Carmen Barrientos

The search for phosphorus-bearing species in the interstellar medium (ISM) has become a compelling topic in the last years due to its significance in prebiotic chemistry. Following the detection of the glycolonitrile molecule (HOCH2CN) in the interstellar medium, we employed high-level quantum chemistry methodologies to predict the structure and spectroscopic properties of the gauche and anti conformers of HOCH2CP, the phosphorus-bearing analogue of glycolonitrile. In particular, we provide a detailed characterization of their equilibrium geometries, relative stabilities, rotational constants, rovibrational parameters, and infrared spectra using a composite scheme and including anharmonic corrections at the CCSD(T) level. We found that the gauche conformer is 1.22 kcal mol−1 more stable than the anti one, and the interconversion barrier for the aforementioned conformer is only 0.35 kcal mol−1 (≈ 175 K), indicating that both conformers may coexist in dense, cold molecular clouds. Also, we studied possible reactions that could lead to its formation.

Context . The recent interstellar detection of the high-energy O-protonated carbonyl sulfide isomer (HOCS ⁺ ) toward the molecular cloud G+0.693-0.027 contrasts with the non-detection of its lower-energy S-protonated counterpart, HSCO ⁺ , the global minimum in energy. This raises questions regarding the occurrence of selective formation pathways of these [H,C,S,O] ⁺ isomers in space. Aims . In this work, we aim to explore the most likely gas-phase formation routes for both HOCS ⁺ and HSCO ⁺ beyond the direct protonation of OCS (i.e., HCS ⁺ + OH, HCO ⁺ + SH, HOC ⁺ + SH, and HCO + SH ⁺ ) to help rationalize previous observational results. Methods . We first explored the thermodynamic feasibility of the aforementioned reactions using high-level double-hybrid B2PLYPD3∕aug-cc-pVTZ and CCSD(T)-F12∕cc-pVTZ-F12 computations. For the reaction HCS ⁺ + OH, found to be the most thermodynamically favorable, we characterized the stationary points on its corresponding potential energy surface (PES). In addition, we also used a composite approach to refine relative energies and employed the statistical rate theory and master equation simulations to estimate rate constants and branching ratios. Results . We show that HOCS ⁺ is preferentially formed through the reaction of HCS ⁺ with OH, providing a plausible chemical explanation for its interstellar presence and the non-detection of the low energy isomer. Nevertheless, while the branching ratio computed at a T ~ T _kin (G+0.693) = 70-140 K is qualitatively consistent with the observations, its value is two orders of magnitude larger than the derived HOCS ⁺ /HSCO ⁺ lower limit observational ratio (of ≥2.3). This suggests that if the upper limit of HSCO ⁺ is close to the real abundance, additional formation pathways may also play a significant role in shaping the isomeric ratio. Conclusions . These results highlight that including all isomers in a given family, along with their isomer-preferential formation pathways, in astrochemical models, which are in many cases isomer-insensitive, is essential to understand their formation routes.

Background/Objectives: Understanding the stabilization mechanisms of amino acid conformations in different solvent environments is crucial for elucidating biomolecular interactions and crystallization processes. This study presents a comprehensive computational investigation of glycine, the simplest amino acid, in both its canonical and zwitterionic forms when interacting with dimethyl sulfoxide (DMSO) molecules. Methods: Using density functional theory (DFT) calculations at the B3LYP/6-311++G(d,p) level with empirical dispersion corrections, we examined the conformational landscape of glycine–DMSO clusters with one and two DMSO molecules, as well as implicit solvent calculations, and compared them with analogous water clusters. Results: Our results demonstrate that while a single water molecule is insufficient to stabilize the zwitterionic form of glycine, one DMSO molecule successfully stabilizes this form through specific interactions between the S=O and the methyl groups of DMSO and the NH₃⁺ and the oxoanion group of zwitterionic glycine, respectively. Topological analysis of the electron density using QTAIM and NCI methods reveals the nature of these interactions. When comparing the relative stability between canonical and zwitterionic forms, we found that two DMSO molecules significantly reduce the energy gap to approximately 12 kJ mol⁻¹, suggesting that increasing DMSO coordination could potentially invert this stability. Implicit solvent calculations indicate that in pure DMSO medium, the zwitterionic form becomes more stable below 150 K, while remaining less stable at room temperature, contrasting with aqueous environments where the zwitterionic form predominates. Conclusions: These findings provide valuable insights into DMSO’s unique role in biomolecular stabilization and have implications for protein crystallization protocols where DMSO is commonly used as a co-solvent.

Phosphorus is a crucial biogenic element, yet its astrochemical role remains poorly understood due to its low cosmic abundance and the limited number of detected P-containing molecules in the interstellar medium. Given its significance for prebiotic chemistry, PCO-bearing molecules, such as the phosphorus analogs of isocyanates, are promising candidates for laboratory and interstellar studies. Herein, we present a comprehensive theoretical study on the isomeric landscape of the C ₂ H ₃ PO system, identifying and characterizing 24 low-lying isomers through high-level quantum chemical calculations. The study employs double-hybrid DFT and coupled-cluster methods to refine energy values and structural parameters, while topological analysis of electronic density characterizes chemical bonding. Vinylphosphinidene oxide (CH ₂ CHPO) emerges as the most stable isomer, followed by methylphosphaketene (CH ₃ PCO), with oxygen-bound structures playing a crucial role in stability. Comparisons with the C ₂ H ₃ NO system reveal structural parallels, reinforcing the importance of oxygen-bound species. Cyclic structures were also explored, with three- and four-membered P- and O-heterocycles identified, although they are generally less stable than open-chain isomers. These results provide insights into the chemical behavior and stability of C ₂ H ₃ PO isomers, which could help future spectroscopic studies and detection efforts in the interstellar medium.

The investigation of metal-containing interstellar molecules stands as a prolific field for current astrochemical research. However, the search for many of these systems in the interstellar medium has remained inaccessible to date due to the lack of preliminary spectroscopic data. In this context, pioneering theoretical studies have inspired quantum chemists to study new appealing candidates to enable their subsequent search in space. The aim of this study is to provide high-level theoretical spectroscopic signatures of the tetratomic system [Na, N, C, O]. We have performed a thorough exploration of its potential energy surface employing different state-of-the-art quantum chemical methods and nine different species have been characterized. Moreover, we have evaluated the stability of the most stable isomers against dissociation and explored their main isomerization processes. We therefore suggest sodium isocyanate (NaNCO,¹Σ) and sodium cyanate, (NaOCN, ¹Σ) as the most relevant candidates for laboratory and interstellar detection. To aid in their eventual spectral search by means of rotational spectroscopy, we report a complete set of the required spectroscopic parameters including the nuclear quadrupole coupling constants, which are needed to interpret their complex hyperfine structure. NaNCO and NaOCN present exceptionally high values of the electric dipole moment (11.4 and 13.6 Debyes, respectively at the CCSD(T,rw)/aug-cc-pVTZ level), which strongly support to perform an eventual radio astronomical search. Furthermore, both isomers exhibit rather small vibrational frequencies, which indicates that these species are certainly floppy molecules.

Herein, we report a computational investigation of the binding affinity of dexamethasone, betamethasone, chloroquine and hydroxychloroquine to SARS-CoV-2 main protease using molecular and quantum mechanics as well as molecular docking methodologies. We aim to provide information on the anti-COVID-19 mechanism of the abovementioned potential drugs against SARS-CoV-2 coronavirus. Hence, the 6w63 structure of the SARS-CoV-2 main protease was selected as potential target site for the docking analysis. The study includes an initial conformational analysis of dexamethasone, betamethasone, chloroquine and hydroxychloroquine. For the most stable conformers, a spectroscopic analysis has been carried out. In addition, global and local reactivity indexes have been calculated to predict the chemical reactivity of these molecules. The molecular docking results indicate that dexamethasone and betamethasone have a higher affinity than chloroquine and hydroxychloroquine for their theoretical 6w63 target. Additionally, dexamethasone and betamethasone show a hydrogen bond with the His41 residue of the 6w63 protein, while the interaction between chloroquine and hydroxychloroquine with this amino acid is weak. Thus, we confirm the importance of His41 amino acid as a target to inhibit the SARS-CoV-2 Mpro activity.

Metal cyanides and isocyanides play a relevant role in the metal chemistry of the carbon-rich circumstellar envelope IRC+10216. It is thought that hydrometal cyanides/isocyanides could also be present in these environments; in fact, HMgNC has been detected in the same source that MgCN, MgNC, and AlNC. The aim of this work is to provide information about hydroaluminum cyanide/isocyanide. For this goal, a comprehensive analysis of the doublet and quartet potential energy surfaces of the [Al, C, H, N] system has been carried out. Different quantum chemistry methodologies from density functional theory to ab initio have been employed. For the [Al, C, H, N] isomers, the stability against dissociation and their interconversion processes have been analyzed. Our results show that the most relevant isomers from an experimental point of view are HAlCN and HAlNC. HAlNC has been found to be the most stable isomer followed by HAlCN, which is located at 1.59 kcal mol⁻¹ (0.0689 eV) at the composite level. The interconversion process between HAlCN and HAlNC presents an energy barrier of 10.0 kcal mol⁻¹ (5032 K) that makes this process not viable in the interstellar medium. We provide a complete set of relevant spectroscopic parameters for rotational spectroscopy for both HAlCN and HAlNC isomers using state-of-the-art quantum chemical computations, mandatory to guide an eventual laboratory or interstellar detection. Moreover, both isomers present sizable μ _a dipole moment components (3.7 and 3.3 D, respectively), which are large enough to enable a characterization by means of rotational spectroscopy, further increasing their interest as interstellar candidates.

Context. Cyanoacetamide is a –CN bearing molecule that is also an amide derivative target molecule in the interstellar medium. Aims. The aim of our investigation is to analyze the feasibility of a plausible formation process of protonated cyanoacetamide under interstellar conditions and to provide direct experimental frequencies of the ground vibrational state of the neutral form in the microwave region in order to enable its eventual identification in the interstellar medium. Methods. We used high-level theoretical computations to study the formation process of protonated cyanoacetamide. Furthermore, we employed a high-resolution laser-ablation molecular beam Fourier transform spectroscopic technique to measure the frequencies of the neutral form. Results. We report the first rotational characterization of cyanoacetamide, and a precise set of the relevant rotational spectroscopic constants have been determined as a first step to identifying the molecule in the interstellar medium. We fully explored the potential energy surface to study a gas-phase reaction on the formation process of protonated cyanoacetamide. We found that an exothermic process with no net activation barrier is initiated by the high-energy isomer of protonated hydroxylamine, which leads to protonated cyanoacetamide.

Recently, the first Ca-bearing molecule discovered in space, calcium isocyanide, CaNC, has been detected in the IRC+10216 circumstellar envelope. Related to CaNC are closed-shell stable molecules of [C, Ca, H, N] composition. One of the isomers with this composition is hydrocalcium isocyanide, HCaNC, which belongs to the hydrometal isocyanide/cyanide group of compounds, among which hydromagnesium isocyanide, HMgNC, is, to date, the only one detected in space. In this work, we have performed a study of the [C, Ca, H, N] isomers that are systems of possible interstellar interest by using quantum theoretical methodologies. The analysis of the relative energies predicts three low-lying isomers: c-HCa–NC (¹A′), hydrocalcium isocyanide, HCaNC (¹Σ), and hydrocalcium cyanide, HCaCN (¹Σ). At the composite level, HCaNC (¹Σ) and HCaCN (¹Σ) were located 0.87 and 4.84 kcal mol⁻¹, respectively, above the c-HCa–NC (¹Σ) isomer. Interconversion processes between these isomers have been studied to analyze their stability. Isomer HCaNC is characterized as a transition state and thus directly isomerizes to the c-HCa–NC minimum. The isomerization process of HCaCN → c-HCa–NC shows a small barrier of about 0.76 kcal mol⁻¹ (∼382 K) above HCaCN, at the highest level of theory employed in this work, suggesting that HCaCN could easily isomerize into the most stable isomer, c-HCa–NC. Our results predict two low-lying isomers, namely, c-HCa–NC (¹A′) and hydrocalcium cyanide, HCaCN (¹Σ), as possible candidates for experimental or radioastronomical detection. For these isomers, we provide predictions for their vibrational and rotational spectroscopic parameters that could aid in their eventual characterization in the laboratory or in space.

The metallic cyanoacetylides LiC₃N, NaC₃N, MgC₃N, and CaC₃N have been investigated by combined spectroscopy measurements and theoretical calculations. The theoretical calculations predict for the four species that the linear isomer with the formula MCCCN (M = Li, Na, Mg, and Ca) is the most stable one. We used laser ablation molecular beam Fourier transform microwave (FTMW) spectroscopy to synthesize these species by the reaction of metal vapors, produced by laser ablation, and 3-bromo-2-propynenitrile (BrCCCN). Pure rotational spectra were observed by FTMW spectroscopy in the 2–18 GHz frequency region only for LiCCCN and NaCCCN, while no spectral signatures for MgCCCN and CaCCCN could be detected. Finally, we have searched for LiCCCN and NaCCCN species toward the carbon-rich evolved star IRC +10 216, but only upper limits to their abundances have been obtained.