arXiv subjects

Edgar Mendoza

Publications and source records attributed to Edgar Mendoza.

15 recordsLinked to original sources

arXiv2026

Ab Initio Characterization of C2H4N2 Isomers: Structures, electronic energies, spectroscopic parameters and formation pathways

This work presents a comprehensive theoretical investigation of key isomers of C2H4N2 using state-of-the-art quantum chemical methods. The objective is to characterize their molecular structures, spectroscopic constants, and electronic energies, and to elucidate plausible formation and destruction pathways, providing data critical for astrochemical and atmospheric detection. High-accuracy ab initio methods were employed, notably CCSD(T)-F12/cc-pVTZ-F12 for optimized geometries. Additional calculations were performed at the CCSD(T)/aug-cc-pVTZ, CCSD(T)/cc-pVTZ, MP2/aug-cc-pVTZ, and CIS levels. Intrinsic reaction coordinate (IRC) calculations were performed at the B3LYP/6-31G(d,p) level to explore reaction pathways. Zero-point energy corrections were determined for all isomers considered. Six low-energy C2H4N2 isomers were identified, all within 1 eV of the global minimum. Among them, methylcyanamide (MCA) exhibits the lowest relative energy (~0.2 eV) and a significant electric dipole moment of 5.00 D, making it a strong candidate for gas-phase detection. The rotational constants for MCA, computed at the CCSD(T)-F12/cc-pVTZ-F12 level, are Ae = 34932.44 MHz, Be = 4995.31 MHz, and Ce = 4520.30 MHz. The V3 torsional barrier was found to be 631.19 cm^{-1}. Centrifugal distortion constants were computed up to sextic order for all isomers. Formation pathways for MCA, such as CH3N + HCN -> CH3NHCN and related isomers, were characterized. The combination of large dipole moments and distinct rotational signatures supports the detectability of methylcyanamide and related C2H4N2 isomers via radioastronomy, infrared, and microwave spectroscopy. Isomerization and reaction pathways involving radical-neutral and neutral-neutral processes were found to be key to their formation in gas-phase environments. These results provide a robust foundation for future observational and modeling efforts.

physics.chem-ph↗

arXiv2025

Unmasking the physical information inherent to interstellar spectral line profiles with Machine Learning. I. Application of LTE to HCN and HNC transitions

Physical and chemical conditions (kinetic temperature, volume density, molecular composition) of interstellar clouds are inherent in their mm-submm line spectra, making spectral line profiles powerful diagnostics of source conditions. We introduce a novel bottom-up approach employing Machine Learning (ML) algorithms to directly infer physical conditions from line profiles without using radiative transfer equations. We simulated HCN and HNC emission under representative dense molecular cloud and star-forming region conditions across five rotational transitions (J=1-0 to J=5-4) within 30-500 GHz. The generated data cloud was parameterized using line intensities and widths to infer the physical conditions of the analyzed regions. Three ML algorithms were trained, tested, and compared to unravel the excitation conditions of HCN and HNC and their abundance ratio. ML results obtained with two spectral lines, one for each isomer, were compared with a Local Thermodynamic Equilibrium (LTE) analysis for the cold source R CrA IRS 7B, yielding excitation temperatures and relative abundances in agreement with LTE. The optimized pipeline (training, testing, and prediction) can predict interstellar cloud properties from line profile inputs at lower computational cost than traditional methods. This work represents the first mapping of spectral line profiles to physical conditions by charting isomer abundance ratios and excitation temperatures. Our bottom-up approach, based on simulated and semiempirical spectra, offers a new tool to interpret line observations and estimate interstellar conditions using ML methods.

astro-ph.GA↗

arXiv2025

New routes for PN destruction and formation in the ISM via neutral-neutral gas-phase reactions and an extended database for reactions involving phosphorus

Phosphorus plays an essential role in the chemistry of living organisms, being present in several fundamental biomolecules. The investigation of chemical reactions taking place in different astronomical environments involving phosphorus-containing molecules is essential for understanding how these species are produced and destroyed. Phosphorus monoxide (PO) and phosphorus nitride (PN) are key reservoirs of phosphorus in the Interstellar Medium (ISM). This work presents a computational study of the CPN system to identify viable reaction pathways involving atom-diatom collisions and to explore a potential destruction route for PN in the ISM. We explore the potential energy landscape of the C($\mathrm{^3P}$) + PN($^1\Sigma^+$), N($\mathrm{^4S}$) + CP($^2\Sigma^+$) and P($\mathrm{^4S}$) + CN($^2\Sigma^+$) reactions by performing high-accuracy ab initio calculations and provide their rate coefficients over a wide range of temperatures. The temperature-dependent rate coefficients were fitted to the modified Arrhenius equation: $k(T)=\alpha(T/300)^{\beta}\mathrm{exp}(-\gamma/T)$. An updated chemical network for P-bearing species was used to model the time-dependent abundances and reaction contributions of P, PO, PN, and PH during the chemical evolution of diffuse/translucent and dense clouds. The only neutral-neutral reaction capable of destroying PN without an activation energy seems to be the PN+C one. We have also shown that reactions between CP and N can yield CN and PN barrierless. Chemical models indicate that PO is a crucial species driving the gas-phase formation of PN. Typically, PO/PN ratios exceed 1, though their chemistry is influenced by photon- and cosmic-ray-induced processes. Over time in simulated dense clouds, neutral-neutral reactions such as PO + N, PH + N, P + OH, and PH + O play a significant role in determining the relative abundances of PO and PN.

astro-ph.GA↗

arXiv2024

New SiS destruction and formation routes via neutral-neutral reactions and their fundamental role in interstellar clouds at low and high metallicity values

Among the silicon bearing species discovered in the interstellar medium, SiS and SiO stand out as key tracers due to their distinct chemistry and abundances in interstellar and circumstellar environments. Our objective is to enhance the network of Si- and S-bearing chemical reactions for a gas-grain model in molecular clouds, encompassing both low and high metallicities. We have calculated the energies and rate coefficients for 6 neutral atom-diatom reactions involved in the SiCS triatomic system, with a special focus on the C+SiS and S+SiC collisions. We employ the coupled cluster method with single and double substitutions and a perturbative treatment of triple substitutions (CCSD(T)) refined at the explicitly correlated CCSD(T)-F12 level. With these computational results in conjunction with data from the literature, we construct an extended network of neutral-neutral chemical reactions. We performed time-dependent models employing the Nautilus gas-grain code, setting the gas temperature to 10 K and the density to 2x10$^4$ cm$^{-3}$. The temperature dependence for the reactions involving SiS were modelled using $k(T)=α\left( T/300 \right)^β \exp{(-γ/T)}$. The high-metallicity models significantly boost the SiS production. Higher initial abundances of C, S, and Si, roughly $\sim$2, 190, and 210 times higher, respectively, contribute to this. Around 10$^3$ yr, destruction mechanisms become relevant. The proposed production reaction S + SiC $\rightarrow$ C + SiS, mitigates these effects. By expanding the gas reaction network using a high metallicity model, we derived estimates for the abundances of interstellar molecules. The inclusion of neutral-neutral mechanisms, particularly via Si+HS and S+SiC channels, played a pivotal role in determining SiS abundance. These mechanisms carry a significance on a par with the well-known and fast ion-neutral reactions.

astro-ph.GA↗

arXiv2023

Observations and chemical modeling of the isotopologues of formaldehyde and the cations of formyl and protonated formaldehyde in the hot molecular core G331.512-0.103

In the interstellar cold gas, the chemistry of formaldehyde (H$_2$CO) can be essential to explain the formation of complex organic molecules. On this matter, the massive and energetic protostellar object G331 is still unexplored and, hence, we carried out a comprehensive study of the isotopologues of H$_2$CO and formyl cation (HCO$^+$), and of protonated formaldehyde (H$_2$COH$^+$) through the APEX observations in the spectral window $\sim$159-356~GHz. We employed observational and theoretical methods to derive the physical properties of the molecular gas combining LTE and non-LTE analyses. Formaldehyde was characterized via 35 lines of H$_2$CO, H$_2^{13}$CO, HDCO and H$_2$C$^{18}$O. The formyl cation was detected via 8 lines of HCO$^+$, H$^{13}$CO$^+$, HC$^{18}$O$^+$ and HC$^{17}$O$^+$. Deuterium was clearly detected via HDCO, whereas DCO$^+$ remained undetected. H$_2$COH$^+$ was detected through 3 clean lines. According to the radiative analysis, formaldehyde appears to be embedded in a bulk gas with a wide range of temperatures ($T\sim$20-90 K), while HCO$^+$ and H$_2$COH$^+$ are primarily associated with a colder gas ($T\lesssim$ 30 K). The reaction H$_2$CO+HCO$^+ \rightarrow$ H$_2$COH$^+$ + CO is crucial for the balance of the three species. We used Nautilus gas-grain code to predict the evolution of their molecular abundances relative to H$_2$ which values at time scales $\sim$10$^3$ yr matched with the observations in G331: [H$_2$CO] = (0.2-2) $\times$10$^{-8}$, [HCO$^+$] = (0.5-4) $\times$10$^{-9}$ and [H$_2$COH$^+$] = (0.2-2) $\times$10$^{-10}$. Based on the molecular evolution of H$_2$CO, HCO$^+$ and H$_2$COH$^+$, we hypothesized about the young lifetime of G331, which is consistent with the active gas-grain chemistry of massive protostellar objects.

astro-ph.GA↗

arXiv2023

Could Nucleobases form in the ISM? A Theoretical Study in the Hoursehead nebula

This work presents the results of a theoretical study that analyzed the possibility of nucleobases to form in the interstellar medium, in the Horsehead nebula, which is a region considered an archetype of molecular cloud. Performing the Meudon PDR code, the reactions of the nitrogen bases formation from formamide, which is a precursor compound identified in several interstellar environment, where simulated. The model showed that at least cytosine and uracil presented significant abundances. Finally, from thermochemical and quantum calculations, a investigation was carried out on the formation reactions considered for the nucleobases and no insurmountable energy barrier which would prevent the reactions was found.

astro-ph.GA↗

arXiv2023

Glycolaldehyde formation mediated by interstellar amorphous ice: a computational study

Glycolaldehyde (HOCH2CHO) is the most straightforward sugar detected in the Interstellar Medium (ISM) and participates in the formation pathways of molecules fundamental to life, red such as ribose and derivatives. Although detected in several regions of the ISM, its formation route is still debated and its abundance cannot be explained only by reactions in the gas phase. This work explores a new gas-phase formation mechanism for glycolaldehyde and compares the energy barrier reduction when the same route happens on the surface of amorphous ices. The first step of the mechanism involves the formation of a carbon-carbon bond between formaldehyde (H2CO) and the formyl radical (HCO), with an energy barrier of 27 kJ mol-1 (gas-phase). The second step consists of barrierless hydrogen addition. Density functional calculations under periodic boundary conditions were applied to study this reaction path on 10 different amorphous ice surfaces through an Eley-Rideal type mechanism. It was found that the energy barrier is reduced on average by 49 per cent, leading in some cases to a 100 per cent reduction. The calculated adsorption energy of glycolaldehyde suggests that it can be promptly desorbed to the gas phase after its formation. This work, thus contributes to explaining the detected relative abundances of glycolaldehyde and opens a new methodological framework for studying the formation routes for Complex Organic Molecules (COMs) in interstellar icy grains.

astro-ph.GA↗

arXiv2022

The Si+SO$_2$ collision and an extended network of neutral-neutral reactions between silicon and sulphur bearing species

The Si+SO$_2$ reaction is investigated to verify its impact on the abundances of molecules with astrochemical interest, such as SiS, SiO, SO and others. According to our results Si($^3$P) and SO$_2$ react barrierlessly yielding only the monoxides SO and SiO as products. No favourable pathway has been found leading to other products, and this reaction should not contribute to SiS abundance. Furthermore, it is predicted that SiS is stable in collisions with O$_2$, and that S($^3$P)+SiO$_2$ and O($^3$P)+OSiS will also produce SO+SiO. Using these results and gathering further experimental and computational data from the literature, we provide an extended network of neutral-neutral reactions involving Si- and S-bearing molecules. The effects of these reactions were examined in a protostellar shock model, using the Nautilus gas-grain code. This consisted in simulating the physicochemical conditions of a shocked gas evolving from $i.$ primeval cold core, $ii.$ the shock region itself, $iii.$ and finally the gas bulk conditions after the passage of the shock. Emphasising on the cloud ages and including systematically these chemical reactions, we found that [SiS/H$_2$] can be of the order of $\sim$ 10$^{-8}$ in shocks that evolves from clouds of $t=1\times 10^6$ yr, whose values are mostly affected by the SiS+O $\longrightarrow$SiO+S reaction. Perspectives on further models along with observations are discussed in the context of sources harbouring molecular outflows.

astro-ph.GA↗

arXiv2022

A spectral survey of CH3CCH in the Hot Molecular Core G331.512-0.103

A spectral survey of methyl acetylene (CH3CCH) was conducted toward the hot molecular core/outflow G331.512-0.103. Our APEX observations allowed the detection of 41 uncontaminated rotational lines of CH3CCH in the frequency range between 172-356 GHz. Through an analysis under the local thermodynamic equilibrium assumption, by means of rotational diagrams, we determined Texc = 50 \pm 1 K, N(CH3CCH) = (7.5 \pm 0.4) x 10^{15} cm^{-2}, X[CH3CCH/H2] ~ (0.8-2.8) x 10^{-8} and X[CH3CCH/CH3OH] ~ 0.42 \pm 0.05 for an extended emitting region (~10 arcsec). The relative intensities of the K=2 and K=3 lines within a given K-ladder are strongly negatively correlated to the transitions' upper J quantum-number (r=-0.84). Pure rotational spectra of CH3CCH were simulated at different temperatures, in order to interpret this observation. The results indicate that the emission is characterized by a non-negligible temperature gradient with upper and lower limits of ~45 and ~60 K, respectively. Moreover, the line widths and peak velocities show an overall strong correlation with their rest frequencies, suggesting that the warmer gas is also associated with stronger turbulence effects. The K=0 transitions present a slightly different kinematic signature than the remaining lines, indicating that they might be tracing a different gas component. We speculate that this component is characterized by lower temperatures, and therefore larger sizes. Moreover, we predict and discuss the temporal evolution of the CH3CCH abundance using a two-stage zero-dimensional model of the source constructed with the three-phase Nautilus gas-grain code.

astro-ph.GA↗

arXiv2021

Possible routes for the Formation of Prebiotic Molecules in the Horsehead Nebula

This article presents the results of a study concerning interstellar molecules which are useful for the bookkeeping of the organic content of the universe and for providing a glimpse into prebiotic conditions on Earth and in other environments in the universe. We explored production channels for astrobiological relevant nitrogen-bearing cyclic molecules (N-heterocycles), e. g. pyrrole and pyridine. The present simulations demonstrate how the exploration of a few possible routes of production of N-heterocycles resulted in significant abundances for these species. One particularly efficient class of channels for the production of N-heterocycles incorporates polycyclic aromatic hydrocarbons (PAHs) as catalysts. Thereby, an exploration of a variety of production paths should reveal more species to be target of astrophysical observations.

astro-ph.GA↗

arXiv2021

Isocyanic acid (HNCO) in the Hot Molecular Core G331.512-0.103: Observations and Chemical Modelling

Isocyanic acid (HNCO) is a simple molecule with a potential to form prebiotic and complex organic species. Using a spectral survey collected with the Atacama Pathfinder EXperiment (APEX), in this work we report the detection of 42 transitions of HNCO in the hot molecular core/outflow G331.512-0.103 (hereafter G331). The spectral lines were observed in the frequency interval $\sim$ 160 - 355 GHz. By means of Local Thermodynamic Equilibrium (LTE) analyses, applying the rotational diagram method, we studied the excitation conditions of HNCO. The excitation temperature and column density are estimated to be $T_{ex}$ = 58.8 $\pm$ 2.7 K and $N$ = (3.7 $\pm$ 0.5) $\times$ 10$^{15}$ cm$^{-2}$, considering beam dilution effects. The derived relative abundance is between (3.8 $\pm$ 0.5) $\times $10$^{-9}$ and (1.4 $\pm$ 0.2) $\times $10$^{-8}$. In comparison with other hot molecular cores, our column densities and abundances are in agreement. An update of the internal partition functions of the four CHNO isomers: HNCO; cyanic acid, HOCN; fulminic acid, HCNO; and isofulminic acid, HONC is provided. We also used the astrochemical code Nautilus to model and discuss HNCO abundances. The simulations could reproduce the abundances with a simple zero-dimensional model at a temperature of 60 K and for a chemical age of $\sim$ 10$^5$ years, which is larger than the estimated dynamical age for G331. This result could suggest the need for a more robust model and even the revision of chemical reactions associated with HNCO.

astro-ph.GA↗

arXiv2019

Sulphur-Bearing and Complex Organic Molecules in an Infrared Cold Core

Since the start of ALMA observatory operation, new and important chemistry of infrared cold core was revealed. Molecular transitions at millimeter range are being used to identify and to characterize these sources. We have investigated the 231 GHz ALMA archive observations of the infrared dark cloud region C9, focusing on the brighter source that we called as IRDC-C9 Main. We report the existence of two sub-structures on the continuum map of this source: a compact bright spot with high chemistry diversity that we labelled as core, and a weaker and extended one, that we labelled as tail. In the core, we have identified lines of the molecules OCS(19-18), $^{13}$CS(5-4) and CH$_{3}$CH$_{2}$CN, several lines of CH$_{3}$CHO and the k-ladder emission of $^{13}$CH$_{3}$CN.We report two different temperature regions: while the rotation diagram of CH$_{3}$CHO indicates a temperature of 25 K, the rotation diagram of $^{13}$CH$_{3}$CN indicates a warmer phase at temperature of $\sim450$K. In the tail, only the OCS(19-18) and $^{13}$CS(5-4) lines were detected. We used the $Nautilus$ and the \textsc{Radex} codes to estimate the column densities and the abundances. The existence of hot gas in the core of IRDC-C9 Main suggests the presence of a protostar, which is not present in the tail.

astro-ph.SR↗

arXiv2019

Destruction and multiple ionization of PAHs by X-rays in circumnuclear regions of AGNs

The infrared signatures of polycyclic aromatic hydrocarbons (PAHs) are observed in a variety of astrophysical objects, including the circumnuclear medium of active galactic nuclei (AGNs). These are sources of highly energetic photons (0.2 to 10 keV), exposing the PAHs to a harsh environment. In this work, we examined experimentally the photoionization and photostability of naphthalene (C$_{10}$H$_{8}$), anthracene (C$_{14}$H$_{10}$), 2-methyl-anthracene (C$_{14}$H$_{9}$CH$_{3}$) and pyrene (C$_{16}$H$_{10}$) upon interaction with photons of 275, 310 and 2500 eV. The measurements were performed at the Brazilian Synchrotron Light Laboratory using time-of-flight mass-spectrometry (TOF-MS). We determined the absolute photoionization and photodissociation cross sections as a function of the incident photon energy; the production rates of singly, doubly and triply charged ions; and the molecular half-lives in regions surrounding AGNs. Even considering moderate X-ray optical depth values ($τ= 4.45$) due to attenuation by the dusty torus, the half-lives are not long enough to account for PAH detection. Our results suggest that a more sophisticated interplay between PAHs and dust grains should be present in order to circumvent molecular destruction. We could not see any significant difference in the half-life values by increasing the size of the PAH carbon backbone, N$_C$, from 10 to 16. However, we show that the multiple photoionization rates are significantly greater than the single ones, irrespective of the AGN source. We suggest that an enrichment of multiply charged ions caused by X-rays can occur in AGNs.

astro-ph.GA↗

arXiv2018

ALMA Observations of the massive molecular outflow G331.512-0.103 II: physical properties, kinematics, and geometry modeling

We present observations and analysis of the massive molecular outflow G331.512-0.103, obtained with ALMA band 7, continuing the work from Merello et al. (2013). Several lines were identified in the observed bandwidth, consisting of two groups: lines with narrow profiles, tracing the emission from the core ambient medium; and lines with broad velocity wings, tracing the outflow and shocked gas emission. The physical and chemical conditions, such as density, temperature, and fractional abundances are calculated. The ambient medium, or core, has a mean density of $\sim 5\times 10^6$ cm$^{-3}$ and a temperature of $\sim 70$ K. The SiO and SO$_2$ emission trace the very dense and hot part of the shocked outflow, with values of $n_{\rm H_2}\sim10^9$ cm$^{-3}$ and $T \sim 160-200$ K. The interpretation of the molecular emission suggests an expanding cavity geometry powered by stellar winds from a new-born UCHII region, alongside a massive and high-velocity molecular outflow. This scenario, along with the estimated physical conditions, is modeled using the 3D geometry radiative transfer code MOLLIE for the SiO(J$=8-7$) molecular line. The main features of the outflow and the expanding shell are reproduced by the model.

astro-ph.GA↗

arXiv2018

Herschel Planetary Nebula Survey (HerPlaNS): Hydrogen Recombination Laser Lines in Mz 3

The bipolar nebula Menzel 3 (Mz 3) was observed as part of the \textit{Herschel} Planetary Nebula Survey (\textit{HerPlaNS}), which used the PACS and SPIRE instruments aboard the \textit{Herschel Space Observatory} to study a sample of planetary nebulae (PNe). In this paper, one of the series describing \textit{HerPlaNS} results, we report the detection of H I recombination lines (HRLs) in the spectrum of Mz 3. Inspection of the spectrum reveals the presence of 12 HRLs in the 55 to 680 $μ$m range covered by the PACS and SPIRE instruments (H11$α$ to H21$α$ and H14$β$). The presence of HRLs in this range is unusual for PNe and has not been reported in Mz 3 before. Our analysis indicates that the HRLs we observed are enhanced by laser effect occurring in the core of Mz 3. Our arguments for this are: (i) the available Mz 3 optical to submillimetre HRL $α$ line intensity ratios are not well reproduced by the spontaneous emission of optically thin ionized gas, as would be typical for nebular gas in PNe; (ii) the compact core of Mz 3 is responsible for a large fraction of the Herschel HRLs emission; (iii) the line intensity ratios for Mz 3 are very similar to those in the core emission of the well known star MWC 349A, where laser effect is responsible for the enhancement of HRLs in the Herschel wavelength range; (iv) the physical characteristics relevant to cause laser effect in the core of MWC 349A are very similar to those in the core of Mz 3.

astro-ph.GA↗