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.

Cavity-modified molecular dipole switching dynamics.

Polaritonic states, which are formed by resonances between a molecular excitation and the photonic mode of a cavity, have a number of useful properties that offer new routes to control molecular photochemistry using electric fields. To provide a theoretical description of how polaritonic states affect the real-time electron dynamics in molecules, a new method is described where the effects of strong light-molecule coupling are implemented using real-time electronic structure theory. The coupling between the molecular electronic states and the cavity is described by the Pauli-Fierz Hamiltonian, and transitions between polaritonic states are induced via an external time-dependent electric field using time-dependent configuration interaction (TDCI) theory, producing quantum electrodynamics TDCI (QED-TDCI). This method is used to study laser-induced ultrafast charge transfer and dipole-switching dynamics of the LiCN molecule inside a cavity. The increase in cavity coupling strength is found to have a significant impact on the energies and transition dipole moments of the molecule-cavity system. The convergence of the polaritonic state energies as a function of the number of included electronic and photonic basis states is discussed.

Potential energy surfaces and dynamic properties via ab initio composite and density functional approaches.

Vibrational spectroscopy enables critical insight into the structural and dynamic properties of molecules. Presently, the majority of theoretical approaches to spectroscopy employ wavefunction-based ab initio or density functional methods that rely on the harmonic approximation. This approximation breaks down for large molecules with strongly anharmonic bonds or for molecules with large internuclear separations. An alternative to these methods involves generating molecular anharmonic potential energy surfaces (potentials) and using them to extrapolate the vibrational frequencies. This study examines the efficacy of density functional theory (DFT) and the correlation consistent Composite Approach (ccCA) in generating anharmonic frequencies from potentials of small main group molecules. Vibrational self-consistent field Theory (VSCF) and post-VSCF methods were used to calculate the fundamental frequencies of these molecules from their potentials. Functional choice, basis set selection, and mode-coupling are also examined as factors in influencing accuracy. The absolute deviations for the calculated frequencies using potentials at the ccCA level of theory were lower than the potentials at the DFT level. With DFT resulting in bending modes that are better described than those of ccCA, a multilevel DFT:ccCA approach where DFT potentials are used for single vibrational mode potentials and ccCA is used for vibrational mode-mode couplings can be utilized for larger polyatomic systems. The frequencies obtained with this multilevel approach using VCIPSI-PT2 were closer to experimental frequencies than the scaled harmonic frequencies, indicating the success of utilizing post-VSCF methods to generate more accurate representations of computed infrared spectra.

Correlation consistent basis sets designed for density functional theory: Third-row atoms (Ga-Br).

The correlation consistent basis sets (cc-pVnZ with n = D, T, Q, 5) for the Ga-Br elements have been redesigned, tuning the sets for use for density functional approximations. Steps to redesign these basis sets for an improved correlation energy recovery and efficiency include truncation of higher angular momentum functions, recontraction of basis set coefficients, and reoptimization of basis set exponents. These redesigned basis sets are compared with conventional cc-pVnZ basis sets and other basis sets, which are, in principle, designed to achieve systematic improvement with respect to increasing basis set size. The convergence of atomic energies, bond lengths, bond dissociation energies, and enthalpies of formation to the Kohn-Sham limit is improved relative to other basis sets where convergence to the Kohn-Sham limit is typically not observed.

Tailoring light-induced charge transfer and intersystem crossing in FeCO using time-dependent spin-orbit configuration interaction.

Real-time (RT) electronic structure methods provide a natural framework for describing light-matter interactions in arbitrary time-dependent electromagnetic fields (EMF). Optically induced excited state transitions are of particular interest, which require tuned EMF to drive population transfer to and from the specific state(s) of interest. Intersystem crossing, or spin-flip, may be driven through shaped EMF or laser pulses. These transitions can result in long-lived "spin-trapped" excited states, which are especially useful for materials requiring charge separation or protracted excited state lifetimes. Time-dependent configuration interaction (TDCI) is unique among RT methods in that it may be implemented in a basis of eigenstates, allowing for rapid propagation of the time-dependent Schrödinger equation. The recent spin-orbit TDCI (TD-SOCI) enables a real-time description of spin-flip dynamics in an arbitrary EMF and, therefore, provides an ideal framework for rational pulse design. The present study explores the mechanism of multiple spin-flip pathways for a model transition metal complex, FeCO, using shaped pulses designed to drive controlled intersystem crossing and charge transfer. These results show that extremely tunable excited state dynamics can be achieved by considering the dipole transition matrix elements between the states of interest.

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.

Population analysis and the effects of Gaussian basis set quality and quantum mechanical approach: main group through heavy element species.

Atomic charge and its distribution across molecules provide important insight into chemical behavior. Though there are many studies on various routes for the determination of atomic charge, there are few studies that examine the broader impact of basis set and quantum method used over many types of population analysis methods across the periodic table. Largely, such a study of population analysis has focused on main-group species. In this work, atomic charges were calculated using several population analysis methods including orbital-based methods (Mulliken, Löwdin, and Natural Population Analysis), volume-based methods (Atoms-in-Molecules (AIM) and Hirshfeld), and potential derived charges (CHELP, CHELPG, and Merz-Kollman). The impact of basis set and quantum mechanical method choices upon population analysis has been considered. The basis sets utilized include Pople (6-21G**, 6-31G**, 6-311G**) and Dunning (cc-pVnZ, aug-cc-pVnZ; n = D, T, Q, 5) basis sets for main group molecules. For the transition metal and heavy element species examined, relativistic forms of the correlation consistent basis sets were used. This is the first time the cc-pVnZ-DK3 and cc-pwCVnZ-DK3 basis sets have been examined with respect to their behavior across all levels of basis sets for atomic charges for an actinide. The quantum methods chosen include two density functional (PBE0 and B3LYP), Hartree-Fock, and second-order Møller-Plesset perturbation theory (MP2) approaches.

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).

Thermochemistry of per- and polyfluoroalkyl substances.

The determination of gas phase thermochemical properties of per- and polyfluoroalkyl substances (PFAS) is central to understanding the long-range transport behavior of PFAS in the atmosphere. Prior gas-phase studies have reported the properties of perfluorinated sulfonic acid (PFOS) and perfluorinated octanoic acid (PFOA). Here, this study reports the gas phase enthalpies of formation of short- and long-chain PFAS and their precursor molecules determined using density functional theory (DFT) and ab initio approaches. Two density functionals, two ab initio methods and an empirical method were used to compute enthalpies of formation with the total atomization approach and an isogyric reaction. The performance of the computational methods employed in this work were validated against the experimental enthalpies of linear alkanoic acids and perfluoroalkanes. The gas-phase determinations will be useful for future studies of PFAS in the atmosphere, and the methodological choices will be helpful in the study of other PFAS.

Molecular Screening and Toxicity Estimation of 260,000 Perfluoroalkyl and Polyfluoroalkyl Substances (PFASs) through Machine Learning.

Perfluoroalkyl and polyfluoroalkyl substances (PFASs) are a class of chemicals widely used in industrial applications due to their exceptional properties and stability. However, they do not readily degrade in the environment and are linked to contamination and adverse health effects in humans and wildlife. To find alternatives for the most commonly used PFAS molecules that maintain their desirable chemical properties but are not adverse to biological lifeforms, a novel approach based upon machine learning is utilized. The machine learning model is trained on an existing set of PFAS molecules to generate over 260,000 novel PFAS molecules, which we dub PFAS-AI-Gen. Using molecular descriptors with known relationships to toxicity and industrial suitability followed by molecular docking and molecular dynamics simulations, this set of molecules is screened. In this manner, increasingly complex calculations are performed only for candidate molecules that are most likely to yield the desired properties of low binding affinity toward two selected protein receptors, the human pregnane x receptor (hPXR) and peroxisome proliferator-activated receptor γ (PPAR-γ), and high industrial suitability, defined by critical micelle concentration (CMC). The selection criteria of low binding affinity and high industrial suitability are relative to the popular PFAS alternative GenX. hPXR and PPAR-γ are selected as they are PFAS targets and facilitate a variety of functions, such as drug metabolism and glucose regulation, respectively. Through this approach, 22 promising new PFAS substitutes that may warrant experimental investigation are identified. This integrated approach of molecular screening and toxicity estimation may be applicable to other chemical classes.

Ab initio composite strategies and multireference approaches for lanthanide sulfides and selenides.

The f-block ab initio correlation consistent composite approach was used to predict the dissociation energies of lanthanide sulfides and selenides. Geometry optimizations were carried out using density functional theory and coupled cluster singles, doubles, and perturbative triples with one- and two-component Hamiltonians. For the two-component calculations, relativistic effects were accounted for by utilizing a third-order Douglas-Kroll-Hess Hamiltonian. Spin-orbit coupling was addressed with the Breit-Pauli Hamiltonian within a multireference configuration interaction approach. The state averaged complete active space self-consistent field wavefunctions obtained for the spin-orbit coupling energies were used to assign the ground states of diatomics, and several diagnostics were used to ascertain the multireference character of the molecules.

Adsorption, Structure, and Dynamics of Short- and Long-Chain PFAS Molecules in Kaolinite: Molecular-Level Insights.

The ubiquitous presence of poly- and perfluoroalkyl substances (PFAS) in different natural settings poses a serious threat to environmental and human health. Soils and sediments represent one of the important exposure pathways of PFAS for humans and animals. With increasing bioaccumulation and mobility, it is extremely important to understand the interactions of PFAS molecules with the dominant constituents of soils such as clay minerals. This study reports for the first time the fundamental molecular-level insights into the adsorption, interfacial structure, and dynamics of short- and long-chain PFAS molecules at the water-saturated mesopores of kaolinite clay using classical molecular dynamics (MD) simulations. At environmental conditions, all the PFAS molecules are exclusively adsorbed near the hydroxyl surface of the kaolinite, irrespective of the terminal functional groups and metal cations. The interfacial adsorption structures and coordination environments of PFAS are strongly dependent on the nature of the functional groups and their hydrophobic chain length. The formation of large, aggregated clusters of long-chain PFAS at the hydroxyl surface of kaolinite is responsible for their restricted dynamics in comparison to short-chain PFAS molecules. Such comprehensive knowledge of PFAS at the clay mineral interface is critical to developing novel site-specific degradation and mitigation strategies.

Ab Initio Composite Approaches for Heavy Element Energetics: Ionization Potentials for the Actinide Series of Elements.

The first, second, and third gas-phase ionization potentials have been determined for the actinide series of elements using an ab initio composite scalar and fully relativistic approach, employing the coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) and Dirac Hartree-Fock (DHF) methods, extrapolated to the complete basis set (CBS) limit. The impact of electron correlation and basis set choice within this framework are examined. Additionally, the first three ionization potentials were obtained using an ab initio heavy element correlation-consistent Composite Approach (here referred to as α-ccCA). This is the first utilization of a ccCA for actinide species.

Multi-configuration electron-nuclear dynamics: An open-shell approach.

The multi-configuration electron-nuclear dynamics for open shell systems with a spin-unrestricted formalism is described. The mean fields are evaluated using second-order reduced density matrices for electronic and nuclear degrees of freedom. Applications to light-element diatomics including equilibrium geometries, electronic energies, dipole moments, and absorption spectra are presented. The von Neumann entropies for different spin states of a LiH molecule are compared.

Considering Density Functional Approaches for Actinide Species: The An66 Molecule Set.

The importance of spin-orbit effects on the predictions of energetic properties of actinide compounds has been considered for 18 different density functionals, comparing the spin-orbit and non-spin-orbit ("standard") forms of density functional theory (DFT). A set of enthalpies of formation for 66 small actinide (Th-Am) compounds-the An66 set, for which experimental data are available-have been investigated. The set includes actinide halides, oxides, and oxohalides in the general form AnOmXn, where n = 0-6, m = 0-3, and X = F, Cl, Br, or I. The impact of basis set choice was investigated, and to help account for the impact of relativity, the Stuttgart general and segmented contracted atomic natural orbital (ANO) basis sets paired with small core relativistic effective core potentials (RECP) as well as all-electron calculations utilizing the third-order Douglas-Kroll-Hess were considered.

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.