Molecular Mechanics Study of Oligomeric Models for Poly(ferrocenylsilanes) Using the Extensible Systematic Forcefield (ESFF)

Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach

Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys₄ tetrahedral binding site, was redesigned in order to accommodate a Cys₂His₂ site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.

Tuning chain extender structure to prepare high-performance thermoplastic polyurethane elastomers

In this work, a novel strategy is developed to solve the issue of mutually exclusive high mechanical robustness and thermo-stability for thermoplastic polyurethane (PU). A leaf-like and reticulate interfingering superstructure can be seen. The superstructure of polyurethanes can also be tuned by the polarity of chain extender molecular via changing the number for ferrocene redox centres, thus to further enhance the thermal stability and elasticity of PUs. As a result, by incorporating bisferrocene units into the main chain of PU, a high-performance PU elastomer can be synthesized with a highest initial degradation temperature of T_5% of 345 °C, a highest tensile strength of 42.3 MPa with an elongation over 1000%, as well as a toughness of 19.6 GJ m⁻³. These results conclusively suggest that high-performance thermoplastic polyurethane elastomers had great promise for potential application in a wide range of practical fields.

Ester-containing ferrocenyl diols are introduced as chain extenders to tune the polyurethane superstructure to optimize thermo-stability and elasticity simultaneously.

General van der Waals potential for common organic molecules

This work presents a systematic development of a new van der Waals potential (vdW2016) for common organic molecules based on symmetry-adapted perturbation theory (SAPT) energy decomposition. The Buf-14-7 function, as well as Cubic-mean and Waldman-Hagler mixing rules were chosen given their best performance among other popular potentials. A database containing 39 organic molecules and 108 dimers was utilized to derive a general set of vdW parameters, which were further validated on nucleobase stacking systems and testing organic dimers. The vdW2016 potential is anticipated to significantly improve the accuracy and transferability of new generations of force fields for organic molecules.

Polyferrocenylsilanes: synthesis, properties, and applications

This comprehensive review covers polyferrocenylsilanes (PFSs), a well-established, readily accessible class of main chain organosilicon metallopolymer. The focus is on the recent advances involving PFS homopolymers and block copolymers and the article covers the synthesis, properties, and applications of these fascinating materials.

Diastereoselective Pictet–Spengler Reactions of a Tethered 2-Aminoimidazole

The diastereoselective Pictet–Spengler reaction of aminopropyl-2-aminoimidazole with enantiopure aldehydes has been investigated. With amino acid-derived aldehydes, anti stereochemistry is favoured, with a diastereoselectivity up to 92 % achievable. The absolute stereochemistry of the products was determined through synthesis of a rigid derivative and from NMR data in combination with molecular modelling. The diastereoselectivity was shown to be dependent on the steric bulk of the amino acid side chain and independent of the nitrogen protecting group. Lewis acids catalysed the reaction but did not affect the diastereoselectivity.

De novo design, synthesis and characterisation of MP3, a new catalytic four-helix bundle hemeprotein

A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four-helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix-loop-helix/heme/helix-loop-helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP-like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix-forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe(III)-MP3 possesses peroxidase-like activity comparable to R38A-hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic.

Equivalence of the Wei potential model and Tietz potential model for diatomic molecules

By employing the dissociation energy and the equilibrium bond length for a diatomic molecule as explicit parameters, we generate improved expressions for the well-known Rosen-Morse, Manning-Rosen, Tietz, and Frost-Musulin potential energy functions. It is found that the well-known Tietz potential function that is conventionally defined in terms of five parameters [T. Tietz, J. Chem. Phys. 38, 3036 (1963)] actually only has four independent parameters. It is shown exactly that the Wei [Phys. Rev. A 42, 2524 (1990)] and the well-known Tietz potential functions are the same solvable empirical function. When the parameter h in the Tietz potential function has the values 0, +1, and -1, the Tietz potential becomes the standard Morse, Rosen-Morse, and Manning-Rosen potentials, respectively.

UTILIZATION OF GENERALIZED MORSE PARAMETERS FOR CONVENTIONAL MORSE FUNCTIONS USED IN MOLECULAR MECHANICS

The greater number of parameters in the generalized Morse (GM) potential energy function, as compared with the conventional Morse (CM) potential, allows the former to be more flexible for curve fitting of experimental data. Owing to its simplicity, the CM function has been more widely adopted in molecular modeling softwares. Hence the conversion of the more accurate GM parameters into the commonly used CM parameter is useful for enhancing the latter. This paper proposes three methods for extracting the CM parameter from the GM parameters. The short-range relation was obtained by equating curvatures at the minimum well-depth, whereas the mid-range relation was obtained by equating equal energy integral from equilibrium to dissociation. The long-range relation was obtained by equating the CM parameter with the attractive index of the GM parameter.

Evaluation of Density Functionals, SCC-DFTB, Neglect of Diatomic Differential Overlap (NDDO) Models and Molecular Mechanics Methods for Prolyl-Leucyl-Glycinamide (PLG) and Structural Derivatives

Prolyl-leucyl-glycinamide (PLG) is a unique endogenous peptide that modulates dopamine receptor subtypes of the D(2) receptor family within the CNS. We seek to elucidate the structural basis and molecular mechanism by which PLG and its analogues modulate dopamine receptors, toward the development of new therapeutics to treat Parkinson's disease, tardive dyskinesia and schizophrenia. As a first step toward establishing a validated protocol for accurate computational modeling of PLG and associated peptidomimetic analogues, we evaluated the accuracy of density functional theory (DFT), wavefunction theory (WFT), and molecular mechanics (MM) calculations for PLG and for a library of structurally related small molecules. We first tested twelve local and nonlocal density functionals, Hartree-Fock (HF) theory, four "semiempirical" methods of the neglect of diatomic differential overlap (NDDO) type, and one self-consistent-charge nonorthogonal tight-binding (SCC-DFTB) method as implemented in two software suites, against coupled-cluster benchmark geometries for 4-methylthiazolidine, a small molecule that comprises key structural features present in our PLG analogue library. DFT and HF calculations were done with the MG3S augmented polarized triple-zeta basis set. We find that for 4-methylthiazolidine bond distances, DFT significantly outperforms NDDO, and both SCC-DFTB versions we evaluated perform worse than HF theory and are less accurate than 83% of the density functionals tested. The top five functionals for 4-methylthiazolidine were M05-2X, mPW1PW, B97-2, M06-2X, and PBEh, with mean unsigned errors (MUEs) in bond length of 0.0017, 0.0020, 0.0023, 0.0025 and 0.0027 Å, respectively. The widely used B3LYP functional ranked 11(th) out of twelve functionals evaluated, slightly below SCC-DFTB, and is significantly less accurate for 4-methylthiazolidine bond distances (MUE = 0.0095 Å) than the best local functional (M06-L, MUE = 0.0030 Å), which is far less computationally costly. Based on that initial analysis, we obtained new M05-2X benchmark geometric parameters for PLG and a library of eleven peptidomimetic derivatives, which we in turn used to examine the accuracy of thirty-four popular molecular mechanics (MM) force fields, four NDDO approaches, and SCC-DFTB for the full compound structures. Here, we found that ∼70% of the MM force fields tested superior to the best semiempirical and SCC-DFTB codings. Moreover, AMBER-type force fields proved most accurate among MM methods for this class of small-molecule peptidomimetics; the AMBER-type methods comprised eight out of the top ten molecular mechanics options we tested.

Polyferrocenylsilane-Based Polymer Systems

The study of metallopolymers has blossomed into a mature field over the last few decades. Especially, polyferrocenylsilane (PFS) chemistry has taken a tremendous leap and continues to raise intense interest. Since the discovery of thermal ring-opening polymerization (ROP) of sila[1]ferrocenophanes, PFSs have been also accessed by anionic, cationic, transition-metal-catalyzed, and photolytic anionic ROP methodologies. A plethora of synthetic strategies have been devised, enabling access to a wide variety of copolymers, polyelectrolytes, and nanostructured materials. The distinctive physical properties and functions of many PFS-based polymers have been explored, leading to their apt exploitation in technical applications. Therefore, it is conceivable that PFS-related platforms might be indispensable nano-objects in the near future, as they stand on the verge of a new generation of sophisticated materials.

Competing through-space and through-bond, intramolecular triplet-energy transfer in a supposedly rigid ruthenium(II) tris(2,2'-bipyridine)--fullerene molecular dyad

A ditopic ruthenium(II) tris(2,2'-bipyridyl)-based fullerene conjugate has been synthesized so as to separate the photoactive terminals by way of a short ethynylene spacer group that is expected to act as a rigid rod. Intramolecular triplet-energy transfer from the metal complex to the fullerene is quantitative at all temperatures and there is no indication for competing electron transfer. Temperature dependence studies indicate two pathways for triplet-energy transfer. An activationless route dominates at low temperature and is attributed to through-bond electron exchange that takes place via super-exchange interactions. The triplet energy of the bridging unit lies well above that of the metal complex. An activated process is switched-on at high temperatures and is believed to involve through-space electron exchange within closed conformations. Molecular dynamics simulations predict that, in addition to an extended conformation, the linker can distort in such a way that the terminals come into orbital contact. In fact, the resultant closed conformation possesses an idealised geometry for fast electron exchange.

Electronic Coupling in Mixed-Valence Dinuclear Ferrocenes and Cobaltocenes with Saturated Bridging Groups

We have synthesised a series of new dinuclear metallocenes [{M(Cp*)(C5H4)}2X] (Cp* = eta5-pentamethylcyclopentadienyl; M = Fe, Co, X = CMe2, SiMe2, GeMe2; M = Fe, X = Si2Me4). For the neutral dicobalt complexes, magnetic susceptibility measurements reveal intramolecular antiferromagnetic interactions of -21 and -14 cm(-1) for SiMe2- and GeMe2-bridged species, respectively, but negligible interaction for the CMe2-bridged compound. In contrast, intervalence charge-transfer (IVCT) data for the mixed-valence monocations of both Fe and Co complexes show electronic coupling to decrease in the order CMe2 > SiMe2 > GeMe2. This suggests that electronic coupling is principally through-space in contrast to results found from previous studies. The IVCT data also show much stronger coupling in the dicobalt species versus their diiron analogues.

Molecular simulations to determine the chelating mechanisms of various metal ions to the His-tag motif: a preliminary study

In the present study, molecular simulations were performed to investigate the chelating mechanisms of various metal ions to the His-tag motifs with various His residues. The chelation mostly involved the i and i+2 His residues for Ni(2+), Zn(2+), Cu(2+), and Co(2+), while the cooperation of 3 His residues was necessary when Fe(3+) was involved in chelation with His-tags having more than 4 His residues. Metal ion was best fitted into the pocket formed by the imidazole nitrogens while it was about equally located among these nitrogen atoms. His-tag6 was found to have little effect on the structural integrity while the target protein contains more than 68 amino acid residues. Ni(2+) interacted with the imidazole nitrogen of His3 in the beginning of chelation, and then entered into the pocket formed by His3 and His5 at 4 ns during the 10 ns molecular dynamics simulations. The fast chelating process resulted in successful application of IMAC techniques in efficient protein purification.

An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems

ESFF is a rule-based force field designed for modeling organic, inorganic, and organometallic systems. To cover this broad range of molecular systems, ESFF was developed in an extensible and systematic manner. Several unique features were introduced including pseudoangle and a dot product function representing torsion energy terms. The partial atomic charges that are topology-dependent are determined from ab initio (DFT) calculated electronegativity and hardness for valence orbitals. The van der Waals parameters are charge-dependent, and correlated with the ionization potential for atoms in various valence states. To obtain a set of well-defined and physically meaningful parameters, ESFF employs semiempirical rules to translate atomic-based parameters to parameters typically associated with a covalent valence force field. The atomic parameters depend not only on atom type, but also on internal type, thus resulting in a more accurate force field. This article presents the theory and the method used to develop the force field. The force field has been applied to molecular simulations of a wide variety of systems including nucleic acids, peptides, hydrocarbons, porphyrins, transition metal complexes, zeolites, and organometallic compounds. Agreement with the experimental results indicates that ESFF is a valuable tool in molecular simulations for understanding and predicting both crystal and gas phase molecular structures.

The effect of metal ions on the binding of ethanol to human alcohol dehydrogenase beta2beta2

Molecular docking simulations were performed in this study to investigate the importance of both structural and catalytic zinc ions in the human alcohol dehydrogenase beta(2)beta(2) on substrate binding. The structural zinc ion is not only important in maintaining the structural integrity of the enzyme, but also plays an important role in determining substrate binding. The replacement of the catalytic zinc ion or both catalytic and structural zinc ions with Cu(2+) results in better substrate binding affinity than with the wild-type enzyme. The width of the bottleneck formed by L116 and V294 in the substrate binding pocket plays an important role for substrate entrance. In addition, unfavorable contacts between the substrate and T48 and F93 prevent the substrate from moving too close to the metal ion. The optimal binding position occurs between 1.9 and 2.4 A from the catalytic metal ion.

Polyferrocenylsilane microspheres: synthesis, mechanism of formation, size and charge tunability, electrostatic self-assembly, and pyrolysis to spherical magnetic ceramic particles

Pt(0)-catalyzed ring-opening precipitation copolymerization of [1]silaferrocenophanes fcSiMe(2) (3) and the spirocyclic cross-linker fcSi(CH(2))(3) (4) (fc = Fe(eta(5)-C(5)H(4))(2)) was used to prepare polyferrocenylsilane microspheres (PFSMSs) under mild conditions. By varying the reaction conditions, a wide variety of other morphologies was obtained. The effects of temperature, monomer ratio, solvent composition, catalyst concentration, and time on the observed morphology were investigated and interpreted in terms of a mechanism for microsphere formation. The most well-defined particles were formed using equimolar amounts of 3 and 4, in a 50:50 mixture of xylenes and decane at 60 degrees C with gentle agitation. Chemical oxidation of the polymeric microspheres led to positively charged particles (OPFSMSs) which underwent electrostatically driven self-assembly with negatively charged silica microspheres to form core-corona composite particles. Redox titration with controlled amounts of the one-electron oxidant [N(C(6)H(4)Br-p)(3)][PF(6)] in acetonitrile led to the oxidation of the outer 0.15 microm (ca. 32%) of the PFSMSs. The resulting OPFSMSs were reduced back to their neutral form by reaction with hydrazine in methanol. Pyrolysis of the PFSMSs led to spherical magnetic ceramic replicas with tunable magnetic properties that organize into ordered 2-D arrays at the air-water interface under the influence of a magnetic field.

Study of substrate specificity of human aromatase by site directed mutagenesis

Human aromatase is responsible for estrogen biosynthesis and is implicated, in particular, in reproduction and estrogen-dependent tumor proliferation. The molecular structure model is largely derived from the X-ray structure of bacterial cytochromes sharing only 15-20% identities with hP-450arom. In the present study, site directed mutagenesis experiments were performed to examine the role of K119, C124, I125, K130, E302, F320, D309, H475, D476, S470, I471 and I474 of aromatase in catalysis and for substrate binding. The catalytic properties of mutants, transfected in 293 cells, were evaluated using androstenedione, testosterone or nor-testosterone as substrates. In addition, inhibition profiles for these mutants with indane or indolizinone derivatives were obtained. Our results, together with computer modeling, show that catalytic properties of mutants vary in accordance with the substrate used, suggesting possible differences in substrates positioning within the active site. In this respect, importance of residues H475, D476 and K130 was discussed. These results allow us to hypothesize that E302 could be involved in the aromatization mechanism with nor-androgens, whereas D309 remains involved in androgen aromatization. This study highlights the flexibility of the substrate-enzyme complex conformation, and thus sheds new light on residues that may be responsible for substrate specificity between species or aromatase isoforms.