of Atomic Orbitals Calculations of K2SiF6 Crystal: Structural, Electronic, Elastic, Vibrational and Dielectric Properties.

The results of first-principles calculations of the structural, electronic, elastic, vibrational, dielectric and optical properties, as well as the Raman and infrared (IR) spectra, of potassium hexafluorosilicate (K2SiF6; KSF) crystal are discussed. KSF doped with manganese atoms (KSF:Mn4+) is known for its ability to function as a phosphor in white LED applications due to the efficient red emission from Mn⁴⁺ activator ions. The simulations were performed using the CRYSTAL23 computer code within the linear combination of atomic orbitals (LCAO) approximation of the density functional theory (DFT). For the study of KSF, we have applied and compared several DFT functionals (with emphasis on hybrid functionals) in combination with Gaussian-type basis sets. In order to determine the optimal combination for computation, two types of basis sets and four different functionals (three advanced hybrid-B3LYP, B1WC, and PBE0-and one LDA functional) were used, and the obtained results were compared with available experimental data. For the selected basis set and functional, the above-mentioned properties of KSF were calculated. In particular, the B1WC functional provides us with a band gap of 9.73 eV. The dependencies of structural, electronic and elastic parameters, as well as the Debye temperature, on external pressure (0-20 GPa) were also evaluated and compared with previous calculations. A comprehensive analysis of vibrational properties was performed for the first time, and the influence of isotopic substitution on the vibrational frequencies was analyzed. IR and Raman spectra were simulated, and the calculated Raman spectrum is in excellent agreement with the experimental one.

The use of 1D carbon nanotube interacting with caffeine molecules for applications in solar cells: structure optimisation, Raman analysis and optoelectronic properties

This study proposes a promising candidate for organic solar cells through the creation of a novel nano-hybrid system composed of caffeine molecules encapsulated within a semiconducting single-walled carbon nanotube known as NT14 (14,0). The stability and optoelectronic properties of this hybrid system, designated as CA@NT14, were thoroughly investigated. We determined the optimal diameter for the NT14 nanotube using molecular mechanics, Density Functional Theory, spectral moment’s method, and bond polarizability model, finding it to be approximately 1.18 nm. The encapsulation’s impact on the Raman-active modes, specifically the radial breathing mode and tangential mode, was analyzed through Raman spectra calculations, revealing structural stability and charge transfer from CA to NT14. Notably, the NT14’s Fermi level position increased upon encapsulation, indicating charge transfer and a type-II band alignment. The study further examined the bandgap characteristics of the hybrid system, finding that the encapsulation of CA within semiconducting NT14 nanotubes minimally impacts the nanotube’s bandgap, thus retaining its excellent visible light absorption properties. Conversely, encapsulating CA within metallic nanotubes significantly reduces their bandgap, limiting their light absorption range. The nonresonant Raman responses of NT14 pre- and post-encapsulation corroborated the charge transfer between CA and NT14. Future research will focus on computing the electronic transport characteristics, transmission spectra, I-V characteristics, and yield of CA@NT14 using DFT and Non-Equilibrium Green’s Function ( formalism. An experimental study will be conducted to validate these theoretical findings. These results indicate the potential of CA@NT14 hybrids as effective active layers in organic solar cells, highlighting their significance in advancing optoelectronic applications.

Low‐Temperature Single‐Crystal Structure and Phonon Properties of A‐Site Ordered Double Perovskite CaMnTi2O6

AbstractWe have used high‐pressure methods to synthesize CaMnTi2O6 single crystals with edge lengths of up to 70 μm. Compared to previously reported synthetic pathways, we were able to use gold capsules and smaller pressures of 4 GPa. X‐ray diffraction analysis of the single crystals at low temperatures between 100 and 230 K confirmed that no phase transitions occur in this temperature range. We found square planar‐coordinated Mn ions to shift further out of the plane with lower temperatures which could lead to a higher polarization. The measured Raman spectrum of CaMnTi2O6 has been compared with quantum chemically calculated Raman spectrum to assign the vibrational modes. Calculated single‐crystal Raman spectrum has also been also analyzed from the point of view of direction dependency of the Raman intensities.

(Invited) Extended Hubbard Functionals for Accurate Modeling of Li-Ion Battery Cathode Materials

Designing novel cathode materials for Li-ion batteries necessitates accurate first-principles predictions of their properties. Density-functional theory (DFT) employing standard (semi-)local functionals encounters challenges due to pronounced self-interaction errors within the partially filled d shells of transition-metal (TM) elements. Here, we demonstrate the efficacy of DFT with extended Hubbard functionals in accurately predicting the "digital" change in oxidation states of TM ions for mixed-valence phases at intermediate Li concentrations in phospho-olivine and spinel cathode materials. The resulting voltages exhibit remarkable agreement with experimental data [1,2].Our approach involves the use of onsite U and intersite V Hubbard parameters computed from density-functional perturbation theory with Lowdin-orthogonalized atomic orbitals, thus circumventing empirical factors [3,4]. Notably, the incorporation of intersite Hubbard V interactions proves indispensable for the precise prediction of thermodynamic quantities, particularly when electronic localization occurs amid inter-atomic orbital hybridization.Extending our investigation to vibrational spectroscopy, we calculate Raman spectra for these materials and find very good agreement with available experimental data [5]. Leveraging the robust and accurate computational framework based on extended Hubbard functionals, we embark on a high-throughput screening of Li-containing compounds, aiming to unveil novel and promising candidates for cathodes [6]. Our findings underscore the pivotal role of advanced DFT methodologies in advancing the discovery and design of high-performance battery materials.[1] I. Timrov, F. Aquilante, M. Cococcioni, N. Marzari, PRX Energy 1, 033003 (2022).[2] I. Timrov, M. Kotiuga, N. Marzari, Phys. Chem. Chem. Phys. 25, 9061 (2023).[3] I. Timrov, N. Marzari, M. Cococcioni, Phys. Rev. B 98, 045141 (2021).[4] I. Timrov, N. Marzari, M. Cococcioni, Phys. Rev. B 103, 085127 (2018).[5] L. Bastonero, N. Marzari, I. Timrov, in preparation.[6] C. Malica, L. Bastonero, M. Bercx, N. Marzari, I. Timrov, in preparation.

Quantum Chemical Investigation into the Structural Analysis and Calculated Raman Spectra of Amylose Modeled with Linked Glucose Molecules.

This study presents a quantum chemical investigation into the structural analysis and calculated Raman spectra of modeled amylose with varying units of linked glucose molecules. We systematically examined the rotation of hydroxymethyl groups and intramolecular hydrogen bonds within these amylose models. Our study found that as the number of linked glucose units increases, the linear structure becomes more complex, resulting in curled, cyclic, or helical structures facilitated by establishing various intramolecular interactions. The hydroxymethyl groups were confirmed to form interactions with oxygen atoms and with hydroxymethyl and hydroxyl groups from adjacent rings in the molecular structures. We identified distinct peaks and selected specific bands applicable in various analytical contexts by comparing their calculated Raman spectra. Representative vibrational modes within selected regions were identified across the different lengths of amylose models, serving as characteristic signatures for linear and more coiled structural conformations. Our findings contribute to a deeper understanding of amylose structures and spectroscopic signatures, with implications for theoretical studies and potential applications. This work provides valuable reference points for the detailed assignment of Raman peaks of amylose structure, facilitating their application in broader research on carbohydrate structures and their associated spectroscopic properties.

Structure–spectrum relationship in the calculated Raman spectra of silicates

AbstractSilicate minerals have a rich structural variety consisting of silicon oxide clusters or networks of any dimensionality interdispersed with different types of elements, which is reflected in marked changes in the Raman spectra. Understanding how the changes in the Raman spectra are correlated with the atomic structure would be highly desirable for fast material identification and analysis. Extracting such trends from experimental spectra can be difficult owing to the uncertainties in the structural details of the samples and in ensuring consistency between measurements from different sources. Simulated spectra, however, avoid these problems, making them a good candidate for systematic studies. Here, we study the correlation between the structure and Raman spectral features of 179 silicates derived from a database of Raman spectra simulated using first‐principles calculations. We investigate the spectral similarities with a specific emphasis on materials containing isolated 0D clusters in nesosilicate (SiO4), sorosilicate (Si2O7), and cyclosilicate (Si3O9 and Si4O12) configurations. While trends identified in the previous reports can be confirmed, we find that the variations within each group of similar structural motifs tend to be larger than the changes across groups, and therefore, developing a reliable automated classification algorithm is likely to be challenging.

An electron density clustering based adaptive segmentation method for protein Raman spectrum calculation

Raman spectroscopy is a powerful technique for protein detection, but the calculation of Raman spectrum is a longstanding challenging problem due to the large sizes and complex structures of protein molecules. Dividing proteins into fragments can greatly accelerate the calculation, but this usually introduces large errors originating from ignored interactions between fragments into obtained spectra. In this paper, we proposed a new adaptive segmentation method based on the strength of interactions and molecular shapes and structures, i.e., electron density clustering, to divide proteins. It can reduce errors of obtained Raman spectra by about 20% compared to the uniform segmentation method without a significant increase in computational cost. This method can facilitate the validation and analysis of detected Raman spectra of proteins and promote the application of Raman spectroscopy in biological detection.

A database of computed Raman spectra of inorganic compounds with accurate hybrid functionals

Raman spectroscopy is widely applied in identifying local structures in materials, but the interpretation of Raman spectra is non-trivial. An accurate computational database of reference spectra calculated with a consistent level of theory can significantly aid in interpreting measured Raman spectra. Here, we present a database of Raman spectra of inorganic compounds calculated with accurate hybrid functionals in density functional theory. Raman spectra were obtained by calculating dynamical matrices and polarizability tensors for structures from the Inorganic Crystal Structure Database. The calculated Raman spectra and other phonon properties (e.g., infrared spectra) are stored in a MongoDB database publicly shared through a web application. We assess the accuracy of our Raman calculations by statistically comparing ~80 calculated spectra with an existing experimental Raman database. To date, the database contains 161 compounds and is continuously growing as we add more materials computed with our automated workflow.

Atomistic mechanism of structural and volume relaxation below glass transition temperature in a soda-lime silicate glass revealed by Raman spectroscopy and its DFT calculations.

To elucidate the atomistic origin of volume relaxation in soda-lime silicate glass annealed below the glass transition temperature (Tg), the experimental and calculated Raman spectra were compared. By decomposing the calculated Raman spectra into specific groups of atoms, the Raman peaks at 800, 950, 1050, 1100, and 1150cm-1 were attributed to oxygen and silicon in Si-O-Si, non-bridging oxygen in the Q2 unit, bridging oxygen in low-angle Si-O-Si, non-bridging oxygen in the Q4 unit, and bridging oxygen in high-angle Si-O-Si, respectively. Based on these attributions, we found that by decreasing the fictive temperature by annealing below Tg - 70K, a homogenization reaction Q2 + Q4 → 2Q3 and an increase in average Si-O-Si angle occurred simultaneously. By molecular dynamics simulation, we clarified how the experimentally demonstrated increase in average Si-O-Si angle contributes to volume shrinkage; increasing Si-O-Si angles can expand the space inside the rings, and Na can be inserted into the ring center.

Decoding PFAS contamination via Raman spectroscopy: A combined DFT and machine learning investigation

In this study, density function theory (DFT) is employed to compute Raman spectra of 40 important Perfluoroalkyl substances (PFASs) as listed in Draft Method 1633 by U.S. Environmental Protection Agent. A systematic comparison of their spectral features is conducted, and Raman peaks and vibrational modes are identified. The Raman spectral regions for the main chemical bonds (such as C-C, CF2 & CF3, O-H) and main functional groups (such as -COOH, -SO3H, -C2H4SO3H, and -SO2NH2) are identified and compared. The impacts of branching location in isomer, molecular chain length, and functional groups on the Raman spectra are analyzed. Particularly, the isomers of PFOA alter the peak locations slightly in wavenumber regions of 200 – 800 and 1000 – 1400 cm−1, while for PFOS, spectral features in the 230 – 360, 470 – 680, and 1030 – 1290 cm−1 regions exhibit significant difference. The carbon chain length can significantly increase the number of Raman peaks, while different functional groups give significantly different peak locations. To facilitate differentiation, a spectral database is constructed by introducing controlled noise into the DFT-computed Raman spectra. Subsequently, two chemometric techniques, principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE), are applied to effectively distinguish among these spectra, both for 40 PFAS compounds and the isomers. The findings demonstrate the promising potential of combining Raman spectroscopy with advanced spectral analysis methods to discriminate between distinct PFAS compounds, holding significant implications for improved PFAS detection and characterization methodologies.

NEW MARKERS FOR DETERMINATION OF CAROTENOID MOLECULES ISOMERISM USING RAMAN SPECTROSCOPY

The paper presents an analysis of the experimental and calculated Raman spectra of plant and bacterial carotenoids: neurosporin, spheroiden, lycopene, spirilloxanthin, β-carotene, lutein, ζ-carotene, α-carotene and γ-carotene. A number of characteristic features in the Raman spectra of carotenoids are described for the first time, which make it possible to determine the structure of end groups of molecules and to distinguish their isomers.

Synthesis and characterization of XeAr2 under high pressure.

The binary Xe-Ar system has been studied in a series of high pressure diamond anvil cell experiments up to 60GPa at 300K. In-situ x-ray powder diffraction and Raman spectroscopy indicate the formation of a van der Waals compound, XeAr2, at above 3.5GPa. Powder x-ray diffraction analysis demonstrates that XeAr2 adopts a Laves MgZn2-type structure with space group P63/mmc and cell parameters a = 6.595 Å and c = 10.716 Å at 4GPa. Density functional theory calculations support the structure determination, with agreement between experimental and calculated Raman spectra. Our DFT calculations suggest that XeAr2 would remain stable without a structural transformation or decomposition into elemental Xe and Ar up to at least 80GPa.

In situ synthesis of PuCl3 and corresponding Raman and density functional theory vibrational modes

AbstractThe experimental and calculated Raman spectrum of PuCl3 has been reported for the first time. PuCl3 is a primary species found in plutonium metal refinement, specifically in pyrochemical salt processes including multicycle direct oxide reduction, metal chlorination, and electrorefining. As such, Raman signatures of PuCl3 could serve as potential forensic indicators of material process history. A novel technique for synthesizing PuCl3 from the in situ chlorination of plutonium metal with HCl was developed to establish these signatures. Cerium metal surrogates were utilized to ensure optimization of the plutonium experiments and to minimize personnel exposure, and all experiments were carried out in a Raman reaction chamber designed for air‐tight, high vacuum environments. In situ Raman spectroscopy was employed in conjunction with density functional theory (DFT) to investigate the vibrational modes of PuCl3. Associated mixed oxy and hydroxyl phases are also reported. The combined Raman and DFT results have eliminated inconsistencies in Raman mode assignments for the MX3 family of metal chlorides having P63/m symmetry, and IR modes derived from the DFT calculations are additionally presented. The data observed in this study are of potential interest to nuclear forensic analyses, nuclear sample aging, nuclear energy, plutonium processing, and stockpile stewardship.

Pressure and temperature effects on the Raman spectra of LLM-105

Currently, only one crystal structure of LLM-105 (2,6-diamino-3,5-dinitropyrazine-1-oxide) (P21/n) has been discovered, and there are still debates on its phase transition point and phase diagram. Based on previous work, we performed crystal structure, Raman spectra, and vibrational properties calculations on LLM-105 crystal. Our results indicate that the crystal structure of LLM-105 remains stable until compressed to 49 GPa, beyond which it may undergo two phase transitions at pressure intervals of 49.0–49.1 GPa and 51.4–51.5 GPa, respectively. Analysis of Raman shift results suggests that these two phase transitions may be reversible, with an intermediate phase possibly acting as a transition phase. Additionally, based on the quasi-harmonic approximation, we fitted the experimental data of LLM-105 lattice expansion state, obtaining the volume at zero pressure and using it for Raman spectra calculations. The results demonstrated the accuracy of this quasi-harmonic approximation method in describing the redshift of Raman peaks during the heating process and the excitation ratio of Raman peaks in different wavenumber ranges.

Anisotropic and Finite Effects on Intermolecular Vibration and Relaxation Dynamics: Low-Frequency Raman Spectroscopy of Water Film and Droplet on Graphene by Molecular Dynamics Simulations.

The structural and dynamical properties of water can be greatly altered by the anisotropic interfacial environment. Here, we study the intermolecular vibration and relaxation dynamics of a water film and a water droplet on a graphene surface based on low-frequency Raman spectra calculated from molecular dynamics simulations. The calculated Raman spectra of the interfacial water systems show a weakened libration peak and an enhanced intermolecular hydrogen bond (HB) stretching peak compared to the spectrum of bulk water, which are attributed to softened orientation motion. We also find that the collective polarizability relaxation in the droplet is much slower than that in the film and bulk, which is completely different from the collective dipole relaxation. The slow relaxation is due to a positive correlation between the induced polarizabilities of distinct molecules caused by the global and anisotropic structural fluctuations of the water droplet. Furthermore, we find that the two-dimensional HB network by the orientation-ordered interfacial water molecules leads to different intermolecular vibration dynamics between the parallel and perpendicular components. The present theoretical study demonstrates that low-frequency Raman spectroscopy can reveal the anisotropic and finite effects on the intermolecular dynamics of the water film and droplet.

Molecular Structures and Vibrational Spectra of trans- and cis-Polyacetylene and Their Oligoenes Revisited Using Density Functional Theory Calculations.

Polyacetylene, the most representative synthetic conducting polymer, has attracted much attention because it exhibits high conductivity upon doping. In this paper, molecular structures, electronic excitation energies, and Raman and infrared spectra were calculated using density functional theory for trans- and cis-oligoenes with various chain lengths up to the number of C═C bonds (n) of 100 and trans- and cis-polyacetylenes under one-dimensional periodic boundary condition. The harmonic vibrational frequencies obtained at the B3LYP/6-311G(d,p) level were scaled by the scaling factors determined with respect to the anharmonic vibrational frequencies using the B2PLYP method, in which the coefficients of the functional were optimized for trans-oligoenes. The calculated infrared and Raman frequencies reproduce reasonably well the observed frequencies for trans- and cis-polyacetylene. Based on the chain-length dependence of the calculated Raman spectra of trans-oligoenes, we proposed the possibility of longer conjugated trans-segments observed in the resonance Raman spectra of trans-polyacetylene excited at longer wavelengths of 647.1 and 1064 nm. We also elucidated the origin of the excitation-wavelength dependence of the resonance Raman spectra of trans-polyacetylene and the structure of isomerization intermediates from cis-form to trans-form. In addition, the previous assignments of Raman and infrared spectra of trans- and cis-polyacetylene were reexamined in the present study based on the chain-length dependence of the spectra.

Plasmon-Mediated Selective Chemical Reaction of Aromatic Molecules with Amino and Nitro Functional Groups

The plasmon-mediated chemical reaction (PMCR) of aromatic molecules with different functional groups is the frontier topic in the photochemistry area. In this work, two typical Ag-plasmon-catalyzed reactions in aqueous environments are studied, in which the selective reduction reactions of 2-amino-5-nitrobenzenethiol (2A-5NBT) molecules to 3,3′-dimercapto-4,4′-diaminoazobenzene (M1) and the reduction of M1 to 2,5-aminobenzenethiol (M2) by NaBH4 are observed. The mechanism of these two reactions is discussed combined with the calculated Raman spectra. These results demonstrate that 2A-5NBT molecules are selectively catalyzed to M1 in aqueous environments and M1 can be reduced to form M2 in the presence of NaBH4 as a reducing agent. Furthermore, the kinetics of the reduction reaction are analyzed based on surface-enhanced Raman spectroscopy (SERS), which conforms to the first-order kinetic process. This work provides a new perspective on the modulation of selective surface-catalyzed coupling reactions on 2A-5NBT molecules and facilitates the broadening of the research field of in situ monitoring of PMCRs by SERS technology.

Synergistic effect between Ce-doped SnO2 and bio-carbon for electrocatalytic degradation of tetracycline: Experiment, CFD, and DFT

Carbon-based sandwich-like electrocatalyst with a hierarchical structure, carbon sheet (CS)-loaded Ce-doped SnO2 nanoparticles, were successfully prepared using a simple method, which presented a high-efficiency electrocatalytic performance for tetracycline decomposition. Among them, Sn0.75Ce0.25Oy/CS exhibits superior catalytic activity, such as more than 95% of tetracycline was removed (120 min), and over 90% of total organic carbon was mineralized (480 min). It is found from morphology observation and computational fluid dynamics simulation that the layered structure is conducive to improving the mass transfer efficiency. Through X-Ray powder diffraction, X-ray photoelectron spectroscopy, Raman spectrum, and density functional theory calculation analyze that the structural defect in Sn0.75Ce0.25Oy caused by Ce doping is considered to play the key role. Moreover, electrochemical measurements and degradation experiments further prove that the outstanding catalytic performance is attributable to the initiated synergistic effect established between CS and Sn0.75Ce0.25Oy. These results explain the effectiveness of Sn0.75Ce0.25Oy/CS for the remediation of tetracycline-contaminated water and mitigating the potential risks and imply that the Sn0.75Ce0.25Oy/CS composite has a deeply practical value in tetracycline wastewater degradation and a promise for further application.