Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations

Bi(III)-Catalyzed Michael Addition of Tautomerizable Heterocycles with α,β-Unsaturated Carbonyl Compounds: Regioselective Construction of C-N Bonds

A Bi(III)-catalyzed synthetic strategy for regioselective construction of C-N bonds via a simple Michael addition reaction is reported. A wide range of tautomerizable heterocycles such as benzoxazolones, benzothiazolones, benzimidazolinones, indolinones, and 2-pyridones along with α,β-unsaturated carbonyls (ketones and esters) are employed to create a library of corresponding N-alkylated derivatives exclusively. High regioselectivity, high atom economy, and the participation of a range of tautomerizable heterocycles highlight the uniqueness and generality of the developed methodology.

Tautomeric equilibrium and spectroscopic properties of 8-azaguanine revealed by quantum chemistry methods

8-azaguanine is a triazolopyrimidine nucleobase analog possessing potent antibacterial and antitumor activities, and it has been implicated as a lead molecule in cancer and malaria therapy. Its intrinsic fluorescence properties can be utilized for monitoring its interactions with biological polymers like proteins or nucleic acids. In order to better understand these interactions, it is important to know the tautomeric equilibrium of this compound. In this work, the tautomeric equilibrium of all natural neutral and anionic compound forms (except highly improbable imino-enol tautomers) as well as their methyl derivatives and ribosides was revealed by quantum chemistry methods. It was shown that, as expected, tautomers protonated at positions 1 and 9 dominate neutral forms both in gas phase and in aqueous solution. 8-azaguanines methylated at any position of the triazole ring are protonated at position 1. The computed vertical absorption and emission energies are in very good agreement with the experimental data. They confirm the validity of the assumption that replacing the proton with the methyl group does not significantly change the positions of absorption and fluorescence peaks.

Caracal: A Versatile Ring Polymer Molecular Dynamics Simulation Package

A new open-source program package named Caracal covering simulations of molecular systems with ring polymer molecular dynamics (RPMD) is presented. It combines a powerful RPMD implementation including chemical reaction rate calculations and biased periodic and nonperiodic samplings with a collection of easy to set up potential energy surface (PES) methodologies, thus delivering an all-inclusive approach. Most implemented PESs are based on the QMDFF and EVB-QMDFF methods. Where the quantum mechanically derived force field (QMDFF) can be set up for an arbitrary molecular system in a black-box fashion, the empirical valence bond (EVB)-QMDFF connects two QMDFFs and is able to represent the PES of a chemical reaction. With our previously published flavors of this composite method, PESs for almost arbitrary gas phase thermal ground state reactions can be set up. Given an optimized reaction path, the mechanism of the reaction can be classified and RPMD rate constants can be obtained via umbrella sampling and recrossing calculations on an EVB-QMDFF PES. Further, QMDFFs can be polymerized for the description of liquid systems. In this paper, the internal structure as well as the handling philosophy of Caracal are outlined. Further, examples of the different possible kinds of calculations are given.

Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble

The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of nonreactive force fields. In this formalism, most of the implemented coupling terms are built using functional forms that depend on spatial coordinates, while parameters are fitted against reference data to model the change of chemistry between the participating nonreactive states. In this work, we demonstrate that the use of such coupling terms precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. Alternatively, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating nonreactive force fields, and derive a general expression for the EVB stress tensor suitable for computation. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in nonreactive water. Mass densities and probability distributions for the values of the energy gaps computed in the NPT ensemble reveal a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating for the first time the validity of approximations based on the canonical NVT ensemble, customarily adopted for EVB simulations. The presented formalism also aims to contribute to future implementations and extensions of the EVB method to research the limit of highly concentrated solutions.

Chlorination and tautomerism: a computational and UPS/XPS study of 2-hydroxypyridine ⇌ 2-pyridone equilibrium

The prototropic tautomeric equilibrium in 2-hydroxypyridine serves as a prototype model for the study of nucleobases' behaviour. The position of such an equilibrium in parent and chlorine monosubstituted 2-hydroxypyridine compounds in the gas phase was determined using synchrotron based techniques. The lactim tautomer is dominant for the 5- and 6-substituted compounds, whereas the parent, 3- and 4-substituted isomers have comparable populations for both tautomers. Information was obtained by measuring valence band and core level photoemission spectra at the chlorine L-edge and carbon, nitrogen, and oxygen K-edges. The effect of chlorine on the core ionization potentials of the atoms in the heterocycle was evaluated and reasonable agreement with a simple model was obtained. Basic considerations of resonance structures correctly predicts the tautomeric equilibrium for the 5- and 6-substituted compounds. The vibrationally resolved structure of the low energy portion of the valence band photoionization spectra is assigned based on quantum-chemical calculations of the neutral and charged species followed by simulation of the vibronic structure. It is shown that the first ionization occurs from a π orbital of similar shape for both tautomers. In addition, the highly distinctive vibronic structure observed just above the first ionization of the lactim, for three of the five species investigated, is assigned to the second ionization of the lactam.

Effect of the ortho-Hydroxyl Groups on a Bipyridine Ligand of Iridium Complexes for the High-Pressure Gas Generation from the Catalytic Decomposition of Formic Acid

The hydroxyl groups of a 2,2'-bipyridine (bpy) ligand near the metal center activated the catalytic performance of the Ir complex for the dehydrogenation of formic acid at high pressure. The position of the hydroxyl groups on the ligand affected the catalytic durability for the high-pressure H₂ generation through the decomposition of formic acid. The Ir complex with a bipyridine ligand functionalized with para-hydroxyl groups shows a good durability with a constant catalytic activity during the reaction even under high-pressure conditions, whereas deactivation was observed for an Ir complex with a bipyridine ligand with ortho-hydroxyl groups (2). In the presence of high-pressure H₂ , complex 2 decomposed into the ligand and an Ir trihydride complex through the isomerization of the bpy ligand. This work provides the development of a durable catalyst for the high-pressure H₂ production from formic acid.

Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent

Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.

Synthesis of N-Alkenyl 2-Pyridonyl Ethers via a Au(I)-Catalyzed Rearrangement of 2-Propargyloxypyridines

N-Alkyl 2-pyridones and other enolizable heterocycles are important synthetic constructs, due to their prevalence in natural products and pharmaceutical targets and their capacity to serve as models for a number of biological and chemical processes. The disclosed Au(I)-catalyzed reaction utilizes 2-propargyloxypyridines to access N-alkylated 2-pyridone products derived from both 5-exo and 6-endo addition of the nitrogen to the pendent alkyne. Experimental and computational studies suggest that the desired 5-exo N-alkenyl 2-pyridonyl ethers are formed reversibly in the transformation. After extensive optimization, biaryl Au(I) catalyst 21 was found to overcome the inherent preference for the 6-endo pathway and provide the highest combination of 5-exo selectivity and yield. Herein, we report the application of this new Au(I)-catalyzed C-N bond formation to the preparation of a variety of N-alkenyl 2-pyridonyl ether analogues, which have the potential to serve as an entry point for the synthesis of complex N-alkyl 2-pyridone-containing frameworks.

Reactive force fields made simple

Combining QMDFF with EVB allows to generate reactive force fields of useful quality for widely varying reactions with minimal effort.

Proton-coupled electron transfer in molecular electrocatalysis: theoretical methods and design principles

Molecular electrocatalysts play an essential role in a wide range of energy conversion processes. The objective of electrocatalyst design is to maximize the turnover frequency and minimize the overpotential for the overall catalytic cycle. Typically, the catalytic cycle is dominated by key proton-coupled electron transfer (PCET) processes comprised of sequential or concerted electron and proton transfer steps. Theoretical methods have been developed to investigate the mechanisms, thermodynamics, and kinetics of PCET processes in electrocatalytic cycles. Electronic structure methods can be used to calculate the reduction potentials and pKa's and to generate thermodynamic schemes, free energy reaction pathways, and Pourbaix diagrams, which indicate the most stable species under certain conditions. These types of calculations have assisted in identifying the thermodynamically favorable mechanisms under specified experimental conditions, such as acid strength and overpotential. Such calculations have also revealed linear correlations among the thermodynamic properties, which can be used to predict the impact of modifying the ligands, substituents, or metal centers. The thermodynamic properties can be tuned with electron-withdrawing or electron-donating substituents. Ligand modification can exploit the role of noninnocent ligands. For example, ligand protonation typically decreases the overpotential. Calculations of rate constants for electron and proton transfer, as well as concerted PCET, have assisted in identifying the kinetically favorable mechanisms under specified conditions. The concerted PCET mechanism is thought to lower the overpotential required for catalysis by avoiding high-energy intermediates. Rate constant calculations have revealed that the concerted mechanism involving intramolecular proton transfer will be favored by designing more flexible ligands that facilitate the proton donor-acceptor motion while also maintaining a sufficiently short equilibrium proton donor-acceptor distance. Overall, theoretical methods have assisted in the interpretation of experimental data and the design of more effective molecular electrocatalysts.

Phenol-quinone tautomerism in (arylazo)naphthols and the analogous Schiff bases: benchmark calculations

Tautomerization energies of a series of isomeric [(4-R-phenyl)azo]naphthols and the analogous Schiff bases (R = N(CH3)2, OCH3, H, CN, NO2) are calculated by LPNO-CEPA/1-CBS using the def2-TZVPP and def2-QZVPP basis sets for extrapolation. The performance of various density functionals (B3LYP, M06-2X, PW6B95, B2PLYP, mPW2PLYP, PWPB95) as well as MP2 and SCS-MP2 is evaluated against these results. M06-2X and SCS-MP2 yield results close to the LPNO-CEPA/1-CBS values. Solvent effects (CCl4, CHCl3, CH3CN, and CH3OH) are treated by a variety of bulk solvation models (SM8, IEFPCM, COSMO, PBF, and SMD) as well as explicit solvation (Monte Carlo free energy perturbation using the OPLSAA force field).

Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy

We provide a systematic characterization of the nanosecond ground-state lactam-lactim tautomerization of pyridone derivatives in aqueous solution under ambient conditions using temperature-jump transient 2D IR spectroscopy. Although electronic excited-state tautomerization has been widely studied, experimental work on the ground electronic state, most relevant to chemistry and biology, is lacking. Using 2D IR spectroscopy, lactam and lactim tautomers of 6-chloro-2-pyridone and 2-chloro-4-pyridone are unambiguously identified by their unique cross-peak patterns. Monitoring the correlated exponential relaxation of these signals in response to a laser temperature jump provides a direct measurement of the nanosecond tautomerization kinetics. By studying the temperature, concentration, solvent, and pH dependence, we extract a thermodynamic and kinetic characterization and conclude that the tautomerization proceeds through a two-state concerted mechanism. We find that the intramolecular proton transfer is mediated by bridging water molecules and the reaction barrier is dictated by the release of a proton from pyridone, as would be expected for an efficient Grothuss-type proton transfer mechanism.

Preparation of N-alkyl 2-pyridones via a lithium iodide promoted O- to N-alkyl migration: scope and mechanism

An efficient and inexpensive LiI-promoted O- to N-alkyl migration of 2-benzyloxy-, 2-allyloxy-, and 2-propargyloxypyridines and heterocycles is reported. The reaction produces the corresponding N-alkyl 2-pyridones and analogues under green, solvent-free conditions in good to excellent yields (30 examples, 20-97% yield). This method has been shown to be intermolecular and requires heat and lithium cation to occur.

Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach

We describe a new method for constructing empirical valence bond potential energy surfaces using a parallel multilevel genetic program (PMLGP). Genetic programs can be used to perform an efficient search through function space and parameter space to find the best functions and sets of parameters that fit energies obtained by ab initio electronic structure calculations. Building on the traditional genetic program approach, the PMLGP utilizes a hierarchy of genetic programming on two different levels. The lower level genetic programs are used to optimize coevolving populations in parallel while the higher level genetic program (HLGP) is used to optimize the genetic operator probabilities of the lower level genetic programs. The HLGP allows the algorithm to dynamically learn the mutation or combination of mutations that most effectively increase the fitness of the populations, causing a significant increase in the algorithm's accuracy and efficiency. The algorithm's accuracy and efficiency is tested against a standard parallel genetic program with a variety of one-dimensional test cases. Subsequently, the PMLGP is utilized to obtain an accurate empirical valence bond model for proton transfer in 3-hydroxy-gamma-pyrone in gas phase and protic solvent.

A mechanistic investigation into the zinc carbenoid-mediated homologation reaction by DFT methods: is a classical donor-acceptor cyclopropane intermediate involved?

An extensive density functional theory (DFT, M05-2X) investigation has been performed on the zinc carbenoid-mediated homologation reaction of β-keto esters. The mechanistic existence of a classical donor-acceptor cyclopropane intermediate was probed to test the traditional school of thought regarding these systems. Calculations of the carbenoid insertion step, following enolate formation, unmasked two possible pathways. Pathway B was shown to explain the proposed, but spectroscopically unobservable donor-acceptor cyclopropane intermediate, while the second (pathway A) reveals an alternative to the classical intermediate in that a cyclopropane transition state leads to product.

Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology

The rates of intramolecular proton transfer are calculated on a full-dimensional reactive electronic potential energy surface that incorporates high level ab initio calculations along the reaction path and by using classical Transition State theory, Path-Integral Quantum Transition State Theory, and the Quantum Instanton approach. The specific example problem studied is malonaldehyde. Estimates of the kinetic isotope effect using the latter two methods are found to be in reasonable agreement with each other. Improvements and extensions of this practical, yet chemically accurate framework for the calculations of quantized, reactive dynamics are also discussed.