Refinement of the crystal structure of fresnoite, Ba2TiSi2O8, from Löhley (Eifel district, Germany); Gladstone-Dale compatibility, electronic polarizability and vibrational spectroscopy of minerals and inorganic compounds with pentacoordinated TiIV and a titanyl bond

Most known compounds with five-coordinated Ti⁴⁺ are natural and synthetic titanosilicates. The crystal structure of natural fresnoite, Ba₂TiSi₂O₈ [tetragonal, space group P4bm, a = 8.510 (1) Å, c = 5.197 (1) Å, V = 376.4 (1) ų, Z = 2], has been refined to R = 0.011 on the basis of 807 unique single-crystal reflections with I > 2σ(I). Titanium has fivefold coordination with one short (`titanyl') bond of 1.692 (5) Å. Bonds in the TiO<sub>5</sub> polyhedron are discussed in comparison to analogous coordination polyhedra in other minerals and compounds. A review of all known compounds with Ti<sup>4+</sup>O<sub>5</sub> polyhedra shows that most of them are titanosilicates in which titanium forms a short Ti-O bond (∼1.61 to ∼1.77 Å). Poor Gladstone-Dale compatibility between chemical composition, optical characteristics and density of these compounds is explained by the anomalous contribution of <sup>[5]</sup>Ti<sup>4+</sup> to the optical properties as shown by calculations based on the relationship between electronic polarizabilities and refractive indices. An improved Gladstone-Dale coefficient of 0.29 is suggested for TiO<sub>2</sub> with <sup>[5]</sup>Ti<sup>4+</sup>. A negative correlation between `titanyl' bond lengths and wavenumbers of the bands of Ti-O stretching vibrations (in the range of 890-830 cm^-1) in infrared and Raman spectra is observed.

Ä-Coupling Dielectric Functionality with Magnetic Properties in Coordination Metal Complexes

Significant research has been conducted on molecular ferroelectric materials, including pure organic and inorganic compounds; however, studies on ferroelectric materials based on coordination metal complexes are scarce. Ferroelectric materials based on coordination metal complexes have tunable structures and designs, with coexistence or synergy between the ferroelectric behavior and magnetic properties. Compared to inorganic compounds, few coordination metal complexes exhibit coupling between the magnetic and dielectric properties. Coordination metal complexes with strong coupling between the magnetic and dielectric properties exhibit dielectric permittivity variations under external magnetic fields. Therefore, they have attracted substantial interest for their potential use in magnetoelectric devices. In this review, we discuss recent advances in coordination metal complexes, that exhibit coupled magnetic functionalities and ferroelectricity or dielectric properties, including single-molecule magnets, electron delocalization systems, and external stimuli responsive compounds.

Methyl-Induced Polarization Destabilizes the Noncovalent Interactions of N-Methylated Lysines

Lysine methylation can modify noncovalent interactions by altering lysine's hydrophobicity as well as its electronic structure. Although the ramifications of the former are documented, the effects of the latter remain largely unknown. Understanding the electronic structure is important for determining how biological methylation modulates protein-protein binding, and the impact of artificial methylation experiments in which methylated lysines are used as spectroscopic probes and protein crystallization facilitators. The benchmarked first-principles calculations undertaken here reveal that methyl-induced polarization weakens the electrostatic attraction of amines with protein functional groups - salt bridges, hydrogen bonds and cation-π interactions weaken by as much as 10.3, 7.9 and 3.5 kT, respectively. Multipole analysis shows that weakened electrostatics is due to the altered inductive effects, which overcome increased attraction from methyl-enhanced polarizability and dispersion. Due to their fundamental nature, these effects are expected to be present in many cases. A survey of methylated lysines in protein structures reveals several cases in which methyl-induced polarization is the primary driver of altered noncovalent interactions; in these cases, destabilizations are found to be in the 0.6-4.7 kT range. The clearest case of where methyl-induced polarization plays a dominant role in regulating biological function is that of the PHD1-PHD2 domain, which recognizes lysine-methylated states on histones. These results broaden our understanding of how methylation modulates noncovalent interactions.

Unraveling the High-Activity Origin of Single-Atom Iron Catalysts for Organic Pollutant Oxidation via Peroxymonosulfate Activation

Single-atom catalysts (SACs) have emerged as efficient materials in the elimination of aqueous organic contaminants; however, the origin of high activity of SACs still remains elusive. Herein, we identify an 8.1-fold catalytic specific activity (reaction rate constant normalized to catalyst's specific surface area and dosage) enhancement that can be fulfilled with a single-atom iron catalyst (SA-Fe-NC) prepared via a cascade anchoring method compared to the iron nanoparticle-loaded catalyst, resulting in one of the most active currently known catalysts in peroxymonosulfate (PMS) conversion for organic pollutant oxidation. Experimental data and theoretical results unraveled that the high-activity origin of the SA-Fe-NC stems from the Fe-pyridinic N₄ moiety, which dramatically increases active sites by not only creating the electron-rich Fe single atom as the catalytic site but also producing electron-poor carbon atoms neighboring pyridinic N as binding sites for PMS activation including synchronous PMS reduction and oxidation together with dissolved oxygen reduction. Moreover, the SA-Fe-NC exhibits excellent stability and applicability to realistic industrial wastewater remediation. This work offers a novel yet reasonable interpretation for why a small amount of iron in the SA-Fe-NC can deliver extremely superior specific activity in PMS activation and develops a promising catalytic oxidation system toward actual environmental cleanup.

Accurate Biomolecular Simulations Account for Electronic Polarization

In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules. While the effects of electronic polarization are highly pronounced for molecules with an opposite total charge, they are also non-negligible for interactions with overall neutral molecules. For instance, neglecting these effects in important biomolecules like amino acids and phospholipids affects the structure of proteins and membranes having a large impact on interpreting experimental data as well as building coarse grained models. With the combined advances in theory, algorithms and computational power it is currently realistic to perform simulations with explicit polarizable dipoles on systems with relevant sizes and complexity. Alternatively, the effects of electronic polarization can also be included at zero additional computational cost compared to standard fixed-charge force fields using the electronic continuum correction, as was recently demonstrated for several classes of biomolecules.

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction

The parametrization of classical nonbonded models of metal ions has been widely addressed in the recent years. Despite the continuous development of novel and more physically inspired functional forms, the 12-6 Lennard-Jones plus Coulomb potential is still the most adopted force field in molecular dynamics (MD) codes, owing to its simple form and easy implementation. However, due to the integer formal charge, unpolarizable force fields of ions may suffer from overestimated interatomic electrostatic interactions, leading to nonphysical clustering or repulsion between such full charges. The electronic continuum correction (ECC) can fix this problem through a simple inclusion of solvent polarization effects via ionic charge rescaling. In this work, the development of novel nonbonded models for mono, divalent, and highly charged metal ions is presented. For each metal species, the ionic charge has been scaled, according to the ECC. Lennard-Jones parameters have been optimized using experimental structural and thermodynamic properties as target quantities. Performances of the proposed models are discussed and compared with the literature data, while transferability attitudes among different and well-known water models are evaluated. © 2019 Wiley Periodicals, Inc.

Polarizable force field for RNA based on the classical drude oscillator

RNA molecules are highly dynamic and capable of adopting a wide range of complex, folded structures. The factors driving the folding and dynamics of these structures are dependent on a balance of base pairing, hydration, base stacking, ion interactions, and the conformational sampling of the 2'-hydroxyl group in the ribose sugar. The representation of these features is a challenge for empirical force fields used in molecular dynamics simulations. Toward meeting this challenge, the inclusion of explicit electronic polarization is important in accurately modeling RNA structure. In this work, we present a polarizable force field for RNA based on the classical Drude oscillator model, which represents electronic degrees of freedom via negatively charged particles attached to their parent atoms by harmonic springs. Beginning with parametrization against quantum mechanical base stacking interaction energy and conformational energy data, we have extended the Drude-2017 nucleic acid force field to include RNA. The conformational sampling of a range of RNA sequences were used to validate the force field, including canonical A-form RNA duplexes, stem-loops, and complex tertiary folds that bind multiple Mg2+ ions. Overall, the Drude-2017 RNA force field reproduces important properties of these structures, including the conformational sampling of the 2'-hydroxyl and key interactions with Mg2+ ions. © 2018 Wiley Periodicals, Inc.

CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses

We present an extension of the CHARMM Drude polarizable force field to enable modeling of polysaccharides containing pyranose and furanose monosaccharides. The new force field parameters encompass 1↔2, 1→3, 1→4, and 1→6 pyranose-furanose linkages, 2→1 and 2→6 furanose-furanose linkages, 2→2, 2→3, and 2→4 furanose-pyranose, and 1↔1, 1→2, 1→3, 1→4, and 1→6 pyranose-pyranose linkages. For the glycosidic linkages, both simple model compounds and the full disaccharides with methylation at the reducing end were used for parameter optimization. The model compounds were chosen to be monomers or glycosidic-linked dimers of tetrahydropyran (THP) and tetrahydrofuran (THF). Target data for optimization included one- and two-dimensional potential energy scans of ω and the Φ/Ψ glycosidic dihedral angles in the model compounds and full disaccharides computed by quantum mechanical (QM) RIMP2/cc-pVQZ single point energies on MP2/6-31G(d) optimized structures. Also included in the target data are extensive sets of QM gas phase monohydrate water-saccharide interactions, dipole moments, and molecular polarizabilities for both model compounds and full disaccharides. The resulting polarizable model is shown to be in good agreement with a range of QM data, offering a significant improvement over the additive CHARMM36 carbohydrate force field, as well as experimental data including crystal structures and conformational properties of disaccharides and a trisaccharide in aqueous solution.

A concise synthesis of a highly substituted 6-(1H-benzimidazol-1-yl)-5-nitrosopyrimidin-2-amine: synthetic sequence and the molecular and supramolecular structures of one product and two intermediates

A concise and efficient synthesis of 6-benzimidazolyl-5-nitrosopyrimidines has been developed using Schiff base-type intermediates derived from N⁴-(2-aminophenyl)-6-methoxy-5-nitrosopyrimidine-2,4-diamine. 6-Methoxy-N⁴-{2-[(4-methylbenzylidene)amino]phenyl}-5-nitrosopyrimidine-2,4-diamine, (I), and N⁴-{2-[(ethoxymethylidene)amino]phenyl}-6-methoxy-5-nitrosopyrimidine-2,4-diamine, (III), both crystallize from dimethyl sulfoxide solution as the 1:1 solvates C₁₉H₁₈N₆O₂·C₂H₆OS, (Ia), and C₁₄H₁₆N₆O₃·C₂H₆OS, (IIIa), respectively. The interatomic distances in these intermediates indicate significant electronic polarization within the substituted pyrimidine system. In each of (Ia) and (IIIa), intermolecular N-H...O hydrogen bonds generate centrosymmetric four-molecule aggregates. Oxidative ring closure of intermediate (I), effected using ammonium hexanitratocerate(IV), produced 4-methoxy-6-[2-(4-methylphenyl-1H-benzimidazol-1-yl]-5-nitrosopyrimidin-2-amine, C₁₉H₁₆N₆O₂, (II) [Cobo et al. (2018). Private communication (CCDC 1830889). CCDC, Cambridge, England], where the extent of electronic polarization is much less than in (Ia) and (IIIa). A combination of N-H...N and C-H...O hydrogen bonds links the molecules of (II) into complex sheets.

Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model

In this work, we have combined the polarizable force field based on the classical Drude oscillator with a continuum Poisson-Boltzmann/solvent-accessible surface area (PB/SASA) model. In practice, the positions of the Drude particles experiencing the solvent reaction field arising from the fixed charges and induced polarization of the solute must be optimized in a self-consistent manner. Here, we parameterized the model to reproduce experimental solvation free energies of a set of small molecules. The model reproduces well-experimental solvation free energies of 70 molecules, yielding a root mean square difference of 0.8 kcal/mol versus 2.5 kcal/mol for the CHARMM36 additive force field. The polarization work associated with the solute transfer from the gas-phase to the polar solvent, a term neglected in the framework of additive force fields, was found to make a large contribution to the total solvation free energy, comparable to the polar solute-solvent solvation contribution. The Drude PB/SASA also reproduces well the electronic polarization from the explicit solvent simulations of a small protein, BPTI. Model validation was based on comparisons with the experimental relative binding free energies of 371 single alanine mutations. With the Drude PB/SASA model the root mean square deviation between the predicted and experimental relative binding free energies is 3.35 kcal/mol, lower than 5.11 kcal/mol computed with the CHARMM36 additive force field. Overall, the results indicate that the main limitation of the Drude PB/SASA model is the inability of the SASA term to accurately capture non-polar solvation effects. © 2018 Wiley Periodicals, Inc.

Current status of protein force fields for molecular dynamics simulations

The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.

Evidence of electronic polarization of the As ion in the superconducting phase of F-doped LaFeAsO

Understanding the nature of superconductivity in iron-based compounds is essential in the development of new strategies to increase T c. Using a charge density analysis based on synchrotron radiation X-ray powder diffraction data, we found that the charge carriers only accumulated in the iron layer of the superconducting phase of LaFeAsO1 - x F x at low temperatures. Analysis of the electrostatic potential distribution revealed the concerted enhancement of the electronic polarization of the As ions and the carrier redistribution. This suggests that the enhanced electronic polarization of the As ion plays an important role in inducing high T c superconductivity, and that the polaron concept, which has been previously regarded as an untenable mechanism, should be reconsidered for the description of the iron-arsenide superconducting phase.