Gas-Phase reactions of NO2− with nitrobenzenes and quinones. Electron transfer, clusters and formation of phenoxide and quinoxide negative ions. Use of NO2 as a negative ion chemical ionization reagent

Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C-H Acids

The pKa of C-H acids is an important parameter in the fields of organic synthesis, drug discovery, and materials science. However, the prediction of pKa is still a great challenge due to the limit of experimental data and the lack of chemical insight. Here, a new model for predicting the pKa values of C-H acids is proposed on the basis of graph neural networks (GNNs) and data augmentation. A message passing unit (MPU) was used to extract the topological and target-related information from the molecular graph data, and a readout layer was utilized to retrieve the information on the ionization site C atom. The retrieved information then was adopted to predict pKa by a fully connected network. Furthermore, to increase the diversity of the training data, a knowledge-infused data augmentation technique was established by replacing the H atoms in a molecule with substituents exhibiting different electronic effects. The MPU was pretrained with the augmented data. The efficacy of data augmentation was confirmed by visualizing the distribution of compounds with different substituents and by classifying compounds. The explainability of the model was studied by examining the change of pKa values when a specific atom was masked. This explainability was used to identify the key substituents for pKa. The model was evaluated on two data sets from the iBonD database. Dataset1 includes the experimental pKa values of C-H acids measured in DMSO, while dataset2 comprises the pKa values measured in water. The results show that the knowledge-infused data augmentation technique greatly improves the predictive accuracy of the model, especially when the number of samples is small.

Mechanism of [M + H]+ formation in photoionization mass spectrometry

In this paper we examine the mechanism of [M + H]+ (henceforth MH+) formation by direct photoionization. Based on comparisons of the relative abundance of M+ and MH+ ions for photoionization of a variety of compounds M as vapor in air versus in different solvents, we conclude that the mechanism is M + hnu --> M+ + e- followed by the reaction M+ + S --> MH+ + S(-H). The principal evidence for molecular radical ion formation M+ followed by hydrogen atom abstraction from protic solvent S are: (1) Nearly exclusive formation of M+ for headspace ionization of M in air, (2) significant relative abundance of MH+ in the presence of protic solvents (e.g., CH3OH, H2O, c-hexane), but not in aprotic solvents (e.g., CCl4-), (3) observation of induced equilibrium oscillations in the abundance of MH+ and M+, and (4) correlation of the ratio of MH+/M+ to reaction length in the photoionization source. Thermodynamic models are advanced that explain the qualitative dependence of the MH+/M+ equilibrium ratio on the properties of solvent S and analyte M. Though the hydrogen abstraction reaction is endothermic in most cases, it is shown that the equilibrium constant is still expected to be much greater than unity in most of the cases studied due to the very slow reverse reaction involving the very low abundant MH+ and S(-H) species.

Regioselectivity of the oxygen addition-induced dechlorination of PCBS and DDT metabolites in electron capture mass spectrometry

The electron capture mass spectra of 28 (35)Cl-labeled polychlorinated biphenyls (PCBs) and 4 (37)Cl-labeled 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) metabolites were obtained by using a 20% oxygen in methane mixture as the reagent gas. The degree of regioselectivity of the PCB oxygen addition-induced dechlorination reaction was determined by measurement of the residual amount of label in the M-19 ions produced by addition of O2 and subsequent loss of OCl from the molecule. Chlorine was lost in a random manner from the PCBs, contrary to the dechlorination reaction observed when methane alone was used. For the DDT metabolites, many dechlorination reactions were observed in addition to the one that generated the M-19 ions. Loss of Cl, loss of Cl2, and addition of O2 with the loss of one or two HCl molecules also were seen. These various dechlorination reactions involved only the aliphatic chlorines. Addition of O2 followed by loss of Cl at the beta position of 2,2-bis(4-(37)Cl-chlorophenyl)-1-chloroethylene and 2,2-bis(4-(37)Cl-chlorophenyl)-1,1-dichloroethylene may be due to the ability of the diphenyl methane moiety to stabilize the intermediates. Formation of an ion that corresponds to 4,4'-dichlorobenzophenone also was observed for three of these labeled DDT metabolites.

Isomer differentiation by charge inversion tandem mass spectrometry: an investigation into the structure of the ionic products from an SN(ANRORC) eeaction

Negative ion fast atom bombardment and negative ion chemical ionization tandem mass spectrometry combined with charge inversion reactions are used to confirm that 2-chloro-5nitropyridine reacts with the hydroxide ion by an SN(ANRORC) mechanism in solution to form a ring-opened C5H3N2O 3 (-) anion that has the structure of the (M-H)(-) anion of 2-nitro-4-cyano-2-butenal. The addition of excess hydroxide ion forms the expected 2-oxy5-nitropyridine anion. In the gas phase the same reaction forms only the 2-oxy-5-nitropyridine anion. High energy charge inversion is shown to be an excellent means of differentiating between these isomeric negative ions.