This is a review.
Non-electrolytic compounds typically cross cell membranes by passive diffusion. The rate of permeation is dependent on the chemical properties of the solute and the composition of ...the lipid bilayer membrane. Predicting the permeability coefficient of a solute is important in pharmaceutical chemistry and toxicology. Molecular simulation has proven to be a valuable tool for modeling permeation of solutes through a lipid bilayer. In particular, the solubility-diffusion model has allowed for the quantitative calculation of permeability coefficients. The underlying theory and computational methods used to calculate membrane permeability are reviewed. We also discuss applications of these methods to examine the permeability of solutes and the effect of membrane composition on permeability. The application of coarse grain and polarizable models is discussed. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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•The theory and practice of molecular simulations of membrane permeation are reviewed.•Permeability coefficients can be calculated by the solubility-diffusion model.•88 papers that have used this model to study membrane permeation are summarized.•The effect of the bilayer composition is explained using molecular simulations.•Polarizable and coarse grain models have promise to address limitations in modeling.
The calculation of molecular electric moments, polarizabilities, and electrostatic potentials is a widespread application of quantum chemistry. Although a range of wave function and density ...functional theory (DFT) methods have been applied in these calculations, combined with a variety of basis sets, there has not been a comprehensive evaluation of how accurate these methods are. To benchmark the accuracy of these methods, the dipole moments and polarizabilities of a set of 46 molecules were calculated using a broad set of quantum chemical methods and basis sets. Wave function methods Hartree–Fock (HF), second-order Møller–Plesset (MP2), and coupled cluster-singles and doubles (CCSD) were evaluated, along with the PBE, TPSS, TPSSh, PBE0, B3LYP, M06, and B2PLYP DFT functionals. The cc-pVDZ, cc-pVTZ, aug-cc-pVDZ, aug-cc-pVTZ, and Sadlej cc-pVTZ basis sets were tested. The aug-cc-pVDZ, Sadlej cc-pVTZ, and aug-cc-pVTZ basis sets all yield results with comparable accuracy, with the aug-cc-pVTZ calculations being the most accurate. CCSD, MP2, or hybrid DFT methods using the aug-cc-pVTZ basis set are all able to predict dipole moments with RMSD errors in the 0.12–0.13 D range and polarizabilities with RMSD errors in the 0.30–0.38 Å3 range. Calculations using Hartree–Fock theory systematically overestimated dipole moments and underestimate polarizabilities. The pure DFT functionals included in this study (PBE and TPSS) slightly underestimate dipole moments and overestimate polarizability. Polarization anisotropy and implications for charge fitting are discussed.
Targeted covalent inhibitors (TCIs) have been successfully developed as high-affinity and selective inhibitors of enzymes of the protein kinase family. These drugs typically act by undergoing an ...electrophilic addition with an active-site cysteine residue, so design of a TCI begins with the identification of a “druggable” cysteine. These electrophilic additions generally require deprotonation of the thiol to form a reactive anionic thiolate, so the acidity of the residue is a critical factor. Few experimental measurements of the pK a’s of druggable cysteines have been reported, so computational prediction could prove to be very important in selecting reactive cysteine targets. Here we report the computed pK a’s of druggable cysteines in selected protein kinases that are of clinical relevance for targeted therapies. The pK a’s of the cysteines were calculated using advanced computational methods based on all-atom replica-exchange thermodynamic integration molecular dynamics simulations in explicit solvent. We found that the acidities of druggable cysteines within protein kinases are diverse and elevated, indicating enormous differences in their reactivity. Constant-pH molecular dynamics simulations were also performed on selected protein kinases, and the results confirmed this varied range in the acidities of druggable cysteines. Many of these active-site cysteines have low exposure to solvent molecules, elevating their pK a values. Electrostatic interactions with nearby anionic residues also elevate the pK a’s of cysteine residues in the active site. The results suggest that some cysteine residues within kinase binding sites will be slow to react with a TCI because of their low acidity. Several oncogenic kinase mutations were also modeled and found to have pK a’s similar to that of the wild-type kinase.
Ideal organic syntheses involve the rapid construction of C−C bonds, with minimal use of functional group interconversions. The Suzuki–Miyaura cross‐coupling (SMC) is a powerful way to form biaryl ...linkages, but the relatively similar reactivity of electrophilic partners makes iterative syntheses involving more than two sequential coupling events difficult to achieve without additional manipulations. Here we introduce (hetero)aryl sulfones as electrophilic coupling partners for the SMC reaction, which display an intermediate reactivity between those of typical aryl (pseudo)halides and nitroarenes. The new complementary reactivity allows for rapid sequential cross‐coupling of arenes bearing chloride, sulfone and nitro leaving groups, affording non‐symmetric ter‐ and quateraryls in only 2 or 3 steps, respectively. The SMC reactivity of (hetero)aryl sulfones is demonstrated in over 30 examples. Mechanistic experiments and DFT calculations are consistent with oxidative addition into the sulfone C−S bond as the turnover‐limiting step. The further development of electrophilic cross‐coupling partners with complementary reactivity may open new possibilities for divergent iterative synthesis starting from small pools of polyfunctionalized arenes.
Complementary reactivity: Aryl sulfones undergo Suzuki–Miyaura coupling with intermediate reactivity between aryl halides and nitroarenes, enabling the iterative synthesis of non‐symmetric polyaromatics.
Knowledge of the hydration structure of Na+ and K+ in the liquid phase has wide ranging implications in the field of biological chemistry. Despite numerous experimental and computational studies, ...even basic features such as the coordination number of these alkali ions in liquid water, thought to play a critical role in selectivity, continue to be the subject of intensive debates. Simulations based on accurate potential energy surfaces offer one approach to resolve these issues by providing reliable results on ion hydration. In this article, we report the results from molecular dynamics simulations of Na+ and K+ hydration based on a novel and rigorous strategy designed to overcome the challenges of QM/MM simulations of solvent molecules in the liquid phase. In this method, which we call Flexible Inner Region Ensemble Separator (FIRES), the ion and a fixed number of nearest water molecules form a dynamical and flexible inner region that is represented with high level ab initio quantum mechanical (QM) methods, while the water molecules from the surrounding bulk form an outer region that is represented by a polarizable molecular mechanical (MM) force field. Simulations yield rigorously correct thermodynamic averages as long as the solvent molecules in the flexible inner and outer regions are not allowed to exchange. Extensive FIRES simulations were carried out based on a QM/MM model in which the Na+ or K+ ion and the 12 nearest water molecules were represented by high level ab initio methods (RI-MP2/def2-TZVP and density functional theory with PBE/def2-TZVP), while the surrounding MM water molecules were represented by the polarizable SWM4-NDP potential. On the basis of these results, the ion coordination numbers are estimated to be within the range of 5.7–5.8 for Na+ and 6.9–7.0 for K+.
Penta-, tetra-, tri-, and difluorobenzenes undergo direct arylation with a wide range of arylhalides in high yield. Inverse reactivity is observed compared to the common electrophilic aromatic ...substitution pathway since electron-deficient, C−H acidic arenes react preferentially. Computational studies indicate that C−H bond cleavage occurs via a concerted carbon−palladium and carbon−hydrogen bond cleaving event involving a carbonate or a bromide ligand. The reactions are rapid, require only a slight excess of the perfluoroarene reagent, and utilize commercially available, air-stable catalyst precursors.
Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics ...simulations combined with the inhomogeneous solubility-diffusion model, which requires calculation of the potential of mean force and position-dependent diffusivity of the solute along the transmembrane axis. In this paper, we assess the efficiency and accuracy of several methods for the calculation of the permeability of a model DMPC bilayer to urea, benzoic acid, and codeine. We compare umbrella sampling, replica exchange umbrella sampling, adaptive biasing force, and multiple-walker adaptive biasing force for the calculation of the transmembrane PMF. No definitive advantage for any of these methods in their ability to predict the membrane permeability coefficient P m was found, provided that a sufficiently long equilibration is performed. For diffusivities, a Bayesian inference method was compared to a generalized Langevin method, both being sensitive to chosen parameters and the slow relaxation of membrane defects. Agreement within 1.5 log units of the computed P m with experiment is found for all permeants and methods. Remaining discrepancies can likely be attributed to limitations of the force field as well as slowly relaxing collective movements within the lipid environment. Numerical calculations based on model profiles show that P m can be reliably estimated from only a few data points, leading to recommendations for calculating P m from simulations.
London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 ...Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquidsbenzene, toluene, cyclohexane, n-pentane, and n-hexanewhich resulted in improved accuracy in the computed enthalpies of vaporization despite only having to evaluate a much smaller section of the parameter space.
Ring-opening hydroarylation of cyclopropanes is typically limited to substrates bearing a donor-acceptor motif. Here, the transformation is achieved for monosubstituted cyclopropanes by using ...catalytic Brønsted acid in hexafluoroisopropanol (HFIP) solvent, constituting a rare example where such cyclopropanes engage in intermolecular C-C bond formation. Branched products are obtained when electron-rich arylcyclopropanes react with a broad scope of arene nucleophiles in accord with a simple S
1-type ring-opening mechanism. In contrast, linear products are obtained when cyclopropylketones react with electron-rich arene nucleophiles. In the latter case, mechanistic experiments and DFT-calculations support a homo-conjugate addition pathway.
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