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1. Machine learning the Hohenberg-Kohn map for molecular excited states

   https://doi.org/10.1038/s41467-022-34436-w  

   Bai, Yuanming ; Vogt-Maranto, Leslie ; Tuckerman, Mark E. ; Glover, William J. ( November 2022 , Nature Communications)

   The Hohenberg-Kohn theorem of density-functional theory establishes the existence of a bijection between the ground-state electron density and the external potential of a many-body system. This guarantees a one-to-one map from the electron density to all observables of interest including electronic excited-state energies. Time-Dependent Density-Functional Theory (TDDFT) provides one framework to resolve this map; however, the approximations inherent in practical TDDFT calculations, together with their computational expense, motivate finding a cheaper, more direct map for electronic excitations. Here, we show that determining density and energy functionals via machine learning allows the equations of TDDFT to be bypassed. The framework we introduce is used to perform the first excited-state molecular dynamics simulations with a machine-learned functional on malonaldehyde and correctly capture the kinetics of its excited-state intramolecular proton transfer, allowing insight into how mechanical constraints can be used to control the proton transfer reaction in this molecule. This development opens the door to using machine-learned functionals for highly efficient excited-state dynamics simulations.
2. Preferential N–H⋯:C hydrogen bonding involving ditopic NH -containing systems and N -heterocyclic carbenes

   https://doi.org/10.1039/d0ra08490e  

   Kinney, Zacharias J. ; Rheingold, Arnold L. ; Protasiewicz, John D. ( November 2020 , RSC Advances)

   Hydrogen bonding plays a critical role in maintaining order and structure in complex biological and synthetic systems. N -heterocyclic carbenes (NHCs) represent one of the most versatile tools in the synthetic chemistry toolbox, yet their potential as neutral carbon hydrogen bond acceptors remains underexplored. This report investigates this capability in a strategic manner, wherein carbene-based hydrogen bonding can be assessed by use of ditopic NH -containing molecules. N–H bonds are unique as there are three established reaction modes with carbenes: non-traditional hydrogen bonding adducts (X–H⋯:C), salts arising from proton transfer ([H–C] + [X] − ), or amines from insertion of the carbene into the N–H bond. Yet, there are no established rules to predict product distributions or the strength of these associations. Here we seek to correlate the hydrogen bond strength of symmetric and asymmetric ditopic secondary amines with 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene ( IPr , a representative NHC). In symmetric and asymmetric ditopic amine adducts both the solid-state (hydrogen bond lengths, NHC interior angles) and solution-state ( 1 H Δ δ of NH signals, 13 C signals of carbenic carbon) can be related to the p K a of the parent amine.
3. UV-Vis Photodissociation Action Spectroscopy Reveals Cytosine-Guanine Hydrogen Transfer in DNA Tetranucleotide Cation Radicals upon One-Electron Transfer

   https://doi.org/10.1021/acd.jpcb.0c01693  

   Huang, Shu R. ; Liu, Y. ; Turecek, Frantisek ( April 2020 , The journal of physical chemistry)

   ABSTRACT: We report the generation and spectroscopic study of hydrogen-rich DNA tetranucleotide cation radicals (GATC+2H)+• and (AGTC+2H)+•. The radicals were generated in the gas phase by one-electron reduction of the respective dications (GATC +2H)2+ and (AGTC+2H)2+ and characterized by collision-induced dissociation and photodissociation tandem mass spectrometry and UV−vis photodissociation action spectroscopy. Among several absorption bands observed for (GATC+2H)+•, the bands at 340 and 450 nm were assigned to radical chromophores. Timedependent density functional theory calculations including vibronic transitions in the visible region of the spectrum were used to provide theoretical absorption spectra of several low-energy tetranucleotide tautomers having cytosine-, adenine-, and thymine- based radical chromophores that did not match the experimental spectrum. Instead, the calculations indicated the formation of a new isomer with the 7,8-H-dihydroguanine cation radical moiety. The isomerization involved hydrogen migration from the cytosine N-3−H radical to the C-8 position in N-7-protonated guanine that was calculated to be 87 kJ mol−1 exothermic and had a low-energy transition state. Although the hydrogen migration was facilitated by the spatial proximity of the guanine and cytosine bases in the low-energy (GATC+2H)+• intermediate formed by electron transfer, the reaction was calculated to have a large negative activation entropy. Rice−Ramsperger−Kassel−Marcus (RRKM) and transitionmore »state theory kinetic analysis indicated that the isomerization occurred rapidly in hot cation radicals produced by electron transfer with the population-weighed rate constant of k = 8.9 × 103 s−1. The isomerization was calculated to be too slow to proceed on the experimental time scale in thermal cation radicals at 310 K.« less
4. Experimental and theoretical assessment of protonated Hoogsteen 9-methylguanine–1-methylcytosine base-pair dissociation: kinetics within a statistical reaction framework

   https://doi.org/10.1039/d0cp06682f  

   Moe, May Myat ; Benny, Jonathan ; Sun, Yan ; Liu, Jianbo ( April 2021 , Physical Chemistry Chemical Physics)

   We investigated the collision-induced dissociation (CID) reactions of a protonated Hoogsteen 9-methylguanine–1-methylcytosine base pair (HG-[9MG·1MC + H] + ), which aims to address the mystery of the literature reported “anomaly” in product ion distributions and compare the kinetics of a Hoogsteen base pair with its Watson-Crick isomer WC-[9MG·1MC + H] + (reported recently by Sun et al. ; Phys. Chem. Chem. Phys. , 2020, 22 , 24986). Product ion cross sections and branching ratios were measured as a function of center-of-mass collision energy using guided-ion beam tandem mass spectrometry, from which base-pair dissociation energies were determined. Product structures and energetics were assessed using various theories, of which the composite DLPNO-CCSD(T)/aug-cc-pVTZ//ωB97XD/6-311++G(d,p) was adopted as the best-performing method for constructing a reaction potential energy surface. The statistical Rice–Ramsperger–Kassel–Marcus theory was found to provide a useful framework for rationalizing the dominating abundance of [1MC + H] + over [9MG + H] + in the fragment ions of HG-[9MG·1MC + H] + . The kinetics analysis proved the necessity for incorporating into kinetics modeling not only the static properties of reaction minima and transition states but more importantly, the kinetics of individual base-pair conformers that have formed in collisional activation. The analysis also pinpointedmore »the origin of the statistical kinetics of HG-[9MG·1MC + H] + vs. the non-statistical behavior of WC-[9MG·1MC + H] + in terms of their distinctively different intra-base-pair hydrogen-bonds and consequently the absence of proton transfer between the N1 position of 9MG and the N3′ of 1MC in the Hoogsteen base pair. Finally, the Hoogsteen base pair was examined in the presence of a water ligand, i.e. , HG-[9MG·1MC + H] + ·H 2 O. Besides the same type of base-pair dissociation as detected in dry HG-[9MG·1MC + H] + , secondary methanol elimination was observed via the S N 2 reaction of water with nucleobase methyl groups.« less
5. BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study

   https://doi.org/10.3390/catal12040415  

   Freindorf, Marek ; Kraka, Elfi ( April 2022 , Catalysts)

   In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by themore »CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.« less