Orlando Acevedo

Advances in Quantum and Molecular Mechanical (QM/MM) Simulations for Organic and Enzymatic Reactions

Application of combined quantum and molecular mechanical (QM/MM) methods focuses on predicting activation barriers and the structures of stationary points for organic and enzymatic reactions. Characterization of the factors that stabilize transition structures in solution and in enzyme active sites provides a basis for design and optimization of catalysts. Continued technological advances allowed for expansion from prototypical cases to mechanistic studies featuring detailed enzyme and condensed-phase environments with full integration of the QM calculations and configurational sampling. This required improved algorithms featuring fast QM methods, advances in computing changes in free energies including free-energy perturbation (FEP) calculations, and enhanced configurational sampling. In particular, the present Account highlights development of the PDDG/PM3 semi-empirical QM method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo (MC) simulations, and a polynomial quadrature method for efficient modeling of proton-transfer reactions. The utility of this QM/MM/MC/FEP methodology is illustrated for a variety of organic reactions including substitution, decarboxylation, elimination, and pericyclic reactions. A comparison to experimental kinetic results on medium effects has verified the accuracy of the QM/MM approach in the full range of solvents from hydrocarbons to water to ionic liquids. Corresponding results from ab initio and density functional theory (DFT) methods with continuum-based treatments of solvation reveal deficiencies, particularly for protic solvents. Also summarized in this Account are three specific QM/MM applications to biomolecular systems: (1) a recent study that clarified the mechanism for the reaction of 2-pyrone derivatives catalyzed by macrophomate synthase as a tandem Michael-aldol sequence rather than a Diels-Alder reaction, (2) elucidation of the mechanism of action of fatty acid amide hydrolase (FAAH), an unusual Ser-Ser-Lys proteolytic enzyme, and (3) the construction of enzymes for Kemp elimination of 5-nitrobenzisoxazole that highlights the utility of QM/MM in the design of artificial enzymes.

Development of OPLS-AA Force Field Parameters for 68 Unique Ionic Liquids

OPLS-AA force field parameters have been developed and validated for use in the simulation of 68 unique combinations of room temperature ionic liquids featuring 1-alkyl-3-methylimidazolium [RMIM] (R = Me, Et, Bu, Hex, Oct), N-alkylpyridinium [RPyr], and choline cations, along with Cl(-), PF6(-), BF4(-), NO3(-), AlCl4(-), Al2Cl7(-), TfO(-), saccharinate, and acesulfamate anions. The new parameters were fit to conformational profiles from gas-phase ab initio calculations at the LMP2/cc-pVTZ(-f)//HF/6-31G(d) theory level and compared to experimental condensed-phase structural and thermodynamic data. Monte Carlo simulations of the ionic liquids gave relative deviations from experimental densities of ca. 1-3% at 25 °C for most combinations and also yielded close agreement over a temperature range of 5 to 90 °C. Predicted heats of vaporization compared well with available experimental data and estimates. Transferability of the new parameters to multiple alkyl side-chain lengths for [RMIM] and [RPyr] was determined to give excellent agreement with charges and torsion potentials developed specific to desired alkyl lengths in 35 separate ionic liquid simulations. As further validation of the newly developed parameters, the Kemp elimination reaction of benzisoxazole via piperidine was computed in 1-butyl-3-methylimidazolium hexafluorophosphate [BMIM][PF6] using mixed quantum and molecular mechanics (QM/MM) simulations and was found to give close agreement with the experimental free energy of activation.

Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations.

The impact of acidic and basic ionic liquid 1-ethyl-3-methylimidazolium chloride (EMIC) melts upon cyclopentadiene and methyl acrylate Diels-Alder reaction rates has been investigated using QM/MM calculations. The ability of the ionic liquid to act as a hydrogen bond donor (cation effect), moderated by its hydrogen bond accepting ability (anion effect), has been proposed previously to explain observed endo/exo ratios. However, the molecular factors that endow ionic liquids with their rate enhancing potential remain unknown. New OPLS-AA force field parameters in conjunction with potentials of mean force (PMF) derived from free energy perturbation calculations in Monte Carlo simulations (MC/FEP) are used to compute activation energies. QM/MM simulations using a periodic box of ions reproduce relative rate enhancements for the EMIC melts compared to water and 1-chlorobutane that reproduce kinetic experiments. Solute-solvent interactions in acidic and basic ionic liquid melts have been analyzed at key stationary points along the reaction coordinate. The reaction rate was found to be greater in the acidic rather than the basic melt due to less-dominant ion-pairing in the acidic melt, enabling the EMI cation to better coordinate to the dienophile at the transition state. The simulations suggest that the hydrogen on C2 of the EMI cation does not contribute to stabilization of the transition state, as previously believed, and the interactions with the more sterically exposed hydrogens on C4 and C5 play a larger role. In addition, the relative stabilization of the transition state through electrostatic interactions with the EMI cation in the acidic melt is also greater than that afforded by the weaker Lewis-acid effect provided by hydrogen bonding with water molecules in aqueous solution.

Mechanism of photolytic decomposition of N-halamine antimicrobial siloxane coatings.

Generally, antimicrobial N-halamine siloxane coatings can be rehalogenated repetitively upon loss of their biocidal efficacies, a marked advantage over coatings containing other antimicrobial materials. However, the N-halamine materials tend to slowly decompose upon exposure to ultraviolet irradiation as in direct sunlight. In this work the mechanism of photolytic decomposition for the N-halamine siloxanes has been studied using spectroscopic and theoretical methods. It was found that the N-chlorinated coatings slowly decomposed upon UVA irradiation, whereas the unhalogenated coatings did not. Model compound evidence in this work suggests that upon UVA irradiation, the N-Cl bond dissociates homolytically, followed by a Cl radical migration to the alkyl side chain connected to the siloxane tethering group. An alpha and/or beta scission then occurs causing partial loss of the biocidal moiety from the surface of the coated material, thus precluding complete rechlorination. NMR, FTIR, GCMS, and computations at the DFT (U)B3LYP/6-311++G(2d,p) level of theory have been employed in reaching this conclusion.

Exploring Solvent Effects upon the Menshutkin Reaction using a Polarizable Force Field

The energetics of the Menshutkin reaction between triethylamine and ethyl iodide have been computed using B3LYP and MP2 with the LANL2DZ, LANL2DZd, SVP, MIDI!, 6-311G(d,p), and aug-cc-PVTZ basis sets. Small- and large-core energy-consistent relativistic pseudopotentials were employed. Solvent effect corrections were computed from QM/MM Monte Carlo simulations utilizing free-energy perturbation theory, PDDG/PM3, and both a nonpolarizable OPLS and polarizable OPLS-AAP force field. The B3LYP/MIDI! theory level provided the best DeltaG(++) values with a mean absolute error (MAE) of 4.9 kcal/mol from experiment in cyclohexane, CCl(4), THF, DMSO, acetonitrile, water, and methanol. However, the relative rates in cyclohexane, and to a certain extent CCl(4), were determined to be greatly underestimated when using the nonpolarizable OPLS force field. An overall reduction in the MAE to 3.1 kcal/mol using B3LYP/MIDI!/OPLS-AAP demonstrated the need for a fully polarizable force field when computing solvent effects for highly dipolar transition structures in low-dielectric media. The MAEs obtained with PDDG/PM3/OPLS and OPLS-AAP of 5.3 and 3.8 kcal/mol, respectively, provided comparable results to B3LYP at a fraction of the computational resources. The large rate accelerations observed in the reaction were correlated to an increased stabilization of the emerging charge separation at the transition state via favorable solute-solvent interactions.

Identification of PLX4032-resistance mechanisms and implications for novel RAF inhibitors

BRAF inhibitors improve melanoma patient survival, but resistance invariably develops. Here we report the discovery of a novel BRAF mutation that confers resistance to PLX4032 employing whole‐exome sequencing of drug‐resistant BRAFV600K melanoma cells. We further describe a new screening approach, a genome‐wide piggyBac mutagenesis screen that revealed clinically relevant aberrations (N‐terminal BRAF truncations and CRAF overexpression). The novel BRAF mutation, a Leu505 to His substitution (BRAFL505H), is the first resistance‐conferring second‐site mutation identified in BRAF mutant cells. The mutation replaces a small nonpolar amino acid at the BRAF‐PLX4032 interface with a larger polar residue. Moreover, we show that BRAFL505H, found in human prostate cancer, is itself a MAPK‐activating, PLX4032‐resistant oncogenic mutation. Lastly, we demonstrate that the PLX4032‐resistant melanoma cells are sensitive to novel, next‐generation BRAF inhibitors, especially the ‘paradox‐blocker’ PLX8394, supporting its use in clinical trials for treatment of melanoma patients with BRAF‐mutations.

Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution.

The energetics of methyl-transfer reactions from dimethylammonium, tetramethylammonium, and trimethylsulfonium to dimethylamine were computed with density functional theory, MP2, CBS-QB3, and quantum mechanics/molecular mechanics (QM/MM) Monte Carlo methods. At the CBS-QB3 level, the gas-phase activation enthalpies are computed to be 9.9, 15.3, and 7.9 kcal/mol, respectively. MP2/6-31+G(d,p) activation enthalpies are in best agreement with the CBS-QB3 results. The effects of aqueous solvation on these reactions were studied with polarizable continuum model, generalized Born/surface area (GB/SA), and QM/MM Monte Carlo simulations utilizing free-energy perturbation theory in which the PDDG/PM3 semiempirical Hamiltonian for the QM and explicit TIP4P water molecules in the MM region were used. In the aqueous phase, all of these reactions proceed more slowly when compared to the gas phase, since the charged reactants are stabilized more than the transition structure geometries with delocalized positive charges. In order to obtain the aqueous-phase activation free energies, the gas-phase activation free energies were corrected with the solvation free energies obtained from single-point conductor-like polarizable continuum model and GB/SA calculations for the stationary points along the reaction coordinate.

An Ionic Liquid Dependent Mechanism for Base Catalyzed β-Elimination Reactions from QM/MM Simulations

Ionic liquids have been proposed to induce a mechanistic change in the reaction pathway for the fundamentally important base-induced β-elimination class compared to conventional solvents. The role of the reaction medium in the elimination of 1,1,1-tribromo-2,2-bis(3,4-dimethoxyphenyl)ethane via two bases, piperidine and pyrrolidine, has been computationally investigated using methanol and the ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and hexafluorophosphate [BMIM][BF(4)] and [BMIM][PF(6)], respectively. QM/MM Monte Carlo simulations utilizing free-energy perturbation theory found the ionic liquids did produce a reaction pathway change from an E1cB-like mechanism in methanol to a pure E2 route that is consistent with experimental observations. The origin of the ionic liquid effect has been found as: (1) a combination of favorable electrostatic interactions, for example, bromine-imidazolium ion, and (2) π-π interactions that enhance the coplanarity between aromatic rings maximizing the electronic effects exerted on the reaction route. Solute-solvent interaction energies have been analyzed and show that liquid clathrate solvation of the transition state is primarily responsible for the observed mechanistic changes. This work provides the first theoretical evidence of an ionic liquid dependent mechanism and elucidates the interplay between sterics and electrostatics crucial to understanding the effect of these unique solvents upon chemical reactions.

A Remodeled Protein Arginine Methyltransferase 1 (PRMT1) Generates Symmetric Dimethylarginine

Background: Asymmetric and symmetric dimethylarginine (ADMA and SDMA) residues are biologically distinct products of protein arginine methyltransferase (PRMT) isoforms. Results: Met-48 in PRMT1 regulates the regiochemistry of dimethylation, and SDMA formation is energetically costly. Conclusion: Steric changes in the PRMT1 active site can reprogram product formation. Significance: SDMA-forming PRMTs may require additional factors to overcome the energetic cost of SDMA. Protein arginine methylation is emerging as a significant post-translational modification involved in various cell processes and human diseases. As the major arginine methylation enzyme, protein arginine methyltransferase 1 (PRMT1) strictly generates monomethylarginine and asymmetric dimethylarginine (ADMA), but not symmetric dimethylarginine (SDMA). The two types of dimethylarginines can lead to distinct biological outputs, as highlighted in the PRMT-dependent epigenetic control of transcription. However, it remains unclear how PRMT1 product specificity is regulated. We discovered that a single amino acid mutation (Met-48 to Phe) in the PRMT1 active site enables PRMT1 to generate both ADMA and SDMA. Due to the limited amount of SDMA formed, we carried out quantum mechanical calculations to determine the free energies of activation of ADMA and SDMA synthesis. Our results indicate that the higher energy barrier of SDMA formation (ΔΔG‡ = 3.2 kcal/mol as compared with ADMA) may explain the small amount of SDMA generated by M48F-PRMT1. Our study reveals unique energetic challenges for SDMA-forming methyltransferases and highlights the exquisite control of product formation by active site residues in the PRMTs.

Pairwise Alternatives to Ewald Summation for Calculating Long-Range Electrostatics in Ionic Liquids.

Room temperature ionic liquid calculations require extensive sampling due to the large degree of localized structuring in the liquid phase relative to conventional solutions. Consequently, a large amount of computer time is required for the convergence of solvent properties, much of which is spent evaluating long-range electrostatics via Ewald summations. The damped Coulomb potential and cutoff-neutralized method of Wolf et al. (J. Chem. Phys.1999, 110, 8254) provides the framework for an accurate, linear-scaling alternative to Ewald in the ionic liquid simulations. The method has been the subject of multiple modifications for improved accuracy, including the damped Coulombic potential of Zahn et al. (J. Phys. Chem. B2002, 106, 10725), the damped shifted force method of Fennell and Gezelter (J. Chem. Phys.2006, 124, 234104), and the shifted force gradient of Kale and Herzfeld (J. Chem. Theory Comput.2011, 7, 3620). These pairwise electrostatic interaction alternatives along with the CHARMM shifted force potential and a new method proposed herein, the shifted force third derivative (SF3), have been examined on 59 unique ionic liquid combinations of 1-alkyl-3-methylimidazolium [RMIM] (R = M (methyl), E (ethyl), B (butyl), H (hexyl), and O (octyl)) and N-alkylpyridinium [RPyr] cations, along with Cl(-), PF6(-), BF4(-), NO3(-), AlCl4(-), Al2Cl7(-), and TfO(-) anions. Monte Carlo simulations utilizing our custom OPLS-AA ionic liquid force field and employing the pairwise alternatives with multiple cutoff distances and electrostatic damping values are compared to the energetics from full Ewald sums.