Fatty Alcohol Membrane Model for Quantifying and Predicting Amphiphilicity.

Amphiphilicity is an important property for drug development and self-assembly. This paper introduces a general approach based on a simple fatty alcohol (dodecanol) membrane model that can be used to quantify the amphiphilicity of small molecules that are in good agreement with experimental surface tension data. By applying the model to a systematic series of compounds, it was possible to elucidate the effect of different motifs on amphiphilicity.

How Accurate Are QM/MM Models?

Despite the success and widespread use of QM/MM methods in modeling (bio)chemically important processes, their accuracy is still not well understood. A key reason is because these methods are ultimately approximations to direct QM calculations of very large systems, which are impractical to perform in most cases. We highlight recent progress toward the development of realistic model systems where it is possible to obtain full QM reference data to directly and systematically evaluate the effectiveness of different QM/MM generation schemes.

Characterization of PFOA isomers from PFAS precursors and their reductive defluorination.

Perfluorooctanoic acid (PFOA) including linear and branched isomers is one of only three PFAS included in the Stockholm convention on Persistent Organic Pollutants. Unfortunately, PFOA branched isomers have received less attention than the linear due to analytical difficulties and perceived lower environmental concentrations. In this study, we revealed a environmentally relevant pathway for the formation of branched PFOA from PFAS precursors.

A High-capacity Benzoquinone Derivative Anode for All-organic Long-cycle Aqueous Proton Batteries.

Quinone compounds, with the ability to uptake protons, are promising electrodes for aqueous batteries. However, their applications are limited by the mediocre working potential range and inferior rate performance. Herein, we examined quinones bearing different substituents, and for the first time introduce tetraamino-1,4-benzoquinone (TABQ) as anode material for proton batteries.

The Quality of Embedding Charges Is Critical for Convergence of Many-Body Expansions When BSSE Is Absent.

There is conflicting evidence in the literature concerning the benefits of charge embedding on the convergence of many-body expansions (MBEs). Using a systematic series of water and ion-water clusters of varying size, this study indicates that the effects of charge embedding can be masked by basis set superposition error (BSSE). When BSSE is removed, this study demonstrates that charge embedding can significantly accelerate MBE convergence, where the electrostatically embedded two-body method, EE-MBE(2), can often yield accuracy close to the four-body method, MBE(4).

In Search of the Best Low-Cost Methods for Efficient Screening of Conformers.

Locating the lowest energy conformer is crucial for the accurate computation of equilibrium properties of molecular systems. This paper examines the performance of efficient low-cost methods in terms of the alignment and relative energies of their energy minima against the benchmark revDSD-PBEP86-D4/def2-TZVPP//MP2/cc-pVTZ potential energy surface. The low-cost methods considered include GFN-FF, GFN2-xTB, DFTB3, HF-3c, B97-3c, PBEh-3c, and rSCAN-3c composite methods against a diverse test set of 20 compounds including alkanes, perfluoroalkyl molecules, peptides, open-shell radicals, and Zn(II) complexes of varying sizes.

Binding of Per- and Polyfluoroalkyl Substances to β-Lactoglobulin from Bovine Milk.

Per- and polyfluoroalkyl substances (PFAS) are known for their high environmental persistence and potential toxicity. The presence of PFAS has been reported in many dairy products. However, the mechanisms underlying the accumulation of PFAS in these products remain unclear.

Maximizing Aqueous Drug Encapsulation: Small Nanoparticles Formation Enabled by Glycopolymers Combining Glucose and Tyrosine.

Highly potent heterocyclic drugs are frequently poorly water soluble, leading to limited or abandoned further drug development. Nanoparticle technology offers a powerful delivery approach by enhancing the solubility and bioavailability of hydrophobic therapeutics. However, the common usage of organic solvents causes unwanted toxicity and process complexity, therefore limiting the scale-up of nanomedicine technology for clinical translation.

Simple Composite Approach to Efficiently Estimate Basis Set Limit CCSD(T) Harmonic Frequencies and Reaction Thermochemistry.

We introduce a simple strategy that combines the G3(MP2) composite method and explicitly correlated coupled cluster CCSD(T)-F12 method to efficiently estimate complete basis set CCSD(T) molecular geometries and harmonic vibrational frequencies at the cost of a double-ζ basis set calculation. Based on a large test set of 61 neutral, ionic, and open-shell molecules, and additionally 31 molecules in the HFREQ2014 data set, we demonstrate that this composite strategy has an average accuracy of 2 cm or better relative to complete basis set CCSD(T) values. Using this approach, we estimated 696 CCSD(T)/CBS reaction energies of small to medium-sized systems containing up to 6 heavy atoms and confirmed existing approximations that use small basis set density functional theory methods [e.

High-Level Quantum Chemical Prediction of C-F Bond Dissociation Energies of Perfluoroalkyl Substances.

In this study, 550 C-F bond dissociation energies (BDEs) of a variety of per- and polyfluoroalkyl substances (PFASs) obtained from high-level DLPNO-CCSD(T)/CBS calculations were used to assess the accuracy of contemporary density functional theory (DFT) and semiempirical methods. DLPNO-CCSD(T)/CBS gas phase C-F BDEs fall between 404.9-550.

Molecular Geometries and Vibrational Contributions to Reaction Thermochemistry Are Surprisingly Insensitive to the Choice of Basis Sets.

Calculation of molecular geometries and harmonic vibrational frequencies are pre-requisites for thermochemistry calculations. Contrary to conventional wisdom, this paper demonstrates that quantum chemical predictions of the thermochemistry of many gas and solution phase chemical reactions appear to be very insensitive to the choice of basis sets. For a large test set of 80 diverse organic and transition-metal-containing reactions, variations in reaction free energy based on geometries and frequencies calculated using a variety of double and triple-zeta basis sets from the Pople, Jensen, Ahlrichs, and Dunning families are typically less than 4 kJ mol, especially when the quasiharmonic oscillator correction is applied to mitigate the effects of low-frequency modes.

MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4.

Carbonic anhydrase is an attractive drug target for the treatment of many diseases. This paper examines the ability of end-state MM/GBSA methods to rank inhibitors of carbonic anhydrase in terms of their binding affinities. The MM/GBSA binding energies were evaluated using different atomic charge schemes (Mulliken, ESP and NPA) at different levels of theories, including Hartree-Fock, B3LYP-D3(BJ), and M06-2X with the 6-31G(d,p) basis set.

Quantum Chemical Prediction of the Acidities of Sulfonamide Inhibitors of Carbonic Anhydrase.

This study examined two p calculation approaches (direct and proton exchange schemes) that employ high-level quantum chemical methods and implicit solvent models to predict aqueous Brønsted acidities of a large set of sulfonamides. For gas-phase deprotonation energies, the DSD-PBEP86-D3(BJ) double-hybrid functional provided the best agreement with the LNO-CCSD(T)/CBS benchmark with a mean absolute deviation less than 2 kJ mol when the aug-cc-pVTZ or larger basis sets are used. For a large test set of 54 primary and secondary sulfonamides, the use of the DSD-PBEP86-D3(BJ)/aug-cc-pVTZ level of theory in conjunction with SM12 solvation free energies predict their p values with a mean accuracy of 0.

Predicting Solvent Effects on S2 Reaction Rates: Comparison of QM/MM, Implicit, and MM Explicit Solvent Models.

Solvents are one of the key variables in the optimization of a synthesis yield or properties of a synthesis product. In this paper, contemporary solvent models are applied to predict the rates of S2 reactions in a range of aqueous and non-aqueous solvents. High-level CCSD(T)/CBS//M06-2X/6-31+G(d) gas phase energies were combined with solvation free energies from SMD, SM12, and ADF-COSMO-RS continuum solvent models, as well as molecular mechanics (MM) explicit solvent models with different atomic charge schemes to predict the rate constants of three S2 reactions in eight protic and aprotic solvents.

Molecular Crowding Electrolytes for Stable Proton Batteries.

Proton electrochemistry is promising for developing post-lithium energy storage devices with high capacity and rate capability. However, some electrode materials are vulnerable because of the co-intercalation of free water molecules in traditional acid electrolytes, resulting in rapid capacity fading. Here, the authors report a molecular crowding electrolyte with the usage of poly(ethylene glycol) (PEG) as a crowding agent, achieving fast and stable electrochemical proton storage and expanded working potential window (3.

Improving the Accuracy of Quantum Mechanics/Molecular Mechanics (QM/MM) Models with Polarized Fragment Charges.

This paper introduces an economical approach for improving the accuracy and convergence of quantum mechanics/molecular mechanics (QM/MM) models. The approach is tested on a series of neutral and charged amino acids embedded in a 160-water cluster, where their intramolecular proton transfer energies (neutral amino acid → zwitterionic amino acid) were previously obtained at the ωB97X-D/6-31G(d) level of theory. When the charges on the MM atoms were replaced with those obtained at the same QM level of theory used to treat the QM atoms, this significantly improved the accuracy and convergence of the QM/MM models.

Hydrogen-Bond Disrupting Electrolytes for Fast and Stable Proton Batteries.

Rechargeable aqueous proton batteries are promising competitors for the next generation of energy storage systems with the fast diffusion kinetics and wide availability of protons. However, poor cycling stability is a big challenge for proton batteries due to the attachment of water molecules to the electrode surface in acid electrolytes. Here, a hydrogen-bond disrupting electrolyte strategy to boost proton battery stability via simultaneously tuning the hydronium ion solvation sheath in the electrolyte and the electrode interface is reported.

Development of an Albumin-Polymer Bioconjugate via Covalent Conjugation and Supramolecular Interactions.

Preexisting serum albumin-polymer bioconjugates have been formed either through covalent conjugation or supramolecular interactions. However, the viability of producing a bioconjugate where both covalent conjugation and supramolecular interactions have been adopted is yet to be explored. In this work, the noncovalent interaction of two polymers bearing fatty acid-based end-functionalities were compared and the superior binder was carried forward for testing with serum albumin that possessed a polymer conjugated to its Cys34 residue.

Accurate Quantum Chemical Prediction of Gas-Phase Anion Binding Affinities and Their Structure-Binding Relationships.

This paper systematically examines the performance of contemporary wavefunction and density functional theory methods to identify robust and cost-efficient methods for predicting gas-phase anion binding energies. This includes the local coupled cluster LNO-CCSD(T) and DLPNO-CCSD(T), as well as double-hybrid DSD-PBEP86-D3(BJ) and various hybrid functionals M06-2X, B3LYP-D3(BJ), ωB97M-V, and ωB97X-V. The focus is on dual-hydrogen-bonding anion receptors that are commonly found in supramolecular chemistry and organocatalysis, namely, (thio)ureas, deltamides, (thio)squaramides, and croconamides as well as the yet-to-be-explored rhodizonamides.

"Water-in-Sugar" Electrolytes Enable Ultrafast and Stable Electrochemical Naked Proton Storage.

Proton is an ideal charge carrier for rechargeable batteries due to its small ionic radius, ultrafast diffusion kinetics and wide availability. However, in commonly used acid electrolytes, the co-interaction of polarized water and proton (namely hydronium) with electrode materials often causes electrode structural distortions. The hydronium adsorption on electrode surfaces also facilitates hydrogen evolution as an unwanted side reaction.

Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions.

Despite recent advances in the development of machine learning potentials (MLPs) for biomolecular simulations, there has been limited effort on developing stable and accurate MLPs for enzymatic reactions. Here we report a protocol for performing machine-learning-assisted free energy simulation of solution-phase and enzyme reactions at the ab initio quantum-mechanical/molecular-mechanical (-QM/MM) level of accuracy. Within our protocol, the MLP is built to reproduce the -QM/MM energy and forces on both QM (reactive) and MM (solvent/enzyme) atoms.

On the Accuracy of QM/MM Models: A Systematic Study of Intramolecular Proton Transfer Reactions of Amino Acids in Water.

This work presents a systematic assessment of QM/QM' and QM/MM models with respect to direct QM calculations for the tautomerization (neutral to zwitterion) reactions of amino acids (glycine, alanine, valine, aspartate, and neutral and protonated histidine) solvated in a 160 water cluster. The effect of varying QM region size and choice of embedding potentials, including fixed-charge and polarizable molecular mechanics force fields (TIP3P and EFP) and various semiempirical QM methods (PM7, GFN2-xTB, DFTBA, DFTB3, HF-3c, and PBEh-3c), on the accuracy of the models was examined. A surprising finding was that molecular mechanics force fields outperformed many of the semiempirical methods.

Polyphenylglyoxamide-Based Amphiphilic Small Molecular Peptidomimetics as Antibacterial Agents with Anti-Biofilm Activity.

The rapid emergence of drug-resistant bacteria is a major global health concern. Antimicrobial peptides (AMPs) and peptidomimetics have arisen as a new class of antibacterial agents in recent years in an attempt to overcome antibiotic resistance. A library of phenylglyoxamide-based small molecular peptidomimetics was synthesised by incorporating an -alkylsulfonyl hydrophobic group with varying alkyl chain lengths and a hydrophilic cationic group into a glyoxamide core appended to phenyl ring systems.

Diaminomethylenemalononitriles and Diaminomethyleneindanediones as Dual Hydrogen Bond Donors for Anion Recognition.

Diaminomethylenemalononitriles (DMMs) and diaminomethyleneindanediones (DMIs) are dual H-bond donors that have previously been used as organocatalysts, but their anion binding ability has not been investigated. We report the synthesis of both alkyl- and aryl-substituted DMMs and DMIs, together with a comparison of their anion binding ability with that of the analogous thioureas. The DMMs display affinity for monovalent anions, with similar anion binding affinities observed to that of the thioureas in acetonitrile, albeit with differing trends for the '-dialkyl versus '-diaryl compounds.