Rational prioritization strategy allows the design of macrolide derivatives that overcome antibiotic resistance.

Antibiotic resistance is a major threat to global health; this problem can be addressed by the development of new antibacterial agents to keep pace with the evolutionary adaptation of pathogens. Computational approaches are essential tools to this end since their application enables fast and early strategical decisions in the drug development process. We present a rational design approach, in which acylide antibiotics were screened based on computational predictions of solubility, membrane permeability, and binding affinity toward the ribosome.

Equilibrium Structures of the Phosphorus Trihalides PF and PCl, and the Phosphoranes PHF, PF, PClF, and PCl.

Among the title species, a reliable and accurate equilibrium geometry ( r structure) is available only for PF, which has been determined experimentally more than 20 years ago. Here, we report accurate r structures for all title molecules, which were obtained using a composite computational approach based on explicitly correlated coupled-cluster theory (CCSD(T)-F12b) in conjunction with a large correlation-consistent basis set (cc-pCVQZ-F12) to take core-valence electron correlation into account. Additional terms were included to correct for the effects of iterative triple excitations (CCSDT), noniterative quadruple excitations (CCSDT(Q)), and scalar relativistic contributions (DKH2-CCSD(T)).

QM/MM study of the taxadiene synthase mechanism.

Combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the reaction mechanism of taxadiene synthase (TXS). TXS catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to taxadiene (T) and four minor cyclic products. All these products originate from the deprotonation of carbocation intermediates.

Semiempirical Quantum-Chemical Methods with Orthogonalization and Dispersion Corrections.

We present two new semiempirical quantum-chemical methods with orthogonalization and dispersion corrections: ODM2 and ODM3 (ODM x). They employ the same electronic structure model as the OM2 and OM3 (OM x) methods, respectively. In addition, they include Grimme's dispersion correction D3 with Becke-Johnson damping and three-body corrections E for Axilrod-Teller-Muto dispersion interactions as integral parts.

On the convergence of multi-scale free energy simulations.

In this work we employ simple model systems to evaluate the relative performance of two of the most important free energy methods: The Zwanzig equation (also known as "Free energy perturbation") and Bennett's acceptance ratio method (BAR). Although our examples should be transferable to other kinds of free energy simulations, we focus on applications of multi-scale free energy simulations. Such calculations are especially complex, since they connect two different levels of theory with very different requirements in terms of speed, accuracy, sampling and parallelizability.

Big data analysis of ab Initio molecular integrals in the neglect of diatomic differential overlap approximation.

Most modern semiempirical quantum-chemical (SQC) methods are based on the neglect of diatomic differential overlap (NDDO) approximation to ab initio molecular integrals. Here, we check the validity of this approximation by computing all relevant integrals for 32 typical organic molecules using Gaussian-type orbitals and various basis sets (from valence-only minimal to all-electron triple-ζ basis sets) covering in total more than 15.6 million one-electron (1-e) and 10.

Mechanism of the Visible-Light-Mediated Copper-Catalyzed Coupling Reaction of Phenols and Alkynes.

A recent experimental study reported a visible-light-mediated aerobic oxidative coupling reaction of phenol with alkynes that produces hydroxyl-functionalized aryl ketones using inexpensive CuCl as catalyst under mild conditions. Here we apply the complete active space self-consistent field (CASSCF) method and multistate second-order perturbation (MS-CASPT2) theory in combination with density functional theory (DFT) to systematically explore the entire photocatalytic reaction between phenol and phenylacetylene in acetonitrile solution in the presence of molecular oxygen and CuCl. Our main findings are as follows: (1) The visible-light-driven conversion of phenylacetylene to PhCCCu(I) occurs thermally because of efficient excited-state deactivation to the S state.

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.

Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model.

Nonadiabatic Excited-State Dynamics with Machine Learning.

We show that machine learning (ML) can be used to accurately reproduce nonadiabatic excited-state dynamics with decoherence-corrected fewest switches surface hopping in a 1-D model system. We propose to use ML to significantly reduce the simulation time of realistic, high-dimensional systems with good reproduction of observables obtained from reference simulations. Our approach is based on creating approximate ML potentials for each adiabatic state using a small number of training points.

Analytic gradient and derivative couplings for the spin-flip extended configuration interaction singles method: Theory, implementation, and application to proton transfer.

We present the formalism of analytic gradients and derivative couplings for the spin-flip extended configuration interaction with single excitations (SF-XCIS) method. We report an efficient implementation of the SF-XCIS method in the framework of semiempirical quantum chemistry that allows fast excited-state calculations for large systems. The performance of the SF-XCIS method in combination with semiempirical orthogonalization-corrected models (OMx) is statistically evaluated for vertical singlet excitation energies.

1-Butanol as a Solvent for Efficient Extraction of Polar Compounds from Aqueous Medium: Theoretical and Practical Aspects.

The extraction of polar molecules from aqueous solution is a challenging task in organic synthesis. 1-Butanol has been used sporadically as an eluent for polar molecules, but it is unclear which molecular features drive its efficiency. Here, we employ free energy simulations to study the partitioning of 15 solutes between water and 1-butanol.

Toward Accurate QM/MM Reaction Barriers with Large QM Regions Using Domain Based Pair Natural Orbital Coupled Cluster Theory.

The hydroxylation reaction catalyzed by p-hydroxybenzoate hydroxylase and the Baeyer-Villiger reaction catalyzed by cyclohexanone monooxygenase are investigated by means of quantum mechanical/molecular mechanical (QM/MM) calculations at different levels of QM theory. The geometries of the stationary points along the reaction profile are obtained from QM/MM geometry optimizations, in which the QM region is treated by density functional theory (DFT). Relative energies are determined from single-point QM/MM calculations using the domain-based local pair natural orbital coupled cluster DLPNO-CCSD(T) method as QM component.

The rotation-vibration spectrum of methyl fluoride from first principles.

Accurate ab initio calculations on the rotation-vibration spectrum of methyl fluoride (CH3F) are reported. A new nine-dimensional potential energy surface (PES) and dipole moment surface (DMS) have been generated using high-level electronic structure methods. Notably, the PES was constructed from explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and considered additional energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction.

An efficient implementation of semiempirical quantum-chemical orthogonalization-corrected methods for excited-state dynamics.

We present an efficient implementation of configuration interaction with single excitations (CIS) for semiempirical orthogonalization-corrected OMx methods and standard modified neglect of diatomic overlap (MNDO)-type methods for the computation of vertical excitation energies as well as analytical gradients and nonadiabatic couplings. This CIS implementation is combined with Tully's fewest switches algorithm to enable surface hopping simulations of excited-state nonadiabatic dynamics. We introduce an accurate and efficient expression for the semiempirical evaluation of nonadiabatic couplings, which offers a significant speedup for medium-size molecules and is suitable for use in long nonadiabatic dynamics runs.

Ultrafast action chemistry in slow motion: atomistic description of the excitation and fluorescence processes in an archetypal fluorescent protein.

We report quantum mechanical/molecular mechanical non-adiabatic molecular dynamics simulations on the electronically excited state of green fluorescent protein mutant S65T/H148D. We examine the driving force of the ultrafast (τ < 50 fs) excited-state proton transfer unleashed by absorption in the A band at 415 nm and propose an atomistic description of the two dynamical regimes experimentally observed [Stoner Ma et al., J.

Molecular dynamics study of taxadiene synthase catalysis.

Molecular dynamics (MD) simulations have been performed to study the dynamic behavior of noncovalent enzyme carbocation complexes involved in the cyclization of geranylgeranyl diphosphate to taxadiene catalyzed by taxadiene synthase (TXS). Taxadiene and the observed four side products originate from the deprotonation of carbocation intermediates. The MD simulations of the TXS carbocation complexes provide insights into potential deprotonation mechanisms of such carbocations.

QM/MM Studies on Photoisomerization Dynamics of Azobenzene Chromophore Tethered to a DNA Duplex: Local Unpaired Nucleobase Plays a Crucial Role.

The photoresponsive azobenzene-tethered DNAs have received growing experimental attention because of their potential applications in biotechnology and nanotechnology; however, little is known about the initial photoisomerization of azobenzene in these systems. Herein we have employed quantum mechanics/molecular mechanics (QM/MM) methods to explore the photoisomerization dynamics of an azobenzene-tethered DNA duplex. We find that in the S state the trans-cis photoisomerization path is much steeper in DNA than in vacuo, which makes the photoisomerization much faster in the DNA environment.

Half-Sandwich Ruthenium Carbene Complexes Link trans-Hydrogenation and gem-Hydrogenation of Internal Alkynes.

The hydrogenation of internal alkynes with [Cp*Ru]-based catalysts is distinguished by an unorthodox stereochemical course in that E-alkenes are formed by trans-delivery of the two H atoms of H. A combined experimental and computational study now provides a comprehensive mechanistic picture: a metallacyclopropene (η-vinyl complex) is primarily formed, which either evolves into the E-alkene via a concerted process or reacts to give a half-sandwich ruthenium carbene; in this case, one of the C atoms of the starting alkyne is converted into a methylene group. This transformation represents a formal gem-hydrogenation of a π-bond, which has hardly any precedent.

Computational Insights into an Enzyme-Catalyzed [4+2] Cycloaddition.

The enzyme SpnF, involved in the biosynthesis of spinosyn A, catalyzes a formal [4+2] cycloaddition of a 22-membered macrolactone, which may proceed as a concerted [4+2] Diels-Alder reaction or a stepwise [6+4] cycloaddition followed by a Cope rearrangement. Quantum mechanics/molecular mechanics (QM/MM) calculations combined with free energy simulations show that the Diels-Alder pathway is favored in the enzyme environment. OM2/CHARMM free energy simulations for the SpnF-catalyzed reaction predict a free energy barrier of 22 kcal/mol for the concerted Diels-Alder process and provide no evidence of a competitive stepwise pathway.

Solvent water interactions within the active site of the membrane type I matrix metalloproteinase.

Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly formed N-terminus (amine) and C-terminus (carboxylate) protein fragments from the site of catalysis coupled with the inclusion of one or more solvent waters.

Hot and Cold Charge-Transfer Mechanisms in Organic Photovoltaics: Insights into the Excited States of Donor/Acceptor Interfaces.

The evolution of the excited-state manifold in organic D/A aggregates (e.g., the prototypical P3HT/PCBM) is investigated through a bottom-up approach via first-principles calculations.

Catalytic Reductive Pinacol-Type Rearrangement of Unactivated 1,2-Diols through a Concerted, Stereoinvertive Mechanism.

A catalytic pinacol-type reductive rearrangement reaction of internal 1,2-diols is reported herein. Several scaffolds not usually amenable to pinacol-type reactions, such as aliphatic secondary-secondary diols, undergo the transformation well without the need for prefunctionalization. The reaction uses a simple boron catalyst and two silanes and proceeds through a concerted, stereoinvertive mechanism that enables the preparation of highly enantiomerically enriched products.

Structure-based sampling and self-correcting machine learning for accurate calculations of potential energy surfaces and vibrational levels.

We present an efficient approach for generating highly accurate molecular potential energy surfaces (PESs) using self-correcting, kernel ridge regression (KRR) based machine learning (ML). We introduce structure-based sampling to automatically assign nuclear configurations from a pre-defined grid to the training and prediction sets, respectively. Accurate high-level ab initio energies are required only for the points in the training set, while the energies for the remaining points are provided by the ML model with negligible computational cost.

Elucidation of the Catalytic Mechanism of a Miniature Zinc Finger Hydrolase.

To improve our mechanistic understanding of zinc metalloenzymes, we report a joint computational and experimental study of a minimal carbonic anhydrase (CA) mimic, a 22-residue Zn-finger hydrolase. We combine classical molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) geometry optimizations, and QM/MM free energy simulations with ambient and high-pressure kinetic measurements to investigate the mechanism of the hydrolysis of the substrate p-nitrophenylacetate (pNPA). The zinc center of the hydrolase prefers a pentacoordinated geometry, as found in most naturally occurring CAs and CA-like enzymes.

Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations.

In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1-matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shell of a complex biomolecule.