Structure and Spectroscopic Insights for CH3PCO Isomers: A High-Level Quantum Chemical Study.

The exploration of phosphorus-bearing species stands as a prolific field in current astrochemical research, particularly within the context of prebiotic chemistry. Herein, we have employed high-level quantum chemistry methodologies to predict the structure and spectroscopic properties of isomers composed of a methyl group and three P, C, and O atoms. We have computed relative and dissociation energies, as well as rotational, rovibrational, and torsional parameters using the B2PLYPD3 functional and the explicitly correlated coupled cluster CCSD(T)-F12b method. Based upon our study, all the isomers exhibit a bent heavy atom skeleton with CH3PCO being the most stable structure, regardless of the level theory employed. Following in energy, we found four high-energy isomers, namely, CH3OCP, CH3CPO, CH3COP, and CH3OPC. The computed adiabatic dissociation energies support the stability of all [CH3, P, C, O] isomers against fragmentation into CH3 and [P, C, O]. Torsional barrier heights associated with the methyl internal rotation for each structure have been computed to evaluate the occurrence of possible A-E splittings in the rotational spectra. For the most stable isomer, CH3PCO, we found a V3 barrier of 82 cm-1, which is slightly larger than that obtained experimentally for the N-counterpart, CH3NCO, yet still very low. Therefore, the analysis of its rotational spectrum can be anticipated as a challenging task owing to the effect of the CH3 internal rotation. The complete set of spectroscopic constants and transition frequencies reported here for the most stable isomer, CH3PCO, is intended to facilitate eventual laboratory searches.

Computational study on the affinity of potential drugs to SARS-CoV-2 main protease.

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.

Infrared-Assisted Synthesis of Prebiotic Glycine.

A novel approach has been developed to synthesize complex organic molecules (COMs) relevant to prebiotic chemistry, using infrared (IR) radiation to trigger the reaction. An original laboratory reactor working at low gas density and using IR irradiation was developed. In this way, glycine, the simplest brick of life, has been synthesized by assisting ion-molecule reaction with IR laser light. The ion-molecule complex constituted by acetic acid and hydroxylamine was formed in a mass spectrometer reactor and then irradiated with IR photons. As photoproducts, we obtained both glycine structures and some of its isomers. Anharmonic vibrational frequency calculations and fragmentation dynamics simulations allow for a better interpretation of the experimental data. This novel approach can be now extended to study other new synthetic pathways responsible for the formation of further COMs also with potential prebiotic relevance.

Alkaline and Alkaline-earth Cyanoacetylides: A Combined Theoretical and Rotational Spectroscopic Investigation.

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 formula MCCCN (M= Li, Na, Mg and Ca) is the most stable one. We used the laser ablation molecular beam Fourier transform microwave spectroscopy to synthesize these species by the reaction of metal vapors, produced by laser ablation, and the 3-bromo-2-propynenitrile (BrCCCN). The pure rotational spectra were observed by Fourier transform microwave 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 towards the carbon-rich evolved star IRC + 10216 but only upper limits to their abundances have been obtained.

Intrinsic Antioxidant Potential of the Aminoindole Structure: A Computational Kinetics Study of Tryptamine.

A computational kinetics study of the antioxidant activity of tryptamine toward HO• and HOO• radicals in water at 298 K has been carried out. Density functional methods have been employed for the quantum chemical calculations, and the conventional transition state theory was used for rate constant evaluation. Different mechanisms have been considered: radical adduct formation (RAF), single electron transfer (SET), and hydrogen atom transfer (HAT). For the reaction of tryptamine with the hydroxyl radical, nearly all channels are diffusion-controlled, and the overall rate constant is very high, 6.29 × 1010 M-1 s-1. The RAF mechanism has a branching ratio of 55%, followed by the HAT mechanism (31%), whereas the SET mechanism accounts just for 13% of the products. The less hindered carbon atom neighboring to the nitrogen of the indole ring seems to be the preferred site for the RAF mechanism, with a branching ratio of 16%. The overall rate constant for the reaction of tryptamine with the HOO• radical is 3.71 × 104 M-1 s-1, suggesting that it could be a competitive process with other reactions of hydroperoxyl radicals in biological environments. For this reaction only the HAT mechanism seems viable. Furthermore, only two centers may contribute to the HAT mechanism, the nitrogen atom of the indole ring and a carbon atom of the aminoethyl chain, the former accounting for more than 91% of the total products. Our results suggest that tryptamine could have a noticeable scavenging activity toward radicals, and that this activity is mainly related to the nitrogen atom of the indole ring, thus showing the relevance of their behavior in the study of aminoindoles.

Structural Trends in Monoboronyl Compounds: Analysis of the Interaction of Second-Row Elements with BO.

A theoretical study of the monoboronyl compounds of second-row elements, [XBO] (X = Na, Si, P, S, Cl), has been carried out. It is observed that the preference for the XBO arrangement is higher when moving to the right of the period. In the case of sodium monoboronyl three minima were characterized, all lying rather close in energy: linear NaBO, linear NaOB, and an L-shaped structure. Linear NaBO and the L-shaped structure are nearly isoenergetic, whereas linear NaOB is located 2.11 kcal/mol above linear NaBO. The barrier for the conversion of the L-shaped structure into linear NaBO is about 5.1 kcal/mol, suggesting that both species could be potential targets for experimental detection. For silicon monoboronyl, two minima, linear SiBO and linear SiOB, are found, the latter lying about 13 kcal/mol above SiBO. The barrier for the isomerization of SiOB into SiBO is estimated to be 11.4 kcal/mol. For phosphorus, sulfur, and chlorine monoboronyls the linear XBO isomer is clearly the most stable one, and the barriers for the conversion into XOB species are relatively high, suggesting that quite likely the linear XBO isomer should be the main experimental target. All studied monoboronyls are relatively stable, with dissociation energies increasing from left to right of the second-row (69.8 kcal/mol for NaBO and 118.98 kcal/mol for ClBO). An analysis of the bonding for second-row monoboronyls has been carried out, emphasizing the different characteristics of the X-B and X-O bonds along the second row.

Gas Phase Synthesis of Protonated Glycine by Chemical Dynamics Simulations.

In the present work, we investigated the reaction dynamics that will possibly lead to the formation of protonated glycine by an ion-molecule collision. In particular, two analogous reactions were studied: NH3OH+ + CH3COOH and NH2OH2+ + CH3COOH that were suggested by previous experiments to be able to form protonated glycine loosing a neutral water molecule. Chemical dynamics simulations show that both reactants can form a molecule with the mass of the protonated glycine but with different structures, if some translational energy is given to the system. The reaction mechanisms for the most relevant product isomers are discussed as well as the role of collision energy in determining reaction products. Finally, in comparing collision dynamics at room and at very low initial internal temperature of the reactants, the same behavior was obtained for forming the protonated glycine isomers products. This supports the use of standard gas phase ion-chemistry setups to study collision-induced reactivity as a model for astrophysical cold conditions, when some relative translation energy is given to the system.

Metallic monoboronyl compounds: Prediction of their structure and comparison with the cyanide analogues.

A theoretical study of monoboronyls of different metals has been carried out. We have chosen Mg as representative of s-block elements, Al for the p-block, and Group 11 metals (Cu, Ag, and Au) for the d-block. Different behaviors are observed: bonding through the oxygen atom is preferred in the case of Al, for all Group 11 monoboronyls bonding through the boron atom prevails and both interactions give rise to almost isoenergetic compounds in the case of Mg. Predictions for the spectroscopic parameters relevant for rotational and vibrational spectroscopy of the different competitive species are provided. Al and Group 11 boronyls have relatively high dissociation energies, whereas Mg boronyl has moderate dissociation energy. The molecular structure of metal boronyls has been rationalized through an analysis of the bonding. The similarities and differences between metal boronyls and their isoelectronic cyanide analogues have been discussed. © 2017 Wiley Periodicals, Inc.

Metallic cyanoacetylides of copper, silver and gold: generation and structural characterization.

The metallic cyanoacetylides CuCCCN, AgCCCN, and AuCCCN have been synthesized in the throat of a pulsed supersonic expansion by reaction of metal vapors, produced by laser ablation, and BrCCCN. Their pure rotational spectra in the (X1Σ+) electronic ground state were observed by Fourier transform microwave spectroscopy in the 2-10 GHz frequency region. Importantly, the rotational spectroscopy constants determined from the analysis of the rotational spectra clearly established the existence of metal-CCCN arrangements for all the mentioned cyanoacetylides. A study of the chemical bonding by means of a topological analysis of the electron density helps to understand the preference for metal-C bonding over metal-N bonding.

Molecular Structure and Bonding in Plutonium Carbides: A Theoretical Study of PuC3.

The most relevant species of plutonium tricarbide were characterized using theoretical methods. The global minimum is predicted to be a fan structure where the plutonium atom is bonded to a quasi-linear C3 unit. A rhombic isomer, shown to be a bicyclic species with transannular C-C bonding, lies about 39 kJ/mol above the fan isomer. A linear PuCCC isomer and a three-membered ring CPuC2 isomer were found to be higher in energy (150 and 195 kJ/mol, respectively, above the predicted global minimum). The possible processes for the formation of these species are discussed, and the IR spectra were predicted to help in possible experimental detection. The nature of the Pu-C interaction has been analyzed in terms of a topological analysis of the electronic density, showing that Pu-C bonding is essentially ionic with a certain degree of covalent character.

Structure and spectroscopic properties of neutral and cationic tetratomic [C,H,N,Zn] isomers: A theoretical study.

The structure and spectroscopic parameters of the most relevant [C,H,N,Zn] isomers have been studied employing high-level quantum chemical methods. For each isomer, we provide predictions for their molecular structure, thermodynamic stabilities as well as vibrational and rotational spectroscopic parameters which could eventually help in their experimental detection. In addition, we have carried out a detailed study of the bonding situations by means of a topological analysis of the electron density in the framework of the Bader's quantum theory of atoms in molecules. The analysis of the relative stabilities and spectroscopic parameters suggests two linear isomers of the neutral [C,H,N,Zn] composition, namely, cyanidehydridezinc HZnCN ((1)Σ) and hydrideisocyanidezinc HZnNC ((1)Σ), as possible candidates for experimental detections. For the cationic [C,H,N,Zn](+) composition, the most stable isomers are the ion-molecule complexes arising from the direct interaction of the zinc cation with either the nitrogen or carbon atom of either hydrogen cyanide or hydrogen isocyanide, namely, HCNZn(+) ((2)Σ) and HCNZn(+) ((2)Σ).

Generation and structural characterization of aluminum cyanoacetylide.

Combined spectroscopy measurements and theoretical calculations bring to light a first investigation of a metallic cyanoacetylide, AlC3N, using laser ablation molecular beam Fourier transform microwave spectroscopy. This molecule was synthesized in a supersonic expansion by the reaction of aluminum vapour with C3N, produced from solid aluminum rods and BrCCCN in a newly constructed ablation-heating nozzle device. A set of accurate rotational and (27)Al and (14)N nuclear quadrupole coupling constants have been determined from the analysis of the rotational spectrum and compared with those predicted in a high-level ab initio study, conducting to the assignment of the observed species to linear AlCCCN. We have searched for this species towards the carbon-rich evolved star IRC + 10216 but only an upper limit to its abundance has been obtained.

Halogen-abstraction reactions from chloromethane and bromomethane molecules by alkaline-earth monocations.

The reactions, in the gas phase, between alkali-earth monocations (Mg(+), Ca(+), Sr(+), Ba(+)) and CH3X (X = Cl, Br) have been theoretically studied. The stationary points on the potential energy surfaces were characterized at the Density Functional Theory level on the framework of the mPW1K functional with the QZVPP Ahlrichs's basis sets. A complementary kinetics study has also been performed using conventional/variational microcanonical transition state theory. In the reactions of Mg(+) with either chloro- or bromomethane the transition structure lies in energy clearly above the reactants rendering thermal activation of CH3Cl or CH3Br extremely improbable. The remaining reactions are exothermic and barrierless processes; thus carbon-halogen bonds in chloro- or bromomethane can be activated by calcium, strontium or barium monocations to obtain the metal halogen cation and the methyl radical. The Mulliken population analysis for the stationary points of the potential energy surfaces supports a "harpoon"-like mechanism for the halogen-atom abstraction processes. An analysis of the bonding situation for the stationary points on the potential energy surface has also been performed in the framework of the quantum theory of atoms in molecules.

Computational study of peptide bond formation in the gas phase through ion-molecule reactions.

A computational study of peptide bond formation from gas-phase ion-molecule reactions has been carried out. We have considered the reaction between protonated glycine and neutral glycine, as well as the reaction between two neutral glycine molecules for comparison purposes. Two different mechanisms, concerted and stepwise, were studied. Both mechanisms show significant energy barriers for the neutral reaction. The energy requirements for peptide bond formation are considerably reduced upon protonation of one of the glycine molecules. For the reaction between neutral glycine and N-protonated glycine the lowest energy barrier is observed for the concerted mechanism. For the reaction between neutral glycine and protonated glycine at carbonyl oxygen, the preferred mechanism is the stepwise one, with a relatively small energy barrier (23 kJ mol(-1) at 0 K) and leading to the lowest-lying protonated glycylglycine isomer. In the case that the reaction could be initiated by protonated glycine at hydroxyl oxygen the process would be barrier-free and clearly exothermic. In that case peptide bond formation could take place even under interstellar conditions if glycine is present in space.

Kinetics studies of the reactions of main fourth-period monocations (Ga+, Ge+, As+, and Se+) with methyl fluoride.

Thermodynamics and kinetics theoretical studies on the gas-phase reactions of fluoromethane with main fourth-period monocations (Ga(+), Ge(+), As(+), and Se(+)) have been carried out. Density functional theory (in particular mPW1K functional) was employed in the description of the potential energy surfaces, and refinement of the energies were done at the CCSD(T) level. The reaction rate constants were estimated using variational/conventional microcanonical transition state theory. From a thermodynamic viewpoint, the fluorine abstraction product is predicted for Ga(+) and Ge(+), whereas for As(+) and Se(+) the elimination product, MCH2(+) (M = As, Se) + HF, is the preferred one. Nevertheless, the most favorable channel for the reactions of CH3F with Ga(+) and Se(+) cations present a net activation barrier. In the case of Ga(+), the reaction proceeds via an addition channel forming the adduct complex, CH3FGa(+), whereas for Se(+) no reaction is found, in agreement with the experiments. The predicted reaction rate constants are in reasonable good agreement with the experimental values available. Apart from the harpoon-like mechanism, our results suggest that an oxidative addition mechanism seems to play a relevant role.

Molecular structure of uranium carbides: isomers of UC3.

In this article, the most relevant isomers of uranium tricarbide are studied through quantum chemical methods. It is found that the most stable isomer has a fan geometry in which the uranium atom is bonded to a quasilinear C3 unit. Both, a rhombic and a ring CU(C2) structures are found about 104-125 kJ/mol higher in energy. Other possible isomers including linear geometries are located even higher. For each structure, we provide predictions for those molecular properties (vibrational frequencies, IR intensities, dipole moments) that could eventually help in their experimental detection. We also discuss the possible routes for the formation of the different UC3 isomers as well as the bonding situation by means of a topological analysis of the electron density.

Reactivity of first-row transition metal monocations (Sc+, Ti+, V+, Zn+) with methyl fluoride: a computational study.

The gas-phase reactivity of methyl fluoride with selected first-row transition metal monocations (Sc(+), Ti(+), V(+), and Zn(+)) has been theoretically investigated. Our thermochemical and kinetics study shows that early transition-metal cations exhibit a much more active chemistry than the latest transition metal monocation Zn(+). The strong C-F bond in methyl fluorine can be activated by scandium, titanium, and vanadium monocations yielding the metal fluorine cation, MF(+). However, the rate efficiencies vary dramatically along the period 0.73 (Sc), 0.91 (Ti), and 0.028 (V) in agreement with the experimental observation. The kinetics results show the relative importance of the entrance and exit channels, apart from the "inner" bottleneck, to control the global rate constant of these reactions. At the mPW1K/QZVPP level our computed kglobal (at 295 K), 1.99 × 10(-9) cm(3) molecule(-1) s(-1) (Sc(+)), 1.29 × 10(-9) cm(3) molecule(-1) s(-1) (Ti(+)), and 3.46 × 10(-10) cm(3) molecule(-1) s(-1) (V(+)) are in good agreement with the experimental data at the same temperature. For the reaction of Zn(+) and CH3F our predicted value for kouter, at 295 K, 3.79 × 10(-9) cm(3) molecule(-1) s(-1), is in accordance with the capture rate constant. Our study suggests that consideration of the lowest excited states for Ti(+) and V(+) is mandatory to reach agreement between calculations and experimental measurements.

Small carbides of third-row main group elements: structure and bonding in C3X compounds (X = K-Br).

The molecular structures of third-row main group tricarbides C(3)X (X = K-Br) have been studied by quantum chemical methods. It is found that less electronegative elements (K, Ca, Ga, Ge) favor either fan or rhombic structures (resulting from side interactions with either linear or triangular C(3) units), whereas the more electronegative elements (As, Se, Br) favor linear or three-membered ring structures (resulting from σ-type interactions with either linear or triangular C(3) units). The predicted global minima are of fan type for C(3)K, rhombic for C(3)Ca, C(3)Ga, and C(3)Ge, linear for C(3)As and C(3)Se, and a three-membered ring for C(3)Br. In order to aid in their possible experimental identification the molecular geometries, vibrational frequencies, IR intensities, and dipole moments have been provided. The nature of the interactions has been characterized through an analysis of the electronic charge density. In addition, the relative stability of the different isomers has been also rationalized in terms of an energy decomposition analysis.

On the molecular structure of uranium dicarbide: T-shape versus linear isomers.

A theoretical study of the molecular structure of uranium dicarbide has been carried out employing DFT, coupled cluster, and multiconfigurational methods. A triangular species, corresponding to a (5)A(2) electronic state, has been found to be the most stable UC(2) species. A triplet linear CUC species, which has been observed in recent infrared spectroscopy experiments, lies much higher in energy. A topological analysis of the electronic density has also been carried out. The triangular species is shown to be in fact a T-shape structure with a U-C interaction which can be considered to be a closed-shell interaction.

Computational study of the reaction of P+ with acetylene: does spin-crossing play a significant role?

A computational study of the reaction of P(+)((3)P) with acetylene has been carried out. The only exothermic products correlating with the reactants are PCCH(+)((2)Π) + H((2)S). Two different pathways leading to these products that are apparently barrier-free have been found. Both pathways involve isomerization into open-chain intermediates followed by direct elimination of a hydrogen atom. The possibility of spin-crossing has been considered because the species on the singlet surface are considerably more stable than those on the triplet one. On the singlet surface, there are other possible channels for the reaction, namely, cyclic PC(2)H(+)((2)A') + H((2)S) and CCP(+)((1)Σ) + H(2) ((1)Σ(g)(+)). A computational kinetic study shows that, in agreement with the experimental evidence, the major products are PCCH(+)((2)Π) + H((2)S) at all temperatures. Only at very high temperatures is CCP(+)((1)Σ) + H(2) ((1)Σ(g)(+)) formed in non-negligible amounts. Therefore, only PCCH(+) should be formed in the interstellar medium.