Enthalpy Barriers for Asymmetric SN2 Alkyl Cation Transfer Reactions between Neutral and Protonated Alcohols

TSNet: predicting transition state structures with tensor field networks and transfer learning

Transition states are among the most important molecular structures in chemistry, critical to a variety of fields such as reaction kinetics, catalyst design, and the study of protein function. However, transition states are very unstable, typically only existing on the order of femtoseconds. The transient nature of these structures makes them incredibly difficult to study, thus chemists often turn to simulation. Unfortunately, computer simulation of transition states is also challenging, as they are first-order saddle points on highly dimensional mathematical surfaces. Locating these points is resource intensive and unreliable, resulting in methods which can take very long to converge. Machine learning, a relatively novel class of algorithm, has led to radical changes in several fields of computation, including computer vision and natural language processing due to its aptitude for highly accurate function approximation. While machine learning has been widely adopted throughout computational chemistry as a lightweight alternative to costly quantum mechanical calculations, little research has been pursued which utilizes machine learning for transition state structure optimization. In this paper TSNet is presented, a new end-to-end Siamese message-passing neural network based on tensor field networks shown to be capable of predicting transition state geometries. Also presented is a small dataset of S_N2 reactions which includes transition state structures - the first of its kind built specifically for machine learning. Finally, transfer learning, a low data remedial technique, is explored to understand the viability of pretraining TSNet on widely available chemical data may provide better starting points during training, faster convergence, and lower loss values. Aspects of the new dataset and model shall be discussed in detail, along with motivations and general outlook on the future of machine learning-based transition state prediction.

3-D aluminum nanostructure with microhole array synthesized by femtosecond laser radiation for enhanced light extinction

This article presents 3-D aluminum micro-nanostructures for enhanced light absorption. Periodic microhole arrays were created by firing a train of femtosecond laser pulses at megahertz pulse frequency onto the surface of an aluminum target at ambient conditions. The laser trains ablated the target surface and created microholes leading to the generation of deposited nanostructures inside and around the microholes. These micro-nanostructures showed enhanced light absorption, which is attributed to surface plasmonics induced by the generation of both nano- and microstructures. These micro-nanostructures may be promising for solar cell applications.

From the mobile proton to wandering hydride ion: mechanistic aspects of gas-phase ion chemistry

Structural characterization of molecular species by mass spectrometry supposes the knowledge of the type of ions generated and the mechanism by which they dissociate. In this context, a need for a rationalization of electrospray ionization(+)(-) mass spectra of small molecules has been recently expressed. Similarly, at the other end of the mass scale, efforts are currently made to interpret the major fragmentation processes of protonated and deprotonated peptides and their reduced forms produced in electron capture or electron transfer experiments. Most fragmentation processes of molecular and pseudo-molecular ions produced in the ion source of a mass spectrometer may be described by a combination of several key mechanistic steps: simple bond dissociation, formation of ion-neutral complex intermediates, hydrogen atom, hydride ion or proton migrations and nucleophilic attack. Selected crucial aspects of these elementary reactions, occurring inside positively charged ions, will be recalled and illustrated by examples taken in recent mass spectrometry literature. Emphasis will be given on the protonation process and its consequence in terms of structure and energetic.

Magnetism in gold nanoparticles

Gold nanoparticles currently elicit an intense and very broad research activity because of their peculiar properties. Be it in catalysis, optics, electronics, sensing or theranostics, new applications are found daily for these materials. Approximately a decade ago a report was published with magnetometry data showing that gold nanoparticles, most surprisingly, could also be magnetic, with features that the usual rules of magnetism were unable to explain. Many ensuing experimental papers confirmed this observation, although the reported magnetic behaviours showed a great variability, for unclear reasons. In this review, most of the experimental facts pertaining to "magnetic gold" are summarized. The various theories put forth for explaining this unexpected magnetism are presented and discussed. We show that despite much effort, a satisfying explanation is still lacking and that the field of hypotheses should perhaps be widened.

Structures, energetics, and dynamics of gas phase ions studied by FTICR and HPMS

Both Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and high-pressure mass spectrometry (HPMS) are very powerful tools in the field of gas phase ion chemistry. Many experimental method developments based on FTICR-MS and HPMS are summarized, including the coupling of a high-pressure external ion source to a FTICR mass spectrometer, blackbody infrared radiative dissociation (BIRD), coupling laser desorption ionization with HPMS, infrared multiple photon dissociation (IRMPD), radiative association and bimolecular routes to gas phase cluster ion formation. An abundance of thermochemical data, such as proton affinities, gas phase acidities, methyl cation affinities and metal cation affinities, have been obtained. Some of these data are the basis of the standard data listed in the NIST thermochemical databases. Ion-molecule interactions, energetics, reactivities, and structures of molecules have been extensively investigated using the methods developed based on HPMS and FTICR mass spectrometric techniques.

Gas-phase basicities of polyfunctional molecules. Part 1: Theory and methods

The experimental and theoretical methods of determination of gas-phase basicities, proton affinities and protonation entropies are presented in a tutorial form. Particularities and limitations of these methods when applied to polyfunctional molecules are emphasized. Structural effects during the protonation process in the gas-phase and their consequences on the corresponding thermochemistry are reviewed and classified. The role of the nature of the basic site (protonation on non-bonded electron pairs or on pi-electron systems) and of substituent effects (electrostatic and resonance) are first examined. Then, linear correlations observed between gas-phase basicities and ionization energies or substituent constants are recalled. Hydrogen bonding plays a special part in proton transfer reactions and in the protonation characteristics of polyfunctional molecules. A survey of the main properties of intermolecular and intramolecular hydrogen bonding in both neutral and protonated species is proposed. Consequences on the protonation thermochemistry, particularly of polyfunctional molecules are discussed. Finally, chemical reactions which may potentially occur inside protonated clusters during the measurement of gas-phase basicities or inside a protonated polyfunctional molecule is examined. Examples of bond dissociations with hydride or alkyl migrations, proton transport catalysis, tautomerization, cyclization, ring opening and nucleophilic substitution are presented to illustrate the potentially complex chemistry that may accompany the protonation of polyfunctional molecules.

Structures of Heterogeneous Proton-Bond Dimers with a High Dipole Moment Monomer: Covalent vs Electrostatic Interactions

A number of calculated structures of heterogeneous proton-bound dimers containing monomers such as acetonitrile, cyanamide, vinylene carbonate, and propiolactone, which have high dipole moments, are presented. These proton-bound dimers are predicted to have a structural anomaly pertaining to the bond distances between the central proton and the basic sites on each of the monomers. The monomers with the high dipole moments also have the larger proton affinity and, on the basis of difference in proton affinities, it would be expected that the proton would be closer to this monomer than the one with the lower proton affinity. However, the proton is found to lie substantially closer to the monomer with the lower proton affinity in most cases, unless the difference in proton affinity is too large. Simply stated, the difference in proton affinities is smaller than the difference in the affinity to form an ion-dipole complex for the two monomers and it is the larger affinity for the high dipole moment monomer (which also has the higher proton affinity) to form an ion-dipole complex that is responsible for the proton lying closer to the low proton affinity monomer. The bond distances between the central proton and the monomers are found to be related to the difference in proton affinity. It is found, though, that the proton-bound dimers can be grouped into two separate groups, one where the proton-bound dimer contains a high dipole moment monomer and one group where the proton-bound dimer does not contain a high dipole moment monomer. From these plots it has been determined that a high dipole moment monomer is one that has a dipole moment greater than 2.9 D.

Unusual Solvent Effect on a SN2 Reaction. A Quantum-Mechanical and Kinetic Study of the Menshutkin Reaction between 2-Amino-1-methylbenzimidazole and Iodomethane in the Gas Phase and in Acetonitrile

The quaternization reaction between 2-amino-1-methylbenzimidazole and iodomethane was investigated in the gas phase and in liquid acetonitrile. Both experimental and theoretical techniques were used in this study. In the experimental part of this work, accurate second-order rate constants were obtained for this reaction in acetonitrile from conductivity data in the 293-323 K temperature range and at ambient pressure. From two different empirical equations describing the effect of temperature on reaction rates, thermodynamic functions of activation were calculated. In the theoretical part of this work, the mechanism of this reaction was investigated in the gas phase and in acetonitrile. Two different quantum levels (B3LYP/[6-311++G(3df,3pd)/LanL2DZ]//B3LYP/[6-31G(d)/LanL2DZ] and B3LYP/[6-311++G(3df,3pd)/LanL2DZ]//B3LYP/[6-31+G(d)/LanL2DZ]) were used in the calculations, and the acetonitrile environment was modeled using the polarized continuum model (PCM). In addition, an atoms in molecules (AIM) analysis was made aiming to characterize possible hydrogen bonding. The results obtained by both techniques are in excellent agreement and lead to new insight into the mechanism of the reaction under examination. These include the identification and thermodynamic characterization of the relevant stationary species, the rationalization of the mechanistic role played by the solvent and the amine group adjacent to the nucleophile nitrogen atom, the proposal of alternative paths on the modeled potential energy surfaces, and the origin of the marked non-Arrhenius behavior of the kinetic data in solvent acetonitrile. In particular, the AIM analysis confirmed the operation of intermolecular hydrogen bonds between reactants and between products, both in the gas phase and in solution. It is also concluded that the unusual solvent effect on this Menshutkin reaction stems from the conjunction of a nucleophile possessing a relatively complex chemical structure with a dipolar aprotic solvent that is protophobic.

Nitrosative Guanine Deamination: Ab Initio Study of Deglycation of N-Protonated 5-Cyanoimino-4-oxomethylene-4,5-dihydroimidazoles

5-Cyanoimino-4-oxomethylene-4,5-dihydroimidazoles (1) (R at N1) have been discussed as possible intermediates in nitrosative guanine deamination, which are formed by dediazoniation and deprotonation of guaninediazonium ion. The parent system 1 (R = H) and its N1 derivatives 2 (R = Me) and 3 (R = MOM) are considered here. Protonation of 1-3, respectively, may occur either at the cyano-N to form cations 4 (R = H), 6 (R = Me), and 8 (R = MOM) or at the imino-N to form cations 5 (R = H), 7 (R = Me), and 9 (R = MOM), respectively. This protonation is the first step in the acid-catalyzed water addition to form 5-cyanoimino-imidazole-4-carboxylic acid, which then leads to oxanosine. There also exists the option of a substitution reaction by water at the R group of 6-9, and this dealkylation forms N-[4-(oxomethylene)-imidazol-5-yl]carbodiimide (10) and N-[4-(oxomethylene)-imidazol-5-yl]cyanamide (11). In the case of DNA, the R group is a deoxyribose sugar, and attack by water leads to deglycation. To explore this reaction option, the S(N)1 and S(N)2 reactions of 6-9 with water were studied at the MP2/6-31G*//RHF/6-31G* and CCSD/6-31G*//RHF/6-31G* levels, with the inclusion of implicit solvation at the IPCM(MP2/6-31G*)//RHF/6-31G* level, and the electron density distributions of tautomers 1, 10, and 11 were analyzed. The low barriers determined for the MOM transfer show that the deglycation could occur at room temperature but that the process cannot compete with water addition.

IR Spectrum and Structure of Protonated Ethanol Dimer: Implications for the Mobility of Excess Protons in Solution

This Communication reports IR spectra and density functional calculations for the isolated protonated ethanol dimer and its N2-microsolvated complexes, (EtOH)2H+-(N2)n (n = 0-2) to investigate the degree of delocalization of the excess proton in this fundamental building block of an alcohol proton wire. The first spectroscopic characterization of isolated and microsolvated (EtOH)2H+ suggests that the excess proton is (nearly) equally shared between both EtOH units under symmetric solvation conditions (Zundel-type ion, n = 0 and 2), whereas it is largely localized on a single EtOH molecule for asymmetric solvation (Eigen-type ion, n = 1).