Mechanism-Based Inactivation of Cytochrome P450 Enzymes: Computational Insights.

Mechanism-based inactivation (MBI) refers to the metabolic bioactivation of a xenobiotic by cytochrome P450s to a highly reactive intermediate which subsequently binds to the enzyme and leads to the quasi-irreversible or irreversible inhibition. Xenobiotics, mainly drugs with specific functional units, are the major sources of MBI. Two possible consequences of MBI by medicinal compounds are drug-drug interaction and severe toxicity that are observed and highlighted by clinical experiments. Today almost all of these latent functional groups (e.g., thiophene, furan, alkylamines, etc.) are known, and their features and mechanisms of action, owing to the vast experimental and theoretical studies, are determined. In the past decade, molecular modeling techniques, mostly density functional theory, have revealed the most feasible mechanism that a drug undergoes by P450 enzymes to generate a highly reactive intermediate. In this review, we provide a comprehensive and detailed picture of computational advances toward the elucidation of the activation mechanisms of various known groups with MBI activity. To this aim, we briefly describe the computational concepts to carry out and analyze the mechanistic investigations, and then, we summarize the studies on compounds with known inhibition activity including thiophene, furan, alkylamines, terminal acetylene, etc. This study can be reference literature for both theoretical and experimental (bio)chemists in several different fields including rational drug design, the process of toxicity prevention, and the discovery of novel inhibitors and catalysts.

In search of molecular ions for optical cycling: a difficult road.

Optical cycling, a continuous photon scattering off atoms or molecules, plays a central role in the quantum information science. While optical cycling has been experimentally achieved for many neutral species, few molecular ions have been investigated. We present a systematic theoretical search for diatomic molecular ions suitable for optical cycling using equation-of-motion coupled-cluster methods. Inspired by the electronic structure patterns of laser-cooled neutral molecules, we establish the design principles for molecular ions and explore various possible cationic molecular frameworks. The results show that finding a perfect molecular ion for optical cycling is challenging, yet possible. Among various possible diatomic molecules we suggest several candidates, which require further attention from both theory and experiment: YF+, SiO+, PN+, SiBr+, and BO+.

Towards a rational design of laser-coolable molecules: insights from equation-of-motion coupled-cluster calculations.

Access to cold molecules is critical for quantum information science, design of new sensors, ultracold chemistry, and search of new phenomena. These applications depend on the ability to laser-cool molecules. Rigorous theory and qualitative models can play a central role in narrowing down the vast pool of potential candidates amenable to laser cooling. We report a systematic study of structural and optical properties of alkaline earth metal derivatives in the context of their applicability in laser cooling using equation-of-motion coupled-cluster methods. To rationalize and generalize the results from high-level electronic structure calculations, we develop an effective Hamiltonian model. The model explains the observed trends and suggests new principles for the design of laser-coolable molecules.

Improving Performance of the SMD Solvation Model: Bondi Radii Improve Predicted Aqueous Solvation Free Energies of Ions and pKa Values of Thiols.

Calculation of the solvation free energy of ionic molecules is the principal source of errors in the quantum chemical evaluation of pKa values using implicit polarizable continuum solvent models. One of the important parameters affecting the performance of these models is the choice of atomic radii. Here, we assess the performance of the solvation model based on density (SMD) implicit solvation model employing SMD default radii (SMD) and Bondi radii (SMD-B), a set of empirical atomic radii developed based on the crystallographic data. For a set of 112 ions (60 anions and 52 cations), the SMD-B model showed lower mean unsigned error (MUE) for predicted aqueous solvation free energies (4.0 kcal/mol for anions and 2.4 kcal/mol for cations) compared to the standard SMD model (MUE of 5.0 kcal/mol for anions and 2.9 kcal/mol for cations). In particular, usage of Bondi radii improves the aqueous solvation energies of sulfur-containing ions by >5 kcal/mol compared to the SMD default radii. Indeed, for a set of 45 thiols, the SMD-B model was found to dramatically improve the predicted pKa values, with ∼1 pKa unit mean deviation from the experimental values, compared to ∼7 pKa units mean deviation for the SMD model with the default radii. These findings highlight the importance of the choice of atomic radii on the performance of the implicit solvation models.

From Static to Dynamic: Electron Density of HOMO at Biaryl Linkage Controls the Mechanism of Hole Delocalization.

In order to extend the physical length of hole delocalization in a molecular wire, chromophores of increasing size are often desired. However, the effect of size on the efficacy and mechanism of hole delocalization remains elusive. Here, we employ a model set of biaryls to show that with increasing chromophore size, the mechanism of steady-state hole distribution switches from static delocalization in biaryls with smaller chromophores to dynamic hopping, as exemplified in the largest system, tBuHBC2 (i.e., "superbiphenyl"), which displays a vanishingly small electronic coupling. This important finding is analyzed with the aid of Hückel molecular orbital and Marcus-Hush theories. Our findings will enable the rational design of the novel molecular wires with length-invariant redox/optical properties suitable for long-range charge transfer.

An Electron-Rich Calix[4]arene-Based Receptor with Unprecedented Binding Affinity for Nitric Oxide.

Calixarenes have found widespread application as building blocks for the design and synthesis of functional materials in host-guest chemistry. The ongoing desire to develop a detailed understanding of the nature of NO bonding to multichromophoric π-stacked assemblies led us to develop an electron-rich methoxy derivative of calix[4]arene (3), which we show exists as a single conformer in solution at ambient temperature. Here, we examine the redox properties of this derivative, generate its cation radical (3+. ) using robust chemical oxidants, and determine the relative efficacy of its NO binding in comparison with model calixarenes. We find that 3/3+. is a remarkable receptor for NO+ /NO, with unprecedented binding efficacy. The availability of precise experimental structures of this calixarene derivative and its NO complex, obtained by X-ray crystallography, is critically important both for developing novel functional NO biosensors, and understanding the role of stacked aromatic donors in efficient NO binding, which may have relevance to biological NO transport.

An electron-transfer induced conformational transformation: from non-cofacial "sofa" to cofacial "boat" in cyclotetraveratrylene (CTTV) and formation of charge transfer complexes.

Electro-active polychromophoric assemblies that undergo clam-like electromechanic actuation represent an important class of organic functional materials. Here, we show that the readily available cyclotetraveratrylene (CTTV) undergoes oxidation-induced folding, consistent with interconversion from a non-cofacial "sofa" conformation to a cofacial "boat" conformer. It is found that the non-cofacial "sofa" conformer of CTTV forms stable electron donor-acceptor complexes with chloranil and DDQ. Electron-transfer induced conformational transformation in CTTV provides a framework for the rational design of novel organic functional molecules.

Vertical vs. adiabatic ionization energies in solution and gas-phase: probing ionization-induced reorganization in conformationally-mobile bichromophoric actuators using photoelectron spectroscopy, electrochemistry and theory.

Ionization-induced structural and conformational reorganization in various π-stacked dimers and covalently linked bichromophores is relevant to many processes in biological systems and functional materials. In this work, we examine the role of structural, conformational, and solvent reorganization in a set of conformationally mobile bichromophoric donors, using a combination of gas-phase photoelectron spectroscopy, solution-phase electrochemistry, and density functional theory (DFT) calculations. Photoelectron spectral analysis yields both adiabatic and vertical ionization energies (AIE/VIE), which are compared with measured (adiabatic) solution-phase oxidation potentials (Eox). Importantly, we find a strong correlation of Eox with AIE, but not VIE, reflecting variations in the attendant structural/conformational reorganization upon ionization. A careful comparison of the experimental data with the DFT calculations allowed us to probe the extent of charge stabilization in the gas phase and solution and to parse the reorganizational energy into its various components. This study highlights the importance of a synergistic approach of experiment and theory to study ionization-induced structural and conformational reorganization.

FHBC, a Hexa-peri-hexabenzocoronene-Fluorene Hybrid: A Platform for Highly Soluble, Easily Functionalizable HBCs with an Expanded Graphitic Core.

Materials based upon hexa-peri-hexabenzocoronenes (HBCs) show significant promise in a variety of photovoltaic applications. There remains the need, however, for a soluble, versatile, HBC-based platform, which can be tailored by incorporation of electroactive groups or groups that can prompt self-assembly. The synthesis of a HBC-fluorene hybrid is presented that contains an expanded graphitic core that is highly soluble, resists aggregation, and can be readily functionalized at its vertices. This new HBC platform can be tailored to incorporate six electroactive groups at its vertices, as exemplified by a facile synthesis of a representative hexaaryl derivative of FHBC. Synthesis of new FHBC derivatives, containing electroactive functional groups that can allow controlled self-assembly, may serve as potential long-range charge-transfer materials for photovoltaic applications.

From Intramolecular (Circular) in an Isolated Molecule to Intermolecular Hole Delocalization in a Two-Dimensional Solid-State Assembly: The Case of Pillarene.

To achieve long-range charge transport/separation and, in turn, bolster the efficiency of modern photovoltaic devices, new molecular scaffolds are needed that can self-assemble in two-dimensional (2D) arrays while maintaining both intra- and intermolecular electronic coupling. In an isolated molecule of pillarene, a single hole delocalizes intramolecularly via hopping amongst the circularly arrayed hydroquinone ether rings. The crystallization of pillarene cation radical produces a 2D self-assembly with three intermolecular dimeric (sandwich-like) contacts. Surprisingly, each pillarene in the crystal lattice bears a fractional formal charge of +1.5. This unusual stoichiometry of oxidized pillarene in crystals arises from effective charge distribution within the 2D array via an interplay of intra- and intermolecular electronic couplings. This important finding is expected to help advance the rational design of efficient solid-state materials for long-range charge transfer.

The Role of Torsional Dynamics on Hole and Exciton Stabilization in π-Stacked Assemblies: Design of Rigid Torsionomers of a Cofacial Bifluorene.

Exciton and charge delocalization across π-stacked assemblies is of importance in biological systems and functional polymeric materials. To examine the requirements for exciton and hole stabilization, cofacial bifluorene (F2) torsionomers were designed, synthesized, and characterized: unhindered (model) Me F2, sterically hindered tBu F2, and cyclophane-like C F2, where fluorenes are locked in a perfect sandwich orientation via two methylene linkers. This set of bichromophores with varied torsional rigidity and orbital overlap shows that exciton stabilization requires a perfect sandwich-like arrangement, as seen by strong excimeric-like emission only in C F2 and Me F2. In contrast, hole delocalization is less geometrically restrictive and occurs even in sterically hindered tBu F2, as judged by 160 mV hole stabilization and a near-IR band in the spectrum of its cation radical. These findings underscore the diverse requirements for charge and energy delocalization across π-stacked assemblies.

Poly-p-hydroquinone Ethers: Isoenergetic Molecular Wires with Length-Invariant Oxidation Potentials and Cation Radical Excitation Energies.

Typical poly-p-phenylene wires are characterized by strong interchromophoric electronic coupling with redox and optical properties being highly length-dependent. Herein we show that an incorporation of a pair of para-methoxy groups at each p-phenylene unit in poly-p-phenylene wires (i.e., PHEn) changes the nodal structure of HOMO that leads to length-invariant oxidation potentials and cation radical excitation energies. As such, PHEn represents a unique class of isoenergetic wires where hole delocalization mainly occurs via dynamic hopping and thus may serve as an efficient medium for long-range charge transfer. Availability of these wires will allow demonstration of long-range electron transfer via incoherent hopping using donor-bridge-acceptor systems with isoenergetic PHEn-based wires as bridges.

Unraveling the Coulombic Forces in Electronically Decoupled Bichromophoric Systems during Two Successive Electron Transfers.

Coulombic forces are vital in modulating the electron transfer dynamics in both synthetic and biological polychromophoric assemblies, yet quantitative studies of the impact of such forces are rare, as it is difficult to disentangle electrostatic forces from simple electronic coupling. To address this problem, the impact of Coulombic interactions in the successive removal of two electrons from a model set of spirobifluorenes, where the interchromophoric electronic coupling is nonexistent, is quantitatively assessed. By systematically varying the separation of the bifluorene moieties using model compounds, ion pairing, and solvation, these interactions, with energies up to about 0.4 V, are absent at distances greater than about 9 Å. These findings can be (quantitatively) applied for the design of polychromophoric assemblies, whereby the redox properties of donors and/or acceptors can be tuned by judicious positioning of the charged groups to control the electron-transfer dynamics.

Dihedral-Angle-Controlled Crossover from Static Hole Delocalization to Dynamic Hopping in Biaryl Cation Radicals.

In cases of coherent charge-transfer mechanism in biaryl compounds the rates follow a squared cosine trend with varying dihedral angle. Herein we demonstrate using a series of biaryl cation radicals with varying dihedral angles that the hole stabilization shows two different regimes where the mechanism of the hole stabilization switches over from (static) delocalization over both aryl rings to (dynamic) hopping. The experimental data and DFT calculations of biaryls with different dihedral angles unequivocally support that a crossover from delocalization to hopping occurs at a unique dihedral angle where the electronic coupling (Hab ) is one half of reorganization (λ), that is, Hab =λ/2. The implication of this finding in non-coherent charge-transfer rates is being investigated.

Energy Gap between the Poly-p-phenylene Bridge and Donor Groups Controls the Hole Delocalization in Donor-Bridge-Donor Wires.

Poly-p-phenylene wires are critically important as charge-transfer materials in photovoltaics. A comparative analysis of a series of poly-p-phenylene (RPPn) wires, capped with isoalkyl (iAPPn), alkoxy (ROPPn), and dialkylamino (R2NPPn) groups, shows unexpected evolution of oxidation potentials, i.e., decrease (-260 mV) for iAPPn, while increase for ROPPn (+100 mV) and R2NPPn (+350 mV) with increasing number of p-phenylenes. Moreover, redox/optical properties and DFT calculations of R2NPPn/R2NPPn+• further show that the symmetric bell-shaped hole distribution distorts and shifts toward one end of the molecule with only 4 p-phenylenes in R2NPPn+•, while shifting of the hole occurs with 6 and 8 p-phenylenes in ROPPn+• and iAPPn+•, respectively. Availability of accurate experimental data on highly electron-rich dialkylamino-capped R2NPPn together with ROPPn and iAPPn allowed us to demonstrate, using our recently developed Marcus-based multistate model (MSM), that an increase of oxidation potentials in R2NPPn arises due to an interplay between the electronic coupling (Hab) and energy difference between the end-capped groups and bridging phenylenes (Δε). A comparison of the three series of RPPn with varied Δε further demonstrates that decrease/increase/no change in oxidation energies of RPPn can be predicted based on the energy gap Δε and coupling Hab, i.e., decrease if Δε < Hab (i.e., iAPPn), increase if Δε > Hab (i.e., R2NPPn), and minimal change if Δε ≈ Hab (i.e., ROPPn). MSM also reproduces the switching of the nature of electronic transition in higher homologues of R2NPPn+• (n ≥ 4). These findings will aid in the development of improved models for charge-transfer dynamics in donor-bridge-acceptor systems.

Genetic algorithm optimization of point charges in force field development: challenges and insights.

Evolutionary methods, such as genetic algorithms (GAs), provide powerful tools for optimization of the force field parameters, especially in the case of simultaneous fitting of the force field terms against extensive reference data. However, GA fitting of the nonbonded interaction parameters that includes point charges has not been explored in the literature, likely due to numerous difficulties with even a simpler problem of the least-squares fitting of the atomic point charges against a reference molecular electrostatic potential (MEP), which often demonstrates an unusually high variation of the fitted charges on buried atoms. Here, we examine the performance of the GA approach for the least-squares MEP point charge fitting, and show that the GA optimizations suffer from a magnified version of the classical buried atom effect, producing highly scattered yet correlated solutions. This effect can be understood in terms of the linearly independent, natural coordinates of the MEP fitting problem defined by the eigenvectors of the least-squares sum Hessian matrix, which are also equivalent to the eigenvectors of the covariance matrix evaluated for the scattered GA solutions. GAs quickly converge with respect to the high-curvature coordinates defined by the eigenvectors related to the leading terms of the multipole expansion, but have difficulty converging with respect to the low-curvature coordinates that mostly depend on the buried atom charges. The performance of the evolutionary techniques dramatically improves when the point charge optimization is performed using the Hessian or covariance matrix eigenvectors, an approach with a significant potential for the evolutionary optimization of the fixed-charge biomolecular force fields.

Electrostatic point charge fitting as an inverse problem: Revealing the underlying ill-conditioning.

Atom-centered point charge (PC) model of the molecular electrostatics-a major workhorse of the atomistic biomolecular simulations-is usually parameterized by least-squares (LS) fitting of the point charge values to a reference electrostatic potential, a procedure that suffers from numerical instabilities due to the ill-conditioned nature of the LS problem. To reveal the origins of this ill-conditioning, we start with a general treatment of the point charge fitting problem as an inverse problem and construct an analytical model with the point charges spherically arranged according to Lebedev quadrature which is naturally suited for the inverse electrostatic problem. This analytical model is contrasted to the atom-centered point-charge model that can be viewed as an irregular quadrature poorly suited for the problem. This analysis shows that the numerical problems of the point charge fitting are due to the decay of the curvatures corresponding to the eigenvectors of LS sum Hessian matrix. In part, this ill-conditioning is intrinsic to the problem and is related to decreasing electrostatic contribution of the higher multipole moments, that are, in the case of Lebedev grid model, directly associated with the Hessian eigenvectors. For the atom-centered model, this association breaks down beyond the first few eigenvectors related to the high-curvature monopole and dipole terms; this leads to even wider spread-out of the Hessian curvature values. Using these insights, it is possible to alleviate the ill-conditioning of the LS point-charge fitting without introducing external restraints and/or constraints. Also, as the analytical Lebedev grid PC model proposed here can reproduce multipole moments up to a given rank, it may provide a promising alternative to including explicit multipole terms in a force field.

Distribution of atmospheric gaseous elemental mercury (Hg(0)) from the Sea of Japan to the Arctic, and Hg(0) evasion fluxes in the Eastern Arctic Seas: Results from a joint Russian-Chinese cruise in 2018.

The Eastern Arctic Seas and the north-western Pacific are among the most poorly investigated areas as far as Hg cycling in marine systems is concerned. Continuous measurements of gaseous elemental mercury (Hg(0)) concentrations in the marine boundary layer and Hg(0) evasion fluxes from the sea surface were performed in these regions in fall 2018. Atmospheric Hg(0) concentrations of 1.02-2.50 ng/m3 were measured (average: 1.45 ± 0.12 ng/m3; N = 2518). Values in the Far Eastern Seas of Russia were lower compared to previous observations, presumably reflecting а global trend of decreasing atmospheric Hg(0). Concentration-weighted trajectory analysis highlighted three source regions influencing Hg(0) concentrations in the ambient air during the cruise: 1) the north-eastern China and the Yellow Sea region; 2) the Kuril-Kamchatka region of the Pacific Ocean and the region around the Commander and Aleutian Islands; and 3) the Arctic region. In the Arctic, sea-air Hg(0) evasion fluxes were at the same low levels as those observed earlier in the northern sea areas (0.28-1.35 ng/m2/h, average, 0.70 ± 0.26 ng/m2/h, N = 29). In the Eastern Arctic Seas, Hg(0) evasion fluxes were significantly dependent on river runoff. In the Arctic Ocean, they were negatively correlated with water temperature and positively correlated with salinity, suggesting a proximity to areas with contiguous ice and higher dissolved Hg(0) concentrations in the surface seawater. These findings are consistent with the hypothesis that the Arctic Ocean is a source of atmospheric Hg(0) during late summer and fall.

Long-Range N-N Bonding by Rydberg Electrons.

By using high-level ab initio methods, we examine the nature of bonding between Rydberg electrons hosted by two four-coordinate nitrogen centers embedded in a hydrocarbon scaffold. The electronic structure of these species resembles that of diradicals, yet the diffuse nature of the orbitals hosting the unpaired electrons results in unusual features. The unpaired Rydberg electrons exhibit long-range bonding interactions, leading to stabilization of the singlet state (relative to the triplet) and a reduced number of effectively unpaired electrons. However, thermochemical gains due to through-space bonding are offset by strong Coulomb repulsion between positively charged nitrogen cores. The kinetic stability of these Rydberg diradicals may be controlled by a judicious choice of the molecular scaffold, suggesting possible strategies for their experimental characterization.

Two Cycling Centers in One Molecule: Communication by Through-Bond Interactions and Entanglement of the Unpaired Electrons.

Many applications in quantum information science (QIS) rely on the ability to laser-cool molecules. The scope of applications can be expanded if laser-coolable molecules possess two or more cycling centers, i.e., moieties capable of scattering photons via multiple absorption-emission events. Here we employ the equation-of-motion coupled-cluster method for double electron attachment (EOM-DEA-CCSD) to study the electronic structure of hypermetallic molecules with two alkaline-earth metals connected by an acetylene linker. The electronic structure of the molecules is similar to that of two separated alkali metals; however, the interaction between the two electrons is weak and largely dominated by through-bond interactions. The communication between the two cycling centers is quantified by the extent of the entanglement of the two unpaired electrons associated with the two cycling centers. This contribution highlights the rich electronic structure of hypermetallic molecules that may advance various applications in QIS and beyond.