scholarly journals Identification of DNA Bases and Their Cations in Astrochemical Environments: Computational Spectroscopy of Thymine as a Test Case

2021 ◽  
Vol 8 ◽  
Author(s):  
Yage Zhao ◽  
Majdi Hochlaf ◽  
Malgorzata Biczysko
Keyword(s):  
Near Infrared ◽  
Vacuum Ultraviolet ◽  
Theoretical Calculations ◽  
Photoelectron Spectra ◽  
Test Case ◽  
Molecular Systems ◽  
James Webb Space Telescope ◽  
Computational Spectroscopy ◽  
Robotic Missions ◽  
Combination Bands

Increased importance of vibrational fingerprints in the identification of molecular systems, can be highlighted by the upcoming interstellar medium (ISM) observations by the James Webb Space Telescope, or in a context of other astrochemical environments as meteorites or exoplanets, Mars robotic missions, such as instruments on board of Perseverance rover. These observations can be supported by combination of laboratory experiments and theoretical calculations, essential to verify and predict the spectral assignments. Astrochemical laboratory simulations have shown that complex organic molecules (COMs) can be formed from simple species by vacuum ultraviolet or X-ray irradiation expanding interest in searching for organic biological and prebiotic compounds. In this work an example of nucleobase, thymine, is selected as a test case for highlighting the utility of computational spectroscopic methods in astrochemical studies. We consider mid-infrared (MIR) and near-infrared (NIR) vibrational spectra of neutral (T) and cationic (T+) thymine ground states, and vibrationally-resolved photoelectron (PE) spectra in the far UV range from 8.7 to 9.4 eV. The theoretical framework is based on anharmonic calculations including overtones and combination bands. The same anharmonic wavenumbers are applied into the simulations of vibrationally-resolved photoelectron spectra based on Franck-Condon computations. The infrared and vibrationally-resolved photoelectron spectra are compared with the available experimental counterparts to verify their accuracy and provide assignment of the observed transitions. Finally, reliable predictions of spectra, going beyond currently available experimental data, either dealing with energy ranges, resolution or temperature, which can support astrochemistry studies are provided.

scholarly journals Anharmonicity and Spectra–Structure Correlations in MIR and NIR Spectra of Crystalline Menadione (Vitamin K3)

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6779
Author(s):  
Krzysztof B. Beć ◽  
Justyna Grabska ◽  
Christian W. Huck ◽  
Sylwester Mazurek ◽  
Mirosław A. Czarnecki
Keyword(s):  
Single Molecule ◽  
Near Infrared ◽  
Structural Information ◽  
Molecular System ◽  
Theoretical Calculations ◽  
Vitamin K3 ◽  
Structure Correlations ◽  
Mir Spectra ◽  
Combination Bands ◽  
The Relationship

Mid-infrared (MIR) and near-infrared (NIR) spectra of crystalline menadione (vitamin K3) were measured and analyzed with aid of quantum chemical calculations. The calculations were carried out using the harmonic approach for the periodic model of crystal lattice and the anharmonic DVPT2 calculations applied for the single molecule model. The theoretical spectra accurately reconstructed the experimental ones permitting for reliable assignment of the MIR and NIR bands. For the first time, a detailed analysis of the NIR spectrum of a molecular system based on a naphthoquinone moiety was performed to elucidate the relationship between the chemical structure of menadione and the origin of the overtones and combination bands. In addition, the importance of these bands during interpretation of the MIR spectrum was demonstrated. The overtones and combination bands contribute to 46.4% of the total intensity of menadione in the range of 3600–2600 cm−1. Evidently, these bands play a key role in shaping of the C-H stretching region of MIR spectrum. We have shown also that the spectral regions without fundamentals may provide valuable structural information. For example, the theoretical calculations reliably reconstructed numerous overtones and combination bands in the 4000–3600 and 2800–1800 cm−1 ranges. These results, provide a comprehensive origin of the fundamentals, overtones and combination bands in the NIR and MIR spectra of menadione, and the relationship of these spectral features with the molecular structure.

scholarly journals A multicolor and ratiometric fluorescent sensing platform for metal ions based on arene–metal-ion contact

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Anna Kanegae ◽  
Yusuke Takata ◽  
Ippei Takashima ◽  
Shohei Uchinomiya ◽  
Ryosuke Kawagoe ◽  
...  
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Near Infrared ◽  
Molecular Design ◽  
Theoretical Calculations ◽  
Probe Design ◽  
One Pot ◽  
Fluorescent Sensing ◽  
Sensing Platform ◽  
Ratiometric Detection

AbstractDespite continuous and active development of fluorescent metal-ion probes, their molecular design for ratiometric detection is restricted by the limited choice of available sensing mechanisms. Here we present a multicolor and ratiometric fluorescent sensing platform for metal ions based on the interaction between the metal ion and the aromatic ring of a fluorophore (arene–metal-ion, AM, coordination). Our molecular design provided the probes possessing a 1,9-bis(2′-pyridyl)-2,5,8-triazanonane as a flexible metal ion binding unit attached to a tricyclic fluorophore. This architecture allows to sense various metal ions, such as Zn(II), Cu(II), Cd(II), Ag(I), and Hg(II) with emission red-shifts. We showed that this probe design is applicable to a series of tricyclic fluorophores, which allow ratiometric detection of the metal ions from the blue to the near-infrared wavelengths. X-ray crystallography and theoretical calculations indicate that the coordinated metal ion has van der Waals contact with the fluorophore, perturbing the dye’s electronic structure and ring conformation to induce the emission red-shift. A set of the probes was useful for the differential sensing of eight metal ions in a one-pot single titration via principal component analysis. We also demonstrate that a xanthene fluorophore is applicable to the ratiometric imaging of metal ions under live-cell conditions.

Near-Infrared Combination and Overtone Bands of CH in CHX3, CHX2—CHX2, and CHX2—CX2—CHX2

2005 ◽  
Vol 59 (11) ◽  
pp. 1393-1398 ◽  
Author(s):  
Reikichi Iwamoto ◽  
Akishi Nara ◽  
Toshihiko Matsuda
Keyword(s):  
Excited State ◽  
Near Infrared ◽  
Present Report ◽  
Spectral Characteristics ◽  
The Other ◽  
Coupled Modes ◽  
Third Order ◽  
The Third ◽  
Combination Bands ◽  
Deformation Modes

In the present report we studied spectral characteristics of the near-infrared combination and overtone bands of CH vibrations of a CH sequence. The near-infrared bands of the CH in CHX3 (X, halogen), which were interpreted in terms of the CH stretching and CH deformation fundamentals without any ambiguity, typically showed how the frequency and intensity of a combination or an overtone depend on the vibrational excited state. In the CH–C–CH of CHX2CX2CHX2, the vibrations of one CH are isolated from those of the other CH, and the combination and overtone bands were similarly interpreted as those of the CH, although each of the combination bands was split into two because of non-degeneracy of the CH deformation. In the CH–CH of CHX2CHX2, the CH deformations only have coupled modes. The first combination showed four narrowly separate bands, which were reasonably interpreted on the basis of the CH stretching and the coupled CH deformation modes. We demonstrated that the first combination of coupled modes as well as the combination of up to, at least, the third order of isolated modes have the nature of the characteristic bands.

scholarly journals Fracture of Be and Its Alloys - Webb Space Telescope Revisited

2021 ◽  
Author(s):  
Muhammad Musaddique Ali Rafique
Keyword(s):  
Near Infrared ◽  
Joint Venture ◽  
Coefficient Of Thermal Expansion ◽  
Infrared Range ◽  
Linear Coefficient ◽  
Space Telescope ◽  
Hexagonal Close Packed ◽  
James Webb Space Telescope ◽  
Layer Deposition ◽  
Slip Planes

NASA/ESA/CSA joint venture James Webb Space Telescope is about to be launched. It is hypothesized to operate in near-infrared range. It is also hypothesized to unveil early star formation, galaxies, and universe due to its orbit, point in orbit and orbital motion. It has been under manufacturing for over 20 years at a staggering cost of 10 billion US dollars (most expensive scientific experiment in history). Beryllium (Be) is chosen to be element for construction of its main mirrors due to its high stiffness, low density, low linear coefficient of thermal expansion (α) in cryogenics and high thermal conductivity. It is followed by gold (Au) layer deposition on its (Be) surface to enhance its sensitivity towards infrared radiation as later is hypothesized to bear superior properties. However, serious mistakes have been made in selecting this material for this application. Owing to its crystal structure (hexagonal close packed (hcp)), slip planes (basal, prismatic and pyramidal) and mechanisms of their activation, Be necessitates easy fracture at cryogenic temperature. It has anisotropic properties and prone to transverse fracture under tensile loading. Furthermore, its ductile to brittle transition temperature is very low making it entirely unsuitable for such an application. It is one of most expensive metals on planet. This study constitutes revisiting these fundamental properties and mechanisms which were entirely ignored during materials selection thus rendering whole project useless.

scholarly journals Infrared Absolute Calibration. I. Comparison of Sirius with Fainter Calibration Stars

2022 ◽  
Vol 163 (2) ◽  
pp. 45
Author(s):  
G. H. Rieke ◽  
Kate Su ◽  
G. C. Sloan ◽  
E. Schlawin
Keyword(s):  
Near Infrared ◽  
Spectral Energy Distribution ◽  
Spectral Energy ◽  
Absolute Calibration ◽  
Absolute Flux ◽  
James Webb Space Telescope ◽  
Infrared Spectral ◽  
History Of ◽  
Flux Measurements ◽  
Debris Disk

Abstract A challenge in absolute calibration is to relate very bright stars with physical flux measurements to faint ones within range of modern instruments, e.g., those on large ground-based telescopes or the James Webb Space Telescope (JWST). We propose Sirius as the fiducial color standard. It is an A0V star that is slowly rotating and does not have infrared excesses due to either hot dust or a planetary debris disk; it also has a number of accurate (∼1%–2%) absolute flux measurements. We accurately transfer the near-infrared flux from Sirius to BD +60 1753, an unobscured early A-type star (A1V, V ≈ 9.6, E(B – V) ≈ 0.009) that is faint enough to serve as a primary absolute flux calibrator for JWST. Its near-infrared spectral energy distribution and that of Sirius should be virtually identical. We have determined its output relative to that of Sirius in a number of different ways, all of which give consistent results within ∼1%. We also transfer the calibration to GSPC P330-E, a well-calibrated close solar analog (G2V). We have emphasized the 2MASS K S band, since it represents a large number and long history of measurements, but the theoretical spectra (i.e., from CALSPEC) of these stars can be used to extend this result throughout the near- and mid-infrared.

Detectors for the James Webb Space Telescope near infrared spectrograph (NIRSpec)

2006 ◽  
Author(s):  
Bernard J. Rauscher ◽  
Torsten Böker ◽  
Craig Cabelli ◽  
Guido De Marchi ◽  
Pierre Ferruit ◽  
...  
Keyword(s):  
Near Infrared ◽  
Space Telescope ◽  
James Webb Space Telescope

Vacuum ultraviolet photochemistry of the conformers of the ethyl peroxy radical

2021 ◽  
Vol 23 (38) ◽  
pp. 22096-22102
Author(s):  
Zuoying Wen ◽  
Xiaoxiao Lin ◽  
Xiaofeng Tang ◽  
Bo Long ◽  
Chengcheng Wang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Vacuum Ultraviolet ◽  
Theoretical Calculations ◽  
Peroxy Radical ◽  
Photoionization Mass Spectrometry ◽  
Condon Factors ◽  
Vuv Photoionization ◽  
Franck Condon

C2H5O2 plus its gauche and trans conformers are studied using synchrotron-based VUV photoionization mass spectrometry and theoretical calculations, and it is found that the gauche conformer has favorable Franck–Condon factors in photoionization.

scholarly journals Towards rational design and optimization of near-field enhancement and spectral tunability of hybrid core-shell plasmonic nanoprobes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Debadrita Paria ◽  
Chi Zhang ◽  
Ishan Barman
Keyword(s):  
Single Molecule ◽  
Rational Design ◽  
Near Infrared ◽  
Theoretical Calculations ◽  
Near Field ◽  
Field Enhancement ◽  
Infrared Region ◽  
Core Shell ◽  
Optimization Strategy ◽  
Design And Optimization

Abstract In biology, sensing is a major driver of discovery. A principal challenge is to create a palette of probes that offer near single-molecule sensitivity and simultaneously enable multiplexed sensing and imaging in the “tissue-transparent” near-infrared region. Surface-enhanced Raman scattering and metal-enhanced fluorescence have shown substantial promise in addressing this need. Here, we theorize a rational design and optimization strategy to generate nanostructured probes that combine distinct plasmonic materials sandwiching a dielectric layer in a multilayer core shell configuration. The lower energy resonance peak in this multi-resonant construct is found to be highly tunable from visible to the near-IR region. Such a configuration also allows substantially higher near-field enhancement, compared to a classical core-shell nanoparticle that possesses a single metallic shell, by exploiting the differential coupling between the two core-shell interfaces. Combining such structures in a dimer configuration, which remains largely unexplored at this time, offers significant opportunities not only for near-field enhancement but also for multiplexed sensing via the (otherwise unavailable) higher order resonance modes. Together, these theoretical calculations open the door for employing such hybrid multi-layered structures, which combine facile spectral tunability with ultrahigh sensitivity, for biomolecular sensing.

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