Spectral Simulation Research Articles

Hydrogen bond network structures of protonated dimethylamine clusters H+(DMA)n (n = 3-7).

Infrared spectroscopy of protonated dimethylamine clusters, H+(DMA)n, (n = 3-7), and their Ar-tagged clusters was performed in the NH and CH stretching vibrational region to explore their hydrogen bond network structures. A stable isomer search and vibrational spectral simulations of the clusters were also carried out to support the interpretations of the observed spectra. Weakly hydrogen-bonded NH stretching vibrational bands, which are characteristic of cyclic structures of small-sized protonated clusters, are observed in the spectra of the Ar-tagged clusters of n ≥ 5, while only linear chain type structures are suggested for the Ar-tagged clusters of n = 3-4 and the bare clusters of all the sizes. These results demonstrate that the size and temperature dependence of the hydrogen bond network structures of the protonated dimethylamine clusters is analogous to that of protonated monohydric alcohol clusters.

Field-stepwise-swept solid-state 127I NMR of 1,4-diiodobenzene

Field-stepwise-swept solid-state 127I NMR experiments of 1,4-diiodobenzene, C6H4I2, applied to a Zeeman-perturbed NQR region, have been presented. A series of QCPMG measurements is performed at T = 90 K with resonant frequencies of 271 MHz in the range of magnetic fields from 2.5 T to zero with the interval of 12 mT. The spectral simulation, in which a numerical calculation involves the diagonalization of the combined Zeeman-quadrupolar Hamiltonian, provides quadrupole coupling constant (CQ) = 1863(5) MHz and the asymmetry parameter (ηQ) = 0.04(2). The 127I NQR spectrum is observed at T = 90 K, which is consistent in the above experimental results.

Seismic attributes and quantitative inverse dynamical simulations for characterization of late Cretaceous classical fluvial meander channelized stratigraphic traps system, onshore Indus, Pakistan: Implications for hydrocarbon exploration

Meandering channel systems and point bars (PBRL) of the fluvial depositional system (FDPS) globally form primary stratigraphic traps (PST). These ultra-thin-bedded and sub-seismic features are developed during rising sea-levels (transgressive) and standstill (aggradational parasequences) inside the transgressive system tract (TST). The aggradational parasequences of TST have coarse-grained sandstone-filled PSTs, which have specific thickness, density, velocity, angle of the sedimentary reserves, and depositional and erosional characteristics for the development of seismic reflection configurations. All these implications are the key controlling factors for developing the aggrading parasequence sets of TST throughout a sea-level standstill, which is not feasible to predict using the full spectrum-based time and depth mapping tools. The full spectrum-based amplitude volumes lack the tuning frequency content for achieving the above-addressed implications. They require sophisticated tuned-frequency amplitudes, which are responsible to resolve these PSTs when they are filled with porous (Ps) and gas-saturated (Sgas) sedimentary facies, and hence, they show unique seismic-based expressions (velocity and density). Therefore, all these implications are achieved in this study by operating the spectral attributes and the instantaneous spectral decomposition-based velocity and density reservoir simulations (SVDRS) on a hydrocarbons-producing arena, onshore Indus, Pakistan. The tuning thickness for this FDPS was 8.75 m. The 42-Hz spectral attribute shows ∼13 m parallel and wavy seismic reflection configurations, but failed in predicting the horizontally deposited PST, simulated density and velocity, shelf or basin plain, and lateral distribution of Sgas and Ps point bars along the subsidence zones. SVDRS have predicted the ∼86–95% Sgas; ∼31–35% Ps; 14–16 m thick (on inverted density simulation); 2453–2500 m/s velocity; inside the 2.2–2.3 g/c.c densely-fractured and inclined (<3°) aggradational parasequences with parallel reflection configurations for high sinuosity index (S.I) > 2.2 PBRLs, which implicates the presence of a meandering channelized reservoir stream. These stratigraphic configurations implicate the low-risk and highly rewarding hydrocarbon prospecting zones due to no spilling out of the hydrocarbon from the PST during the sea-level standstills. These hydrocarbon-bearing PBRLs have a lateral extent of >2 km, which is an appreciable signature of velocity and densities to develop these traps as the future stratigraphic prospect. These PBRLs with >90% Sgas and >32% Ps of PST are completely embedded within the topmost and horizontal regions with transgressive shales facies (seal) of TST and low-Ps shaly-sandstones, which implicates the landward shifting of shoreline during the sea-level rising events. The uncertainty analysis for simulated velocity and density validates a strong R2>0.85% and 0.90% along the high sinuosity index (S.I.)>2.2 implicates the presence of meandering channel streams., which have implicated the presence of non-Ps and water-statured (Sw) retrogradational parasequences. This workflow has developed this FDPS into a pure stratigraphic trap, and hence, the presented scheme of exploration may serve to explore the remaining reserves from the exploration zones for global FDPS.

Identification of nonvolatile organic compounds (NVOCs) in biopharmaceuticals through non-target analysis and quantification using complexation-precipitation extraction

Single-use systems in biopharmaceutical manufacturing can potentially release chemical constituents (leachables) into drug products. Prior to conducting toxicological risk assessments, it is crucial to establish the qualitative and quantitative methods for these leachables. In this study, we conducted a comprehensive screening and structure elucidation of 23 leachables (nonvolatile organic compounds, NVOCs) in two antibody drugs using multiple (self-built and public) databases and mass spectral simulation. We identified 7 compounds that have not been previously reported in medical or medicinal extractables and leachables. The confidence levels for identified compounds were classified based on analytical standards, literature references, and fragment assignments. Most of the identified leachables were found to be plasticizers, antioxidants, slip agents or polymer degradants. Polysorbate (namely Tween) is commonly used as an excipient for protein stabilization in biopharmaceutical formulations, but its ionization in liquid chromatography-electrospray ionization mass spectrometry can interfere with compound quantification. To address this, we employed a complexation-precipitation extraction method to reduce polysorbate content and quantify the analytes. The developed quantitative method for target NVOCs demonstrated high sensitivity (limit of quantification: 20 or 50 μg/L), accuracy (recoveries: 77.2 to 109.5 %) and precision (RSD ≤ 8.2 %). Overall, this established method will facilitate the evaluation of NVOC safety in drug products.

Core-level spectroscopy of the photodissociation process of BrCN molecule

Fewest-switches surfacing hopping (FSSH) simulations have been performed with the high-level multi-reference electronic structure method to explore the coupled electronic and nuclear dynamics upon photoexcitation of cyanogen bromide (BrCN). The potential energy surfaces (PES) of BrCN are charted as functions of the Jacobi coordinates (R, θ). An in-depth examination of the FSSH trajectories reveals the temporal dynamics of the molecule and the population changes of the lowest twelve states during BrCN’s photodissociation process, which presents a rich tapestry of dynamical information. Furthermore, the carbon K-edge x-ray absorption spectroscopy (XAS) is calculated with multi-reference inner-shell spectral simulations. The rotation of the CN fragment and the elongation of the C–Br bond are found to be the reason for the peak shifting in the XAS. Our findings offer a nuanced interpretation for inner-shell probe investigations of BrCN, setting the stage for a deeper understanding of the photodissociation process of cyanogen halides molecules.

Geometric Imperfection Simulations in Cee-Shape Cold-Formed Steel Members Based on Newly Developed Machine-Vision Inspection Techniques

This paper insightfully studies geometric imperfection simulations of cee-section CFS members from laser-based measurements. A machine-vision imperfection inspection technique is first developed where an algorithm is implemented to automate imperfection characterization from volumetric data. The measured imperfections are statistically analyzed and resemble past measurements from other researchers. Two imperfection simulation approaches are studied, i.e., the modal imperfection simulation method and the 1D spectral simulation method, where strength performance and deformation are predicted from finite element analysis. The analysis results are compared with those of testing. The 1D spectral simulation method is superior where stochasticity and regularity of real im-perfection can be properly addressed. The study provides feasible access to imperfection simulations of cee-section CFS members that other researchers can directly apply. The prediction results can aid the future direct analysis and design of CFS members.

A framework to generate local spectral skies for spectral daylight simulations

Spectral daylight simulations are becoming increasingly important in predicting non-visual responses to light and more accurate daylight colour and temporal patterns. However, the availability of locally measured spectral sky data is limited and current spectral sky models do not capture the local colour variability of skies. This paper presents a novel framework for generating high-accuracy, location-specific spectral sky data using typically measured atmospheric data at meteorological stations as inputs to physics-based radiative transfer programs like libRadtran. A comparison of measured and simulated data across the year demonstrates that using location-specific atmospheric profiles leads to significantly more accurate predictions of irradiances, spectral global and direct irradiances, and better captures the variability of clear skies regarding colour accuracy and appearance than simulations with default settings.

Rovibronic molecular line list for the N[formula omitted] second positive system

A line list for the N2 second positive system, B3Πg - C3Πu, has been compiled using the PGOPHER spectral simulation software. The line list extends the number of vibrational states of the B3Πg up to v= 29 and a maximum rotational state of J= 150 for simulation temperatures up to 7000 K. New electronic–vibrational transition moments were calculated using refined potential energy curves and a transition dipole moment with the DUO software. Comparisons to experimental data and the SPECAIR software have been used to validate the new line list. The results are available in ASCII ExoMol .state and .trans files and as a PGOPHER input file for use in spectral analysis.

A Hyperspectral Camouflage Colorant Inspired by Natural Leaves.

The unmet spectral mimicry of foliar green in camouflage materials is hampered by the lack of colorants with similar spectral properties to chlorophyll, resulting in substantial risks of exposure from hyperspectral target detection. By drawing inspiration from leaf chromogenesis, a microcapsule colorant with a chloroplast-like structure and chlorophyll-like absorption is developed, and a generic bilayer coating is designed to provide high spectral similarity to leaves with different growth stages, seasons, and species. Specifically, the microcapsule colorant preserves the monomeric absorption of the internal phthalocyanine and features the manufacturability of conventional pigments, such as amenability to painting and patterning, and compatibility to different substrates. The pigmented artificial leaves successfully deceive the hyperspectral classification algorithm in a foliar background, and outperforming the state-of-art spectral simulation materials. This coloration strategy expands the knowledge base of the spectral fine tuning of composite colorants, which are essential for their application in spectral-resolved optical materials.

Ball Pivoting Algorithm and discrete gaussian curvature: A direct way to curved nanographene circularly polarized luminescence spectral simulation

Theoretical innovations for constructing robust computational protocols are of fundamental significance for a variety of advanced chiroptical spectroscopies. The new generation of chiral curved nanographenes offered us the opportunity to study the chiral emission phenomena in the nanometers scale. Herein we reported a distinctive method that combines topological aspects and the density functional theory in order to reach a coherent description of calculated circularly polarized luminescence spectra of negatively curved nanographenes. Our computational plan was defined as a multi-sequence strategy, paying the attention on the relationship between the molecular curvature and the relative spectroscopic properties: 1) the Ball Pivoting Algorithm for the nanographene surface reconstruction; 2) the atom by atom discrete gaussian curvature analysis to establish which DFT functional better approximates the shape of nanographenes backbones; 3) molecular dynamics in the first excited state for accounting the thermal effect; 4) TDDFT benchmark to scrutinize which functional provides the most reliable excitation energies and rotatory strengths for an accurate CPL spectral simulation. The direct merging of the previous steps celebrated the B3LYP (coupled with the 6-311G(d,p) basis set) as the most precise exchange–correlation functional in duplicating exquisitely the CPL profiles of a heterogeneous set of functionalized nanographene.

The Mechanism of Inhibition of Pyruvate Formate Lyase by Methacrylate.

Pyruvate Formate Lyase (PFL) catalyzes acetyl transfer from pyruvate to coenzyme a by a mechanism involving multiple amino acid radicals. A post-translationally installed glycyl radical (G734· in Escherichia coli) is essential for enzyme activity and two cysteines (C418 and C419) are proposed to form thiyl radicals during turnover, yet their unique roles in catalysis have not been directly demonstrated with both structural and electronic resolution. Methacrylate is an isostructural analog of pyruvate and an informative irreversible inhibitor of pfl. Here we demonstrate the mechanism of inhibition of pfl by methacrylate. Treatment of activated pfl with methacrylate results in the conversion of the G734· to a new radical species, concomitant with enzyme inhibition, centered at g = 2.0033. Spectral simulations, reactions with methacrylate isotopologues, and Density Functional Theory (DFT) calculations support our assignment of the radical to a C2 tertiary methacryl radical. The reaction is specific for C418, as evidenced by mass spectrometry. The methacryl radical decays over time, reforming G734·, and the decay exhibits a H/D solvent isotope effect of 3.4, consistent with H-atom transfer from an ionizable donor, presumably the C419 sulfhydryl group. Acrylate also inhibits PFL irreversibly, and alkylates C418, but we did not observe an acryl secondary radical in H2O or in D2O within 10 s, consistent with our DFT calculations and the expected reactivity of a secondary versus tertiary carbon-centered radical. Together, the results support unique roles of the two active site cysteines of PFL and a C419 S-H bond dissociation energy between that of a secondary and tertiary C-H bond.

Multielectronic and multiatomic effects in the U O4,5 x-ray absorption spectroscopy of uranium dioxide

In order to explain all of the spectral features observed in the U O4,5 x-ray absorption spectrum of uranium dioxide (UO2), it is necessary to include both multielectron effects and multiatomic effects. The 5d (core hole)-5f (electron) angular momentum coupling that gives rise to the giant resonance has been treated within ligand field density functional theory, and the electron scattering that generates the extended x-ray absorption fine structure has been included via the spectral simulation program FEFF: both within a UO8 fluorite cluster picture. An atomic model is insufficient to explain all of the observed spectral features.

A critical review of computational efforts towards identifying secondary structure elements in polylactic acid (PLA)

Polylactic acid (PLA) may be regarded as an analogue of a poly-alanine oligo/polypeptide, where the amino group has been replaced by a hydroxyl. As a consequence, a series of studies have explored the possibility that PLA can adopt peptide-type secondary structures – i.e., repetitive structural patterns characterized by intramolecular hydrogen bonds between neighboring functional groups. To this end, computational techniques (molecular mechanics, semiempirical, Hartree-Fock, density functional theory DFT) geometry optimizations of isolated oligomers of lactic acid (generally ten-unit oligomers), or oligomers attached to solid surfaces, or dimers have been reported, as well as spectral simulations thereof - looking at relative stabilities of helices (α, π, 310), and β sheets. A significant variation in the predicted structures and spectra was noted, depending on the computational method employed. With the most accurate method available (a DFT functional parametrized especially for describing non-covalent interactions), in isolated PLA models the π helix was found to be the most likely structure, closely followed by the 310 helix, and β sheets being the least stable. We review here these data and add two important elements: (1) first, a comparison with an experimentally-derived model of PLA, proposed by De Santis, and (2) second, a Ramachandran analysis of the Φ and Ψ angles in the optimized geometries. It is shown that (1) the De Santis structure is in fact slightly more stable than the helices, and (2) the optimized geometries in fact stray far from the initial Φ, Ψ values – to the extent that all of the peptide-like secondary structures in fact end up as turns (mostly type III β turns), while the DFT-optimized De Santis structure has no classical correspondent in the Ramachandran series of secondary structures.

Utilising spectral lighting simulation technique for evaluating transmitted daylight through glazing: Exploring the non-visual effects and colour appearance

Modern humans spend more time indoors than their ancestors. In indoor environments, windows are the primary building elements that provide access to daylight and views. The advancement of the building industry has introduced new glazing and coating technologies for windows. Electrochromic glazing, in particular, has gained popularity in recent decades. These glazings’ tint varies with light exposure and electrical voltage, affecting the spectral power distribution of transmitted daylight. The growing knowledge of the impacts of light on sleep and health encourages an evaluation of the non-visual effects of daylight transmitted through glazing. Therefore, the aim of this paper is to investigate the non-visual effects of transmitted daylight through one clear and one smart glazing and evaluate the colour appearance variations. However, conventional visualisation tools are inadequate for this purpose, necessitating the use of alternative techniques that consider the spectral power distribution of light. To accomplish this, the Radiance-based Lark spectral lighting simulation tool was utilised. The non-visual effects were analysed by examining the responses of the five photoreceptors (Short-, Medium-, Long-wavelength cones, Rods, and ipRGCs) to light using the CIE spectral sensitivity functions. Additionally, the changes in colour appearance were assessed using six attributes: lightness, hue, chroma, vividness, depth, and clarity. The results demonstrate the effect of the studied glazing on non-visual light stimulation and colour appearance while presenting the challenges, applicability, and limitations of spectral simulation techniques. The proposed method yields promising results and can be a valuable tool for evaluating the effects of glazing on humans.

High resolution infrared spectra of neopentane: Rovibrational analysis of bands at 8.3–6.4 μm

High resolution (0.0014 cm−1) infrared spectra of neopentane (2,2-dimethylpropane) have been recorded at 203 K at the Canadian Light Source. Spectra were recorded in the infrared (8.3–6.4 μm) with 8 m of optical path. Neopentane is a spherical top molecule with Td (tetrahedral) symmetry. A low temperature is favorable for a detailed rotational analysis of its fundamental bands.This study focuses on the analysis of 3 band systems of neopentane. The first system is a dyad consisting of a ν15 fundamental band and a ν7 + ν19 combination band located at 1472.5 and 1489 cm−1, respectively. The second system is a ν16 fundamental band located at 1369.4 cm−1 with uncertain band origin. The third band system is a dyad of a ν17 fundamental and a ν8 + ν18 combination band. Only the ν17 fundamental band was analyzed in this last system due to the weaker intensity of the combination band. For all spectral simulations and calculations an ‘XTDS’ program based on tensorial formalism by the Dijon molecular spectroscopy group was used. A subprogram ‘SPVIEW’, paired with XTDS, was used for spectral assignment.

Spectral simulation of hydromagnetic flow with dissipative and radiative heat transfer over an inclined rotating disk within a non‐Darcy porous medium

AbstractThe goal of the research presented in this paper is to examine how a magnetic field affects the unsteady flow of an incompressible nanofluid over a spinning disc that is inclined and stretched while the flow is embedded in a non‐Darcy porous medium. Furthermore, the heat transmission mechanism takes into account Joule heating and viscous dissipation. By imposing thermal radiation to enhance the heat transmission system under the effects of convection, the current article becomes more realistic. A set of nonlinear partial differential equations and associated boundary conditions defines the mathematical problem. Using an appropriate similarity transformation, the mathematical model is converted into a set of nonlinear ordinary differential equations with boundary conditions, which are then solved numerically by the Spectral Quasi Linearization Method (SQLM). Graphs and tables for various flow parameters illustrate the complete results for the exploration of dimensionless velocity and temperature. Regression analysis is used to statistically estimate the local Nusselt number and the skin friction coefficients. From the numerical results, it is found that when the magnetic parameter is increased, the flow velocity in the radial and tangential directions decreases due to the Lorentz force. With the variation of the Forchheimer number, the fluid flow in both directions decreases with increasing inertia coefficient. By increasing the magnetic parameter and Eckart number, the temperature of the fluid increases. The performed quadratic regression analysis reveals that the permeability of the medium and the generated Lorentz force are significant for the skin friction coefficient in the radial direction, whereas the stretching parameter and Forchheimer number are significant for the skin friction coefficient in the tangential direction. Thermal radiation and convective heating are found to significantly affect the heat transfer coefficient.

Intermolecular charge fluxes and terahertz spectral features of liquid methanol

The behavior of electrons that is relevant to the THz spectral features of liquid methanol is examined theoretically through analyses of the dipole derivatives and the electron density derivatives with respect to the molecular translations and rotations of hydrogen-bonded methanol. It is shown that the hydrogen-bond-induced components of these derivatives are reasonably well interpreted or modeled by intermolecular charge fluxes through hydrogen bonds, which represent the modulations of the extent of hydrogen-bond-induced intermolecular charge transfer occurring upon fluctuations of hydrogen-bond lengths. Combining this model with classical molecular dynamics, spectral simulations in the 0–1000 cm−1 region are carried out, resulting in reasonably good agreement with the observed overall spectral features. The spectral simulations are based on two different formulas that are suitable for different ways of spectral decomposition. The factors with regard to intensity generation and molecular motion that are important for each element of the spectral features are discussed.

From design to realization of high diffraction efficiency Littrow configuration diffraction gratings based on multilayer dielectric mirrors patterned with electron beam lithography

Diffraction efficiency (DE) and laser-induced damage threshold of Chirped pulse amplification (CPA) system diffraction gratings (DGs) are one of the main limiting factors for the anticipated progress of high peak power lasers. Optimization of a high reflectivity dielectric multilayer ZrO2/SiO2 stack mirror with a DG etched in the top SiO2 layer was carried out employing the Rigorous coupled wave analysis method. Two families of solutions possessing DE > 0.99 over the bandwidth of the 1030 nm wavelength ultrashort laser and withstanding different fabrication margins were identified for the Littrow configuration. DGs were produced and verified experimentally. Structures permitting variation in both the depth of the DG and filling factor without loss in DE were obtained for the 690 nm thick SiO2 layer. While the 770 nm thick layer permitted separation of the two parameters requiring either rigorous control of the DG depth or filling factor. DG realization technology was proposed employing electron beam lithography and inductively coupled plasma reactive ion etching. Measurements of the fabricated structures demonstrated 0.91 DE for the first diffraction order over the 60 nm bandwidth and under a 6° mounting error from the Littrow configuration. Spectral angular reflectance DE simulations and respective measurements indicated quantitative agreement. The work provides an integrated overview of high DE periodic structure numerical optimization and manufacturing roadmap which could be applied for the high-peak-power laser CPA system development.

Origin of Low-Lying Red States in the Lhca4 Light-Harvesting Complex of Photosystem I.

The antenna complexes of Photosystem I present low-lying states visible as red-shifted and broadened absorption and fluorescence bands. Among these, Lhca4 has the most evident features of these "red" states, with a fluorescence band shifted by more than 25 nm from typical LHC emission. This signal arises from a mixing of exciton and charge-transfer (CT) states within the excitonically coupled a603-a609 chlorophyll (Chl) dimer. Here we combine molecular dynamics, multiscale quantum chemical calculations, and spectral simulations to uncover the molecular mechanism for the formation and tuning of exciton-CT interactions in Lhca4. We show that the coupling between exciton and CT states is extremely sensitive to tiny variations in the Chl dimer arrangement, explaining both the red-shifted bands and the switch between conformations with blue and red emission observed in single-molecule spectroscopy. Finally, we show that mutating the axial ligand of a603 diminishes the exciton-CT coupling, removing any red-state fingerprint.

A linearized approach to radial velocity extraction

ABSTRACT High-precision radial velocity (RV) measurements are crucial for exoplanet detection and characterization. Efforts to achieve ∼10 cm s–1 precision have been made over the recent decades, with significant advancements in instrumentation, data reduction techniques, and statistical inference methods. However, despite these efforts, RV precision is currently limited to ∼50 cm s–1. This value exceeds state-of-the-art spectrographs’ expected instrumental noise floor and is mainly attributed to RV signals induced by stellar variability. In this work, we propose a factorization method to overcome this limitation. The factorization is particularly suitable for controlling the effect of localized changes in the stellar emission profile, assuming some smooth function of a few astrophysical parameters governs them. We use short-time Fourier transforms (STFTs) to infer the RV in a procedure equivalent to least-squares minimization in the wavelength domain and demonstrate the effectiveness of our method in treating arbitrary temperature fluctuations on the star’s surface. The proposed prescription can be naturally generalized to account for other effects, either intrinsic to the star, such as magnetic fields, or extrinsic to it, such as telluric contamination. As a proof-of-concept, we empirically derive a set of factorization terms describing the solar centre-to-limb variation and apply them to a set of realistic SOAP-GPU spectral simulations. We discuss the method’s capability to mitigate variability-induced RV signals and its potential extensions to serve as a tomographic tool.