Calculation Of Spectra Research Articles

Exploring effects of reactant’s chemical environments on adsorption and reaction mechanism by global optimization and IR spectrum calculation, using NO oxidation as a case

Reactant’s chemical environments derived from the type and concentration of surface species on heterogeneous catalysts do great effects on the structures of reactants and reaction pathway. Unraveling the arrangement of surface species and reaction mechanism at different reactant’s chemical environments in theory remains a substantial challenge due to the difficulty in obtaining the global stable configuration of surface species on catalysts and the lack of other theoretical evidences for the identification of surface species and reaction pathway. To solve this problem, a protocol combining the global optimization of surface species at different chemical environments with electronic structure analysis and IR spectrum calculation including frequency and intensity was proposed to unravel the arrangement of surface species and their reaction pathway in this work. Using NO adsorption and oxidation on Pt(111) and O-covered Pt(111) as a case, their stable structures were obtained by the global optimization; then the origins of the structural transformation of NO and NO2 at different environments were elucidated by electronic structure analysis; then the structures and reaction pathway were confirmed by comparing the experimental and calculated IR spectra of NO and NO2 with frequency and intensity. Utilizing this protocol, the stable structures of NO and its transformation, as well as oxidation pathway were revealed under varying chemical environments at the molecular level. It provides solid supports for identifying the stable arrangement of surface species, their transformation and reaction pathway, and can be easily extended to heterogeneous catalysis.

Thermochemistry of Solid-State Formation, Structure, Optical, and Luminescent Properties of Complex Oxides Eu2MeO6 (Me-Mo, W), Eu2W2O9: A Combined Experimental and DFT Study.

Complex oxides Eu2MeO6 (Me-Mo, W), Eu2W2O9 were obtained by a solid-phase reaction between binary oxides. The thermodynamic and kinetic mechanisms of the reaction processes were established using a variety of physical-chemical methods. All compounds obtained in this work crystallize in the low-symmetry monoclinic system, forming complex framework structures, which determine a set of very valuable physical-chemical properties. Comparison of experimental Kubelka-Munk functions and DFT- calculated absorption spectra shows adequate agreement and reveals the origin of the fundamental absorption. In addition, the deficiency in DFT calculations in the part of mutual contribution of CTBs of Mo-O and W-O, from one side, and Eu-O contributions, from the other side, is reported. Calculations of absorption spectra are shown to be superior to band structure analysis in the determination of optical band gaps. Additionally, luminescent properties of Eu2MeO6 and Eu2W2O9 compounds were investigated. These studies provide a better understanding of the electronic and optical properties of the compounds Eu2MeO6 and Eu2W2O9, along with their potential applications in various areas.

First-Principles Studies of the Electronic and Optical Properties of Two-Dimensional Arsenic-Phosphorus (2D As-P) Compounds.

In this work, we propose the construction of a two-dimensional system based on the stable phases previously reported for the 2D arsenic and phosphorus compounds, with hexagonal and orthorhombic symmetries. Therefore, we have modeled one hexagonal and three possible orthorhombic structures. To ensure the dynamical stability, we performed phonon spectra calculations for each system. We found that all phases are dynamically stable. To ensure the thermodynamic and mechanical stabilities, we have calculated cohesive energies and elastic constants. Our results show that the criteria for the stabilities are all fulfilled. For these stable structures, we computed the electronic and optical properties from first-principles studies based on density functional theory. The computation of electronic band gaps was performed by using the GW approximation to overcome the underestimation of the results obtained from standard DFT approaches. To study the optical properties, we have computed the dielectric function imaginary part within the BSE approach, which takes into account the excitonic effects and allows us to calculate the exciton binding energies of each system. The study was complemented by the computation of the absorption coefficient. From our calculations, it can be established that the 2D As-P systems are good candidates for several technological applications.

(Invited) Predicting the Optical Spectra of Fullerenes with Vibronic Coupling

Following the mid-1980s discovery of fullerenes, their optical properties quickly drew a lot of attention as the intrinsically allowed electronic transitions did not seem to alone explain the complexities of their spectra. Even after more than three decades, there is still little knowledge of the intricate details of their absorption and emission spectra. The main issue with these carbon cages is the high density of electronic states in the energy range of interest. From an experimental standpoint, this means that high resolution spectra are needed to accurately distinguish the electronic and vibronic structure. On the other hand, such a high density of electronic states tests the limits of first-principle calculations, as the computational cost for precisely predicting electronic states quickly becomes prohibitive for systems as large as fullerenes.In this presentation, we will discuss the challenges and importance of including vibronic coupling in the Ab initio calculation of fullerenes' optical spectra. This is necessary in order to gain a reliable interpretation of their electronic spectra and make the most of spectroscopy to probe the electronic structure of fullerenes.

The effect of metal-to-ligand charge transfer on linear and nonlinear optical properties of hexaphyrin and metallo-hexaphyrins

Charge transfer from metal to ligand has implications in various fields of chemistry, physics and biology. The manipulation of spin properties would be necessary for controlling charge transfer in spintronics and biological applications. Upon binding to the metal atoms (Ni, Cu, Au, etc.), the spin properties would be modulated in organic conjugated molecules of less intrinsic spin–orbit coupling (SOC) due to SOC coming from the heavy elements. Emission spectra calculation is necessary to validate them as suitable fluorescence quenchers. The nonlinear optical properties like first-order hyperpolarisability β and second-order hyperpolarisability γ calculations are important to find out their relation between fluorescence quenching and higher order nonlinear optical (NLO) properties. From the second-order NLO properties, we computed degenerate four-wave mixing (DFWM) component ( γ ( 2 ) ( − ω ; ω , ω , − ω )) and finally quadratic nonlinear refractive indices of the expanded porphyrins (EPs). How the linear and nonlinear optical properties are dependent on the SOC coming from the heavy materials (Ni, Cu, Au), and charge transfer process is the most interesting question to be addressed for their potential uses for various optoelectronic and spintronic applications.

Optical continuous pulse position modulation-based analog RoF via frequency-domain position estimation.

Analog radio-over-fiber (A-RoF) solutions for mobile fronthaul are regaining wide attention due to their high spectral efficiency and low complexity. However, the performance of A-RoF is usually limited by the fiber link fidelity. In this Letter, we propose and experimentally demonstrate an optical continuous pulse position modulation-based analog radio-over-fiber (OCPPM-RoF) scheme, in which the amplitudes of wireless waveforms are mapped to the time-domain positions of optical pulses to decouple the additive noise. The de-modulation of OCPPM-RoF signals is performed by a frequency-domain continuous position estimation (FD-CPE) algorithm including cross-power spectrum calculation and weighted least square for accurate delay estimation. In the experiment, by adopting appropriate pulse width factors, the recovered signal-to-noise ratio (SNR) can be flexibly adjusted within a wide range from 31.8 to 54.0 dB, supporting the transmission of various formats from 256-QAM to 65536-QAM. The results indicate that OCPPM-RoF can be a promising candidate for future fronthaul.

Femtosecond Core-Level Spectroscopy Reveals Involvement of Triplet States in the Gas-Phase Photodissociation of Fe(CO)5.

Excitation of iron pentacarbonyl [Fe(CO)5], a prototypical photocatalyst, at 266 nm causes the sequential loss of two CO ligands in the gas phase, creating catalytically active, unsaturated iron carbonyls. Despite numerous studies, major aspects of its ultrafast photochemistry remain unresolved because the early excited-state dynamics have so far eluded spectroscopic observation. This has led to the long-held assumption that ultrafast dissociation of gas-phase Fe(CO)5 proceeds exclusively on the singlet manifold. Herein, we present a combined experimental-theoretical study employing ultrafast extreme ultraviolet transient absorption spectroscopy near the Fe M2,3-edge, which features spectral evolution on 100 fs and 3 ps time scales, alongside high-level electronic structure theory, which enables characterization of the molecular geometries and electronic states involved in the ultrafast photodissociation of Fe(CO)5. We assign the 100 fs evolution to spectroscopic signatures associated with intertwined structural and electronic dynamics on the singlet metal-centered states during the first CO loss and the 3 ps evolution to the competing dissociation of Fe(CO)4 along the lowest singlet and triplet surfaces to form Fe(CO)3. Calculations of transient spectra in both singlet and triplet states as well as spin-orbit coupling constants along key structural pathways provide evidence for intersystem crossing to the triplet ground state of Fe(CO)4. Thus, our work presents the first spectroscopic detection of transient excited states during ultrafast photodissociation of gas-phase Fe(CO)5 and challenges the long-standing assumption that triplet states do not play a role in the ultrafast dynamics.

Relativistic calculations of neutron and gamma-ray spectra from beam-target reactions in magnetized plasmas.

We present a fully relativistic analytical model for calculating synthetic spectra from beam-target fusion reactions. When the target particle is assumed at rest, Monte Carlo sampling of reactant velocities can be avoided, and spectrum computations are considerably faster. A fully analytical treatment additionally gives more insight into the spectrum formation. The fully relativistic formulation now makes it possible to handle massless particles in the model, for example from one-step gamma-ray reactions, and the results are corroborated by simulations from established codes.

Statistical data analysis of x-ray spectroscopy data enabled by neural network accelerated Bayesian inference.

Bayesian inference applied to x-ray spectroscopy data analysis enables uncertainty quantification necessary to rigorously test theoretical models. However, when comparing to data, detailed atomic physics and radiation transfer calculations of x-ray emission from non-uniform plasma conditions are typically too slow to be performed in line with statistical sampling methods, such as Markov Chain Monte Carlo sampling. Furthermore, differences in transition energies and x-ray opacities often make direct comparisons between simulated and measured spectra unreliable. We present a spectral decomposition method that allows for corrections to line positions and bound-bound opacities to best fit experimental data, with the goal of providing quantitative feedback to improve the underlying theoretical models and guide future experiments. In this work, we use a neural network (NN) surrogate model to replace spectral calculations of isobaric hot-spots created in Kr-doped implosions at the National Ignition Facility. The NN was trained on calculations of x-ray spectra using an isobaric hot-spot model post-processed with Cretin, a multi-species atomic kinetics and radiation code. The speedup provided by the NN model to generate x-ray emission spectra enables statistical analysis of parameterized models with sufficient detail to accurately represent the physical system and extract the plasma parameters of interest.

CPL of Mellein and Related Natural Compounds: Analysis of the ESIPT Phenomenon.

(R)-(-)-Mellein, (3R,4R)-4-hydroxymellein and (3R,4S)-4-hydroxymellein obtained from fungi, i. e. from Diplodia globulosa, were investigated as a class of natural products presenting ESIPT (excited state intramolecular proton transfer) phenomenon, through fluorescence and CPL (circularly polarized luminescence). The study was preceded by the assessment of the absolute configuration through ECD and VCD (electronic and vibrational circular dichroism) spectroscopies in addition to NMR spectra. It is found that ESIPT takes place in these systems very rapidly, and no dual fluorescence has been observed. The experimental study is backed up by TD-DFT calculations of ECD and CPL spectra, plus MD calculations to follow proton transfer in the excited state and careful analysis of the puckering dynamics of the lactone ring. Deprotonated forms of the three compounds were also investigated by the same chiroptical experimental and theoretical methods, showing how one can find in natural compounds not only biological activity but also biologically compatible sensing probes.

Simulating Chemistry on Bosonic Quantum Devices.

Bosonic quantum devices offer a novel approach to realize quantum computations, where the quantum two-level system (qubit) is replaced with the quantum (an)harmonic oscillator (qumode) as the fundamental building block of the quantum simulator. The simulation of chemical structure and dynamics can then be achieved by representing or mapping the system Hamiltonians in terms of bosonic operators. In this Perspective, we review recent progress and future potential of using bosonic quantum devices for addressing a wide range of challenging chemical problems, including the calculation of molecular vibronic spectra, the simulation of gas-phase and solution-phase adiabatic and nonadiabatic chemical dynamics, the efficient solution of molecular graph theory problems, and the calculations of electronic structure.

Ring Structures of Metal Atom Doped C9, C11, and C13 Clusters from Ab Initio Calculations-The Finding of a Gd@C13 Magnetic Superatom Ring.

Pure C9 clusters have a linear chain structure. However, here, we report using ab initio calculations the transformation of a chain into a cyclic ring structure with the capping of Ca, Sr, and Ba atoms. Further calculations on neutral and charged clusters doped with Sc, Y, and La atoms show stabilization of a cation C9 isoelectronic cyclic ring capped with the metal (M) atom, but anion clusters doped with these trivalent atoms form a C10 like MC9 ring, which deforms to a necklace structure. Both the ring structures correspond to electronic shell closing with 20 delocalized valence electrons in a disk jellium model and have a large highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap. Calculations of IR and Raman spectra show no imaginary frequency, suggesting that the structures are stable. Addition of two C atoms to the ring structure of LaC9 leads to a capped ring structure of the cation LaC11 and an open ring structure of the LaC11 anion. Further addition of two C atoms leads to a La@C13 cation as well as Ca@C13 and Sr@C13 neutral wheel-shaped rings with endohedral doping of the M atom. These novel ring structures have a large HOMO-LUMO gap of more than 4 eV and are magic with electronic shell closing corresponding to 28 delocalized valence electrons in a disk jellium model. There is π aromaticity in this ring satisfying 4n+2 (n = 3) Hückel's rule with 14 valence electrons. Interestingly, when the dopant is a Gd atom, there is a formation of a magnetic superatom ring Gd@C13 + with 7 μB magnetic moments due to seven 4f up-spin states of Gd being fully occupied. Bonding in these novel ring structures is discussed.

New Zosteropenillines and Pallidopenillines from the Seagrass-Derived Fungus Penicillium yezoense KMM 4679.

Ten new decalin polyketides, zosteropenilline M (1), 11-epi-8-hydroxyzosteropenilline M (2), zosteropenilline N (3), 8-hydroxyzosteropenilline G (4), zosteropenilline O (5), zosteropenilline P (6), zosteropenilline Q (7), 13-dehydroxypallidopenilline A (8), zosteropenilline R (9) and zosteropenilline S (10), together with known zosteropenillines G (11) and J (12), pallidopenilline A (13) and 1-acetylpallidopenilline A (14), were isolated from the ethyl acetate extract of the fungus Penicillium yezoense KMM 4679 associated with the seagrass Zostera marina. The structures of isolated compounds were established based on spectroscopic methods. The absolute configurations of zosteropenilline Q (7) and zosteropenilline S (10) were determined using a combination of the modified Mosher's method and ROESY data. The absolute configurations of zosteropenilline M (1) and zosteropenilline N (3) were determined using time-dependent density functional theory (TD-DFT) calculations of the ECD spectra. A biogenetic pathway for compounds 1-14 is proposed. The antimicrobial, cytotoxic and cytoprotective activities of the isolated compounds were also studied. The significant cytoprotective effects of the new zosteropenilline M and zosteropenillines O and R were found in a cobalt chloride (II) mimic in in vitro hypoxia in HEK-293 cells. 1-Acetylpallidopenilline A (14) exhibited high inhibition of human breast cancer MCF-7 cell colony formation with IC50 of 0.66 µM and its anticancer effect was reduced when MCF-7 cells were pretreated with 4-hydroxitamoxifen. Thus, we propose 1-acetylpallidopenilline A as a new xenoestrogen with significant activity against breast cancer.

Mechanistic Insights into UV Spectral Changes of Pyruvic Acid and Pyruvate Part 1: Interaction with Water Molecules

We investigate how the UV spectra of pyruvic acid (PA) and pyruvate are impacted by interactions with water molecules. In particular, we would like to understand the mechanistic origin of the blue shift in the n →− π∗ transition. Pyruvic acid is the simplest α-keto organic acid and is common in the environment. We use density functional theory to optimize geometries to determine excitation energies and find that the excitation energies of the two main pyruvic acid conformers and pyruvate blue shift when interacting with 1 to 4 water molecules, both in vacuo and in a solvent. The excitation wavelength is blue-shifted by 0.9-9.2 nm when adding water molecules to the lowest energy conformer of PA. Calculations of the UV spectra of pyruvic acid (PA) and pyruvate are crucial for understanding the impact of the interactions with water molecules.

Sensitive quantification of mevalonate pathway intermediates and prediction of relative novel analogs by chemical derivatization-based LC-MS/MS

The mevalonate (MVA) pathway plays a crucial role in the occurrence and progression of various diseases, such as osteoporosis, breast cancer, and lung cancer, etc. However, determining all the MVA pathway intermediates is still challenging due to their high polarity, low concentration, chelation effect with metal compartments, and poor mass spectrometric response. In this study, we established a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method coupled with N2, N2, N4, N4-tetramethyl-6-(4-(piperazin-1-ylsulfonyl) phenyl)-1,3,5-triazine-2,4-diamine (Tmt-PP) labeling for the simultaneous analysis of all MVA intermediates in biospecimens. Chemical derivatization significantly improved the chromatographic retention, peak shape, and detection sensitivity of the analytes. Moreover, we employed a method named mass spectrum calculation to achieve the absolute quantification of the isomers, i.e., isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The established method was fully qualified and applied to explore the difference of these metabolites in cisplatin-resistant non-small cell lung cancer (NSCLC) cells. Additionally, several MVA intermediate analogs, including isopentenyl monophosphate or dimethylallyl monophosphate (IMP/DMAMP), geranyl monophosphate (GMP), 5-triphosphomevalonate (MTP), and isopentenyl triphosphate or dimethylallyl triphosphate (ITP/DMATP), were identified for the first time using a knowledge-driven prediction strategy. We further explored the tissue distribution of these novel metabolites. Overall, this work developed a sensitive quantification method for all MVA intermediates, which will enhance our understanding of the role of this pathway in various health and disease conditions. The novel metabolites we discovered warrant further investigations into their biosynthesis and biological functions.

Nonlinear Optical Effects in Europium Melilite Eu2MgSi2O7

Crystals of the family of tetragonal, non‐centrosymmetric melilites have attracted interest as nonlinear optical, piezoelectric, and ferroelectric materials. This work presents an ab initio study of the optical properties of europium melilite, Eu2MgSi2O7. The study includes the calculation of refractive and absorption spectra, with respect to the density of states of the system. The obtained results demonstrate the correlation between the electronic structure of europium melilite and its optical characteristics.

Cross-linkable binder for composite silicon-graphite anodes in lithium-ion batteries

Silicon (Si) is a promising substitute for graphite anode due to the high theoretical specific capacity (4200 mAh g−1). However, too large volume change exists during the lithiation/delithiation process. Composite anode, prepared by mixing Si with graphite, can realize higher specific capacity than graphite and much better cycle performance than Si anode. However, the capacity decay caused by pulverization of Si particles is still a great challenge. Here, a cross-linkable binder rich in nitrile, carboxyl and hydroxyl groups is designed for composite silicon-graphite (Si-C) anode. The nitrile and hydroxyl groups can be in situ cross-linked in the batteries through Ritter reaction. The cross-linked binder has excellent resilience and good adhesion to the active materials and current collector. The cycle performance of the cell with cross-linked binder is much better than the counterpart. Scanning electron microscopy results of the cycled Si-C anode show that the cross-linked binder can suppress the volume expansion and pulverization. Moreover, the investigation with X-ray photoelectronic spectrum and density function theory calculation demonstrate that the decomposition of ester solvent and LiPF6 on Si anode has been mitigated and more stable SEI film is formed on the Si-C anode. Our strategy of in situ cross-linking binder in the batteries has provided a feasible way for designing the next generation of silicon-based anodes with higher specific capacity and longer cycling life.

CLASS-OneLoop: accurate and unbiased inference from spectroscopic galaxy surveys

The power spectrum is the most commonly applied summary statistics to extract cosmological information from the observed three-dimensional distribution of galaxies in spectroscopic surveys. We present CLASS-OneLoop, a new numerical tool, fully integrated into the Boltzmann code CLASS, enabling the calculation of the one-loop power spectrum of biased tracers in spectroscopic surveys. Built upon the Eulerian moment expansion framework for redshift-space distortions, the implemented model incorporates a complete set of nonlinear biases, counterterms, and stochastic contributions, and includes the infrared resummation and the Alcock-Paczynski effect. The code features an evaluation of the loops by either direct numerical integration or Fast Fourier Transform, and employs a fast-slow parameter decomposition, which is essential for accelerating MCMC runs. After presenting performance and validation tests, as an illustration of the capabilities of the code, we apply it to fit the measured redshift-space halo power spectrum wedges on a ΛCDM subset of the AbacusSummit simulation suite and considering scales up to kmax = 0.3 h/Mpc. We find that the one-loop model adeptly recovers the fiducial cosmology of the simulation, while a simplified model commonly used in the literature for sensitivity forecasts yields significantly biased results. Furthermore, we conduct Monte Carlo Markov Chain (MCMC) forecasts for a DESI-like survey, considering a model with a dynamical dark energy component. Our results demonstrate the ability to independently constrain cosmological and nuisance parameters, even in the presence of a large parameter space with twenty-nine variables.

Dark radiation isocurvature from cosmological phase transitions

Cosmological first order phase transitions are typically associated with physics beyond the Standard Model, and thus of great theoretical and observational interest. Models of phase transitions where the energy is mostly converted to dark radiation can be constrained through limits on the dark radiation energy density (parameterized by ΔN eff). However, the current constraint (ΔN eff < 0.3) assumes the perturbations are adiabatic. We point out that a broad class of non-thermal first order phase transitions that start during inflation but do not complete until after reheating leave a distinct imprint in the scalar field from bubble nucleation. Dark radiation inherits the perturbation from the scalar field when the phase transition completes, leading to large-scale isocurvature that would be observable in the CMB. We perform a detailed calculation of the isocurvature power spectrum and derive constraints on ΔN eff based on CMB+BAO data. For a reheating temperature of T rh and a nucleation temperature T *, the constraint is approximately ΔN eff ≲ 10-5 (T */T rh)-4, which can be much stronger than the adiabatic result. We also point out that since perturbations of dark radiation have a non-Gaussian origin, searches for non-Gaussianity in the CMB could place a stringent bound on ΔN eff as well.

Molecular Diversity from Longipinenes of Santolina viscosa Lag. through Acid Catalysis: Biocidal Activity.

The search for new compounds with biocidal potential was carried out, focusing on the longipinenes 1-7 from the plant species Santolina viscosa Lag. Compounds 1, 2, and 5 showed remarkable molecular diversity when treated in acidic reaction conditions. Protonic, Lewis, and heterogeneous compounds were used in the treatment. Three main models of reaction have been observed: isomerization of the double bond (8-10); rearrangements to longibornane-based skeleton (11-15) and ring-opening to himachalane-based skeleton (16-18). Secolongibornane aldehydes 23 and 24 were obtained after epoxide opening under the same reaction conditions. The elucidation of the structures of the new compounds was carried out using spectroscopic data and was supported by computational theoretical calculations of 13C NMR spectra. Additionally, high-resolution mass spectrometry and single-crystal X-ray diffraction analysis were employed for certain compounds. Natural longipinenes 4-7, methyl esters 1-3 of corresponding natural carboxylic acids and the isomerized and derivatives compounds 8-19 exhibit moderate to high insecticidal activity against R. padi and M. persicae insects. Longipinene 5 shows potent inhibition against the root growth of the plants L. perenne and L. sativa, as well as compound 2 on the leaves of L. perenne. Furthermore, significant ixocidal and nematicidal activity was found for this latter compound.