Anchoring the Gas-Phase Acidity Scale from Hydrogen Sulfide to Pyrrole. Experimental Bond Dissociation Energies of Nitromethane, Ethanethiol, and Cyclopentadiene

Resonant electron capture by polycyclic aromatic hydrocarbon molecules: Effects of aza-substitution

Resonant electron capture by aza and diaza derivatives of phenanthrene (7,8-benzoquinoline and 1,10-phenanthroline) and anthracene (acridine and phenazine) at incident free electron energies (Ee) in the range of 0-15 eV was studied. All compounds except 7,8-benzoquinoline form long-lived molecular ions (M-) at thermal electron energies (Ee ∼ 0 eV). Acridine and phenazine also form such ions at epithermal electron energies up to Ee = 1.5-2.5 eV. The lifetimes (τa) of M- with respect to electron autodetachment are proportional to the extent of aza-substitution and increase on going from molecules with bent geometry of the fused rings (azaphenanthrenes) to linear isomers (azaanthracenes). These regularities are due to an increase in the adiabatic electron affinities (EAa) of the molecules. The EAa values of the molecules under study were comprehensively assessed based on a comparative analysis of the measured τa values using the Rice-Ramsperger-Kassel-Marcus theory, the electronic structure analysis using the molecular orbital approach, as well as the density functional calculations of the total energy differences between the molecules and anions. The only fragmentation channel of M- ions from the compounds studied is abstraction of hydrogen atoms. When studying [M-H]- ions, electron autodetachment processes were observed, the τa values were measured, and the appearance energies were determined. A comparative analysis of the gas-phase acidity of the molecules and the EAa values of the [M-H]· radicals revealed their proportionality to the EAa values of the parent molecules.

Proton Transfer in Nitromethane-Ammonia Clusters under VUV Single-Photon Ionization Explored by Infrared Spectroscopy and Theoretical Calculations

It is known that the acidity and reactivity of the CH bond can be enhanced after ionization. Also, this property plays a pivotal role in proton transfer reaction and in the formation of new molecules. Herein, infrared spectroscopy and high-precision quantum chemical calculations are used to study the neutral and cationic clusters of nitromethane-ammonia (CH₃NO₂-NH₃). It is found that in the neutral cluster, CH₃NO₂ and NH₃ are mainly bonded by three intermolecular hydrogen bonds, in which electrostatic contribution plays a major role. After vacuum ultraviolet (VUV) single-photon ionization of CH₃NO₂-NH₃, the positive charge redistributes from the ionized nitrogen atom of NH₃ to the CH₃NO₂ molecule immediately. Then, the proton of CH₃NO₂ transfers to NH₃ to form a proton-transferred type structure CH₂NO₂-NH₄⁺, without any effective energy barrier, due to the positive hyperconjugation of cationic nitromethane. A closed loop of positive charge transfer takes place in the CH₃NO₂-NH₃ cluster after VUV ionization. The present work demonstrates that both the proton transfer reaction and charge transfer process have occurred in the ionized CH₃NO₂-NH₃ cluster. Moreover, it is found that the proton transfer reaction is a result of the highly acidic CH bond caused by hyperconjugation between the σ (CH) bond and π orbital.

Fragmentation and slow autoneutralization of isolated negative molecular ions of phthalocyanine and tetraphenylporphyrin

Macrocyclic tetrapyrrolic compounds, such as naturally occurring or artificial porphyrins and phthalocyanines, have unique and highly attractive properties for applications in medicine and technology. The interaction of free-base phthalocyanine (H₂Pc) and tetraphenylporphyrin (H₂TPP) molecules with low-energy (0-15 eV) electrons was studied in vacuo by means of negative ion resonant electron capture mass spectrometry. Close similarities in formation and decay of negative ions of these compounds were revealed. Efficient formation of long-lived molecular negative ions (MNIs) was observed in the incident electron energy range of 0-8 eV, unprecedentedly wide for organic compounds and comparable to the range characteristic to carbon atomic clusters, fullerenes. Experiments testify to the strong persistence of MNIs of both compounds to dissociative decay, isomerization, and electron autodetachment. Lifetimes of MNIs as a function of incident electron energy were measured and it was concluded that the isolated anions may retain additional electrons in a time scale of up to hundreds of seconds at standard temperature due to the high adiabatic electron affinity of these large molecules. For the representatives of dyes and photochromic compounds comprehensively studied in terms of interaction with light, the present work highlights yet another unique property of these molecules, namely the capability to attach and durably retain an additional electron of low, pre-ionization energy.

Preferred Hydrogen-Bonding Partners of Cysteine: Implications for Regulating Cys Functions

The hydrogen-bonding interactions of cysteine, which can serve as a hydrogen-bond donor and/or acceptor, play a central role in cysteine's diverse functional roles in proteins. They affect the balance between the neutral thiol (SH) or thiolate (S^-) and the charge distribution in the rate-limiting transition state of a reaction. Despite their importance, no study has determined the preferred hydrogen-bonding partners of cysteine serving as a hydrogen-bond donor or acceptor. By computing the free energy for displacing a peptide backbone hydrogen-bonded to cysteine with amino acid side chains in various protein environments, we have evaluated how the strength of the hydrogen bond to the cysteine thiol/thiolate depends on its hydrogen-bonding partner and its local environment. The predicted hydrogen-bonding partners preferred by cysteine are consistent with the hydrogen-bonding interactions made by cysteines in 9138 nonredundant X-ray structures. Our results suggest a mechanism to regulate the reactivity of cysteines and a strategy to design drugs based on the hydrogen-bonding preference of cysteine.