Solid-Phase-Supported Chemoenzymatic Synthesis and Analysis of Chondroitin Sulfate Proteoglycan Glycopeptides.

Proteoglycans (PGs), consisting of glycosaminoglycans (GAGs) linked with the core protein through a tetrasaccharide linkage region, play roles in many important biological events. The chemical synthesis of PG glycopeptides is extremely challenging. In this work, the enzymes required for synthesis of chondroitin sulfate (CS) PG (CSPG) have been expressed and the suitable sequence of enzymatic reactions has been established. To expedite CSPG synthesis, the peptide acceptor was immobilized on solid phase and the glycan units were directly installed enzymatically onto the peptide. Subsequent enzymatic chain elongation and sulfation led to the successful synthesis of CSPG glycopeptides. The CS dodecasaccharide glycopeptide was the longest homogeneous CS glycopeptide synthesized to date. The enzymatic synthesis was much more efficient than the chemical synthesis of the corresponding CS glycopeptides, which could reduce the total number of synthetic steps by 80 %. The structures of the CS glycopeptides were confirmed by mass spectrometry analysis and NMR studies. In addition, the interactions between the CS glycopeptides and cathepsin G were studied. The sulfation of glycan chain was found to be important for binding with cathepsin G. This efficient chemoenzymatic strategy opens new avenues to investigate the structures and functions of PGs.

Unraveling the electronic structure of LuH, LuN, and LuNH: building blocks of new materials.

Advances in superconductor technology have been pursued for decades, moving towards room temperature models, such as a postulated nitrogen-doped lutetium hydride network. While experimental observations have been contradictory, insight into the building blocks of potential new superconductor materials can be gained theoretically, unravelling the fascinating electronic structure of these compounds at a molecular level. Here, the fundamental building blocks of lutetium materials (LuH, LuN, and LuNH) have been examined. The structures, spectroscopic constants for the ground and excited states, and the potential energy curves have been obtained for these species using complete active self-consistent field (CASSCF) and multireference configuration interaction with Davidson's correction (MRCI+Q) methods. For LuNH, the energetic properties of its isomers are determined. The bond dissociation energies of the three building blocks are calculated with the state-of-the-art f-block ab initio correlation consistent composite approach (f-ccCA) and the high accuracy extrapolated ab initio thermochemistry (HEAT) scheme. As well, an analysis of different formation pathways of LuNH has been provided.

Binding of Per- and Polyfluoroalkyl Substances (PFAS) to the PPARγ/RXRα-DNA Complex.

Nuclear receptors are the fundamental building blocks of gene expression regulation and the focus of many drug targets. While binding to DNA, nuclear receptors act as transcription factors, governing a multitude of functions in the human body. Peroxisome proliferator-activator receptor γ (PPARγ) and the retinoid X receptor α (RXRα) form heterodimers with unique properties and have a primordial role in insulin sensitization. This PPARγ/RXRα heterodimer has been shown to be impacted by per- and polyfluoroalkyl substances (PFAS) and linked to a variety of significant health conditions in humans. Herein, a selection of the most common PFAS (legacy and emerging) was studied utilizing molecular dynamics simulations for PPARγ/RXRα. The local and global structural effects of PFAS binding on the known ligand binding pockets of PPARγ and RXRα as well as the DNA binding domain (DBD) of RXRα were inspected. The binding free energies were predicted computationally and were compared between the different binding pockets. In addition, two electronic structure approaches were utilized to model the interaction of PFAS within the DNA binding domain, density functional theory (DFT) and domain-based pair natural orbital coupled cluster with perturbative triples (DLPNO-CCSD(T)) approaches, with implicit solvation. Residue decomposition and hydrogen-bonding analysis were also performed, detailing the role of prominent residues in molecular recognition. The role of l-carnitine is explored as a potential in vivo remediation strategy for PFAS interaction with the PPARγ/RXRα heterodimer. In this work, it was found that PFAS can bind and act as agonists for all of the investigated pockets. For the first time in the literature, PFAS are postulated to bind to the DNA binding domain in a nonspecific manner. In addition, for the PPARγ ligand binding domain, l-carnitine shows promise in replacing smaller PFAS from the pocket.

Multireference Wavefunction-Based Investigation of the Ground and Excited States of LrF and LrO.

Complete active space self-consistent field (CASSCF) and multireference configuration interaction with Davidson correction (MRCI+Q) calculations have been carried out for lawrencium fluoride (LrF) and lawrencium oxide (LrO) molecules, detailing 19 and 20 electronic states for LrF and LrO, respectively. For LrF, two dissociation channels were considered, Lr(2P)+F(2P) and Lr(2D)+F(2P). However, due to the more complex electronic manifold of LrO, three dissociation channels were computed: Lr(2P)+O(3P), Lr(2D)+O(3P), and Lr(2P)+O(1D). In addition, equilibrium bond lengths, harmonic vibrational frequencies ωe, anharmonicity constants ωeχe, ΔG1/2 values, and excitation energies Te for the ground and several excited electronic states were calculated for both molecules, for the first time. Bond dissociation energies (BDEs) were calculated for LrF and LrO using several different levels of theory: unrestricted coupled-cluster with single, double, and perturbative triple excitations (UCCSD(T)), density functional theory (B3LYP, TPSS, M06-L, and PBE), and the correlation-consistent composite approach developed for f-elements (f-ccCA).

Multireference calculations on the ground and lowest excited states and dissociation energy of LuF.

High level multireference calculations were performed for LuF for a total of 132 states, including four dissociation channels Lu(2D) + F(2P), Lu(2P) + F(2P), and two Lu(4F) + F(2P). The 6s, 5d, and 6p orbitals of lutetium, along with the valence 2p and 3p orbitals of fluorine, were included in the active space, allowing for the accurate description of static and dynamic correlation. The Lu(4F) + F(2P) channel has intersystem spin crossings with the Lu(2P) + F(2P) and Lu(2D) + F(2P) channels, which are discussed herein. To obtain spectroscopic constants, bond lengths, and excited states, multi-reference configuration interaction (MRCI) was used at a quadruple-ζ basis set level, correlating also the 4f electrons and corresponding orbitals. Core spin-orbit (C-MRCI) calculations were performed, revealing that 13Π0- is the first excited state closely followed by 13Π0+. In addition, the dissociation energy of LuF was determined at different levels of theory, with a range of basis sets. A balance between core correlation and a relativistic treatment of electrons is fundamental to obtain an accurate description of the dissociation energy. The best prediction was obtained with a combination of coupled-cluster single, double, and perturbative triple excitations /Douglas-Kroll-Hess third order Hamiltonian methods at a complete basis set level with a zero-point energy correction, which yields a dissociation value of 170.4 kcal mol-1. Dissociation energies using density functional theory were calculated using a range of functionals and basis sets; M06-L and B3LYP provided the closest predictions to the best ab initio calculations.

Binding of Per- and Polyfluoro-alkyl Substances to Peroxisome Proliferator-Activated Receptor Gamma.

Peroxisome proliferator receptor gamma (PPARγ), a type II nuclear receptor, fundamental in the regulation of genes, glucose metabolism, and insulin sensitization has been shown to be impacted by per- and poly-fluoroalkyl substances (PFASs). To consider the influence of PFASs upon PPARγ, the molecular interactions of 27 PFASs have been investigated. Two binding sites have been identified on the PPARγ homodimer structure: the dimer pocket and the ligand binding pocket, the former has never been studied prior. Molecular dynamics calculations were performed to gain insights about PFASs-PPARγ binding and the role of acidic and basic residues. The electrostatic interactions for acidic and basic residues far from the binding site were probed, together with their effect on PPARγ recognition. Short-range electrostatic and van der Waals interactions with nearby residues and their influence on binding energies were investigated. As the negative effects of perfluorooctane sulfonate acid were previously shown to be alleviated by one of its natural ligands, l-carnitine, here, the utility of l-carnitine as a possible inhibitor for other PFASs has been considered. A comparison of the binding patterns of l-carnitine and PFASs provides insights toward mitigation strategies for PFASs.

SAMPL7: Host-guest binding prediction by molecular dynamics and quantum mechanics.

Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges provide routes to compare chemical quantities determined using computational chemistry approaches to experimental measurements that are shared after the competition. For this effort, several computational methods have been used to calculate the binding energies of Octa Acid (OA) and exo-Octa Acid (exoOA) host-guest systems for SAMPL7. The initial poses for molecular dynamics (MD) were generated by molecular docking. Binding free energy calculations were performed using molecular mechanics combined with Poisson-Boltzmann or generalized Born surface area solvation (MMPBSA/MMGBSA) approaches. The factors that affect the utility of the MMPBSA/MMGBSA approaches including solvation, partial charge, and solute entropy models were also analyzed. In addition to MD calculations, quantum mechanics (QM) calculations were performed using several different density functional theory (DFT) approaches. From SAMPL6 results, B3PW91-D3 was found to overestimate binding energies though it was effective for geometry optimizations, so it was considered for the DFT geometry optimizations in the current study, with single-point energy calculations carried out with B2PLYP-D3 with double-, triple-, and quadruple-ζ level basis sets. Accounting for dispersion effects, and solvation models was deemed essential for the predictions. MMGBSA and MMPBSA correlated better to experiment when used in conjunction with an empirical/linear correction.

Ab initio investigation of the ground and excited states of RuO+,0,- and their reaction with water.

High-level quantum chemical calculations on RuO0,± elucidate the electronic structure of their low-lying electronic states. For thirty-two states, we report the electronic configurations, bond lengths, vibrational frequencies, spin-orbit splittings, and excitation energies. The electronic states of RuO can be generated from those of RuO+ by adding one electron to the σ non-bonding orbital closely resembling the 5s atomic orbital of Ru. The ground states for RuO and RuO- are clearly identified as 5Δ and 4Δ, but the two states (4Δ and 2Π) compete for RuO+. The difficulty of calculations is revealed by our small binding energies compared to the experimental values. In addition, we studied the reaction of the three species with water in their ground and selected low-lying electronic states. We found a consistent decrease of the activation energy barriers and higher exothermicity as we add electrons to the system. RuO- is found to facilitate the reaction for both kinetic and thermodynamic reasons.

O-H and C-H Bond Activations of Water and Methane by RuO2+ and (NH3)RuO2+: Ground and Excited States.

Investigation of the ground and excited states of RuO2+ is carried out using multireference quantum chemical methodologies. The electronic structure is explored in detail, and accurate spectroscopic constants for 12 states are reported. Although ruthenium belongs to the same group as iron, the ground state of RuO2+ is 1Σ+ with a strong oxo character as opposed to the 3Δ of FeO2+ with primarily oxyl character. To see the effect of the different electronic structure of RuO2+ on the O-H and C-H bond activation processes, we studied its reaction with one water or methane molecule. Reaction energies and activation barriers are given for six low-lying electronic states of singlet, triplet, and quintet spin multiplicities. It is found that the higher-energy quintet state (5Σ+) provides the lowest activation energies and is the same state responsible for the C-H activation for FeO2+ complexes. The reason is attributed to its weaker metal-oxygen bond (longer bond length), which is "prepared" to be activated at the same time with the O-H and C-H bonds. The effect of an ammonia ligand in the chemical activity is also discussed.

Stability and Electronic Features of Calcium Hexa-, Hepta-, and Octa-Coordinated Ammonia Complexes: A First-Principles Study.

Neutral and positively charged calcium ammonia complexes are investigated by means of high-level quantum chemical calculations. We report optimal structures, binding energies, and vibrational spectra for Ca(NH3)1-80,+. The bigger Ca(NH3)6-80,+ complexes can be classified as solvated electron precursors (SEPs) and are best described as a Ca(NH3)6-82+ core with two or one peripheral electrons. In their ground state, only ∼10% of the outer electron density is estimated to be within the calcium van der Waals radius. For these systems, we calculated several low-lying electronic states, where electrons populate diffuse outer orbitals. The Aufbau principle for the outer electrons is found to be identical to previously studied SEPs: 1s, 1p, 1d, 1f, 2s, and 2p. We show that going from Ca(NH3)5, which has an incomplete first coordination shell and the two valence electrons that are mainly in the valence sphere of calcium, to Ca(NH3)6, both the vibrational and electronic features change abruptly. Infrared, visible, and ultraviolet spectroscopy can be used to identify and characterize calcium SEPs.

Electronic and structural features of octa-coordinated yttrium-ammonia complexes: the first neutral solvated electron precursor with eight ligands and three outer electrons.

The neutral and charged yttrium metal-ammonia complexes, [Y(NH3)8]0,±, are investigated using state-of-the-art quantum chemical calculations. The electronic structure of these complexes is described as an Y(NH3)83+ core with two, three, and four electrons orbiting in its periphery. Unlike the so far reported solvated electron precursors containing alkali, alkaline earth or first-row transition metals, yttrium complexes are the only ones which can accommodate eight ammonia ligands and up to four peripheral electrons. For the neutral species, two electrons occupy the diffuse s-type orbital (1s) and one diffuse p-type orbital (1p). For the cationic counterpart one electron is removed from the 1p orbital, while for the anion another electron is added to the 1p shell. The calculated low-lying electronic states with excitation energies up to 2.0 eV populate the 1s, 1p, and 1d outer orbitals. The first ionization energy of Y(NH3)8 is 2.74 eV and its electron affinity is 0.64 eV. The present results suggest that saturated yttrium ammonia solutions will turn into solids (liquid or expanded metals), where a grid of Y(NH3)83+ centers will be surrounded by "free" electrons.

Transition-metal solvated-electron precursors: diffuse and 3d electrons in V(NH3).

Ground and excited electronic states of V(NH3)0,±6 complexes, investigated with ab initio electronic structure theory, consist of a V(NH3)62+ core with up to three electrons distributed over its periphery. This result extends the concept of super-atomic, solvated-electron precursors from alkali and alkaline-earth complexes to a transition metal. In the approximately octahedral ground state of V(NH3)6, three unpaired electrons occupy 3dxz, 3dyz and 3dxy (t2g) orbitals of vanadium and two electrons occupy a diffuse 1s outer orbital. The lowest excitations involve promotion of diffuse 1s electrons to 1p or 1d diffuse orbitals, followed by a 3d (t2g → eg) transition. V(NH3)6+ is produced by removing a diffuse 1s electron, whereas the additional electron in V(NH3)6- populates a 1p diffuse orbital. The adiabatic ionization energy and electron affinity of V(NH3)6 equal 3.50 and 0.48 eV, respectively.

Ab initio calculations on the ground and excited electronic states of neutral and charged palladium monoxide, PdO0,+,.

Multi-reference configuration interaction and coupled cluster calculations were carried out for the ground and several low-lying excited electronic states for PdO, PdO+, and PdO-. Spin-orbit coupling, core-correlation effects, and large correlation-consistent basis sets were employed. We report bond lengths, spectroscopic constants, energetics, and potential energy curves for all of the considered states. Our calculations settle the assignment for the previously recorded peaks of the experimental PdO- photoelectron spectrum. We found that the spin-orbit effects mix considerably the Λ-S states of PdO, changing dramatically the order of its low-lying electronic states. The ground states of these species were found to be 4Σ- for PdO+, 3Σ- for PdO, and 2Π for PdO-. Going from PdO to PdO+, the electron detaches from a σ orbital which is localized on the metal. Going from PdO to PdO-, the additional electron attaches a π orbital, which is more localized on oxygen. For PdO- we found six electronic states bound with respect to PdO.

Investigation of challenging spin systems using Monte Carlo configuration interaction and the density matrix renormalization group.

We investigate if a range of challenging spin systems can be described sufficiently well using Monte Carlo configuration interaction (MCCI) and the density matrix renormalization group (DMRG) in a way that heads toward a more "black box" approach. Experimental results and other computational methods are used for comparison. The gap between the lowest doublet and quartet state of methylidyne (CH) is first considered. We then look at a range of first-row transition metal monocarbonyls: MCO when M is titanium, vanadium, chromium, or manganese. For these MCO systems we also employ partially spin restricted open-shell coupled-cluster (RCCSD). We finally investigate the high-spin low-lying states of the iron dimer, its cation and its anion. The multireference character of these molecules is also considered. We find that these systems can be computationally challenging with close low-lying states and often multireference character. For this more straightforward application and for the basis sets considered, we generally find qualitative agreement between DMRG and MCCI. © 2017 Wiley Periodicals, Inc.

Gelation Landscape Engineering Using a Multi-Reaction Supramolecular Hydrogelator System.

Simultaneous control of the kinetics and thermodynamics of two different types of covalent chemistry allows pathway selectivity in the formation of hydrogelating molecules from a complex reaction network. This can lead to a range of hydrogel materials with vastly different properties, starting from a set of simple starting compounds and reaction conditions. Chemical reaction between a trialdehyde and the tuberculosis drug isoniazid can form one, two, or three hydrazone connectivity products, meaning kinetic gelation pathways can be addressed. Simultaneously, thermodynamics control the formation of either a keto or an enol tautomer of the products, again resulting in vastly different materials. Overall, this shows that careful navigation of a reaction landscape using both kinetic and thermodynamic selectivity can be used to control material selection from a complex reaction network.

Excited States of the Nickel Carbonyls Ni(CO) and Ni(CO)4: Challenging Molecules for Electronic Structure Theory.

We apply a wide range of correlated electronic structure approaches to the excited states of Ni(CO)4 and Ni(CO) as model complexes of saturated and unsaturated transition metal carbonyls respectively to understand the performance of each method, in addition to setting benchmark data for these metal carbonyls. In particular, we apply the coupled-cluster linear response hierarchy, complete-active-space self-consistent field theory, N-electron valence state multireference perturbation theory, Monte Carlo configuration interaction, and time-dependent density functional theory with a range of functionals and basis sets. We find that although the systems can qualitatively be described by a single configuration, electron correlation effects are sufficiently strong to give large single amplitudes in cluster expansions, which cause spurious solutions to the response equations for the intermediate CCn methods. DFT also performs well if care is taken to choose an appropriate functional, although for Ni(CO) several popular functionals give the incorrect ground spin-state, depending on the amount of Hartree-Fock exchange.