Force-Field Development and Molecular Dynamics Simulations of Ferrocene–Peptide Conjugates as a Scaffold for Hydrogenase Mimics

A Quantum-Guided Molecular Mechanics Force Field for the Ferrocene Scaffold

Ferrocene derivatives have a wide range of applications, including as ligands in asymmetric catalysis, due to their chemical stability, rigid backbone, steric bulk, and ability to encode stereochemical information via planar chirality. Unfortunately, few of the available molecular mechanics force fields incorporate parameters for the accurate study of this important building block. Here, we present a MM3* force field for ferrocenyl ligands, which was generated using the quantum-guided molecular mechanics (Q2MM) method. Detailed validation by comparison to DFT calculations and crystal structures demonstrates the accuracy of the parameters and uncovers the physical origin of deviations through excess energy analysis. Combining the ferrocene force field with a force field for Pd-allyl complexes and comparing the crystal structures shows the compatibility with previously developed MM3* force fields. Finally, the ferrocene force field was combined with a previously published transition-state force field to predict the stereochemical outcomes of the aminations of Pd-allyl complexes with different amines and different chiral ferrocenyl ligands, with an R² of ∼0.91 over 10 examples.

On-the-Fly Training of Atomistic Potentials for Flexible and Mechanically Interlocked Molecules

Mechanically interlocked molecules have gained significant attention because of their unique ability to perform well-defined motions originating from their entanglement, which is important for the design of artificial molecular machines. Atomistic simulations based on force fields (FFs) provide detailed insights into such architectures at the molecular level enabling one to predict the resulting functionalities. However, the development of reliable FFs is still challenging and time-consuming, in particular for highly dynamic and interlocked structures such as rotaxanes, which exhibit a large number of different conformers. In the present work, we present an on-the-fly training (OTFT) algorithm. By a guided and nonguided phase space sampling, relevant reference data are automatically and continuously generated and included for the on-the-fly parametrization of the FF based on a population swapping genetic algorithm (psGA). The OTFT approach provides a fast and automated FF parametrization scheme and tackles problems caused by missing phase space information or the need for big data. We demonstrate the high accuracy of the developed FF for flexible molecules with respect to equilibrium and out-of-equilibrium properties. Finally, by applying the ab initio parametrized FF, molecular dynamic simulations were performed up to experimentally relevant time scales (ca. 1 μs) enabling capture in detail of the structural evaluation and mapping out of the free-energy topology. The on-the-fly training approach thus provides a strong foundation toward automated FF developments and large-scale investigations of phenomena in and out of thermal equilibrium.

Properties of Conjugated Materials from Quantum Chemistry Coupled to Molecular Dynamics Generated Ensembles

We provide a set of molecular dynamics simulations employing a force field specifically parameterized for organic π-conjugated materials. The resulting conformation ensemble was coupled to quantum chemistry calculations, and quantities of interest for optoelectronic applications, namely, ground- and excited-state energies, oscillator strengths, and dipole moments were extracted. This combined approach allowed not only exploration of the configurational landscape but also of the resulting electronic properties of each frame within the simulation and thus probe the link between conformation and property. A study was made of the sampling and convergence requirements to yield reliable averages over the ensemble. Typically between 800 and 1000 conformations were sufficient to ensure convergence of properties. However, for some oligomers, more configurations were required to achieve convergence of the oscillator strength and magnitude of the dipole moment.

Recognition of HIV-inactivating peptide triazoles by the recombinant soluble Env trimer, BG505 SOSIP.664

Peptide triazole (PT) antagonists interact with gp120 subunits of HIV-1 Env trimers to block host cell receptor interactions, trigger gp120 shedding, irreversibly inactivate virus and inhibit infection. Despite these enticing functions, understanding the structural mechanism of PT-Env trimer encounter has been limited. In this work, we combined competition interaction analysis and computational simulation to demonstrate PT binding to the recombinant soluble trimer, BG505 SOSIP.664, a stable variant that resembles native virus spikes in binding to CD4 receptor as well as known conformationally-dependent Env antibodies. Binding specificity and computational modeling fit with encounter through complementary PT pharmacophore Ile-triazolePro-Trp interaction with a 2-subsite cavity in the Env gp120 subunit of SOSIP trimer similar to that in monomeric gp120. These findings argue that PTs are able to recognize and bind a closed prefusion state of Env trimer upon HIV-1 encounter. The results provide a structural model of how PTs exert their function on virion trimeric spike protein and a platform to inform future antagonist design. Proteins 2017; 85:843-851. © 2016 Wiley Periodicals, Inc.

Molecular structures and solvation of free monomeric and dimeric ferriheme in aqueous solution: insights from molecular dynamics simulations and extended X-ray absorption fine structure spectroscopy

CHARMM force field parameters have been developed to model nonprotein bound five-coordinate ferriheme (ferriprotoporphyrin IX) species in aqueous solution. Structures and solvation were determined from molecular dynamics (MD) simulations at 298 K of monomeric [HO-ferriheme](2-), [H2O-ferriheme](-), and [H2O-ferriheme](0); π-π dimeric [(HO-ferriheme)2](4-), [(H2O-ferriheme)(HO-ferriheme)](3-), [(H2O-ferriheme)2](2-), and [(H2O-ferriheme)2](0); and μ-oxo dimeric [μ-(ferriheme)2O](4-). Solvation of monomeric species predominated around the axial ligand, meso-hydrogen atoms of the porphyrin ring (Hmeso), and the unligated face. Existence of π-π ferriheme dimers in aqueous solution was supported by MD calculations where such dimers remained associated over the course of the simulation. Porphyrin rings were essentially coplanar. In these dimers major and minor solvation was observed around the axial ligand and Hmeso positions, respectively. In μ-oxo ferriheme, strong solvation of the unligated face and bridging oxide ligand was observed. The solution structure of the μ-oxo dimer was investigated using extended X-ray absorption fine structure (EXAFS) spectroscopy. The EXAFS spectrum obtained from frozen solution was markedly different from that recorded on dried μ-oxo ferriheme solid. Inclusion of five solvent molecules obtained from spatial distribution functions in the structure generated from MD simulation was required to produce acceptable fits to the EXAFS spectra of the dimer in solution, while the solid was suitably fitted using the crystal structure of μ-oxo ferriheme dimethyl ester which included no solvent molecules.

Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase

Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexible in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of Cα and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H2-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.

Unusual carbamate-directed CH-activation at an annulated ferrocenophane framework

The tetrahydroazepine-annulated [3]ferrocenophane carbamate (4) was synthesized by two different linear routes starting from the readily available α-dimethylamino[3]ferrocenophane-ortho-carbaldehyde rac-6. The carbamate directed lithiation of 4 resulted in a selective attack at a (Cp)C-H bond at the higher substituted "lower" [3]ferrocenophane Cp-ring to eventually yield the respective ester (18) after treatment with ClCO(2)Me.