Chemical Bonding and the Role of Node-Induced Electron Confinement.

The chemical bond is the cornerstone of chemistry, providing a conceptual framework to understand and predict the behavior of molecules in complex systems. However, the fundamental origin of chemical bonding remains controversial and has been responsible for fierce debate over the past century. Here, we present a unified theory of bonding, using a separation of electron delocalization effects from orbital relaxation to identify three mechanisms [node-induced confinement (typically associated with Pauli repulsion, though more general), orbital contraction, and polarization] that each modulate kinetic energy during bond formation. Through analysis of a series of archetypal bonds, we show that an exquisite balance of energy-lowering delocalizing and localizing effects are dictated simply by atomic electron configurations, nodal structure, and electronegativities. The utility of this unified bonding theory is demonstrated by its application to explain observed trends in bond strengths throughout the periodic table, including main group and transition metal elements.

Large Computational Survey of Intrinsic Reactivity of Aromatic Carbon Atoms with Respect to a Model Aldehyde Oxidase.

Aldehyde oxidase (AOX) and other related molybdenum-containing enzymes are known to oxidize the C-H bonds of aromatic rings. This process contributes to the metabolism of pharmaceutical compounds and, therefore, is of vital importance to drug pharmacokinetics. The present work describes an automated computational workflow and its use for the prediction of intrinsic reactivity of small aromatic molecules toward a minimal model of the active site of AOX. The workflow is based on quantum chemical transition state searches for the underlying single-step oxidation reaction, where the automated protocol includes identification of unique aromatic C-H bonds, creation of three-dimensional reactant and product complex geometries via a templating approach, search for a transition state, and validation of reaction end points. Conformational search on the reactants, products, and the transition states is performed. The automated procedure has been validated on previously reported transition state barriers and was used to evaluate the intrinsic reactivity of nearly three hundred heterocycles commonly found in approved drug molecules. The intrinsic reactivity of more than 1000 individual aromatic carbon sites is reported. Stereochemical and conformational aspects of the oxidation reaction, which have not been discussed in previous studies, are shown to play important roles in accurate modeling of the oxidation reaction. Observations on structural trends that determine the reactivity are provided and rationalized.

Oligoprogression in Metastatic, Castrate-Resistant Prostate Cancer-Prevalence and Current Clinical Practice.

Aims: Oligoprogression is poorly defined in current literature. Little is known about the natural history and significance of oligoprogression in patients with hormone-resistant prostate cancer on abiraterone or enzalutamide treatment [termed androgen receptor-targeted therapy (ARTT)]. The aim of this study was to determine the prevalence of oligoprogression, describe the characteristics of oligoprogression in a cohort of patients from a single center, and identify the number of patients potentially treatable with stereotactic body radiotherapy (SBRT). Methods: Castration-resistant prostate cancer (CRPC) patients who radiologically progressed while on ARTT were included. Patients with oligoprogressive disease (OPD) (≤3 lesions) on any imaging were identified in a retrospective analysis of electronic patient records. Kaplan-Meier method and log-rank test were used to calculate progression-free and overall survival. Results: A total of 102 patients with metastatic CRPC on ARTT were included. Thirty (29%) patients presented with oligoprogression (46 lesions in total); 21 (21% of total) patients had lesions suitable for SBRT. The majority of lesions were in the bone (21, 46%) or lymph nodes (15, 33%). Patients with oligoprogression while on ARTT had a significantly better prostate-specific antigen (PSA) response on commencing ARTT as compared to patients who later developed polyprogression. However, PSA doubling time immediately prior to progression did not predict OPD. Median progression-free survival to oligoprogression versus polyprogression was 16.8 vs. 11.7 months. Time to further progression after oligoprogression was 13.6 months in those treated with radiotherapy (RT) for oligoprogression vs. 5.7 months in those treated with the continuation of ARTT alone. Conclusions: In this study, nearly a third of patients on ARTT for CRPC were found to have OPD. OPD patients had a better PSA response on ART and a longer duration on ARTT before developing OPD as compared to those developing polyprogressive disease (Poly-PD). The majority of patients (70%) with OPD had lesions suitable for SBRT treatment. Prospective randomized control trials are needed to establish if there is a survival benefit of SBRT in oligoprogressive prostate cancer and to determine predictive indicators.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package.

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

The Dark Triad trait of psychopathy and message framing predict risky decision-making during the COVID-19 pandemic.

The effects of framing on risky decision-making have been studied extensively in research using Kahneman and Tversky's (1981) hypothetical scenario about a contagious Asian disease. The COVID-19 pandemic offers a unique opportunity to test how message framing affects risky decision-making when millions of real lives are at stake worldwide. In a sample of US adults (N = 294), we investigated the effects of message framing and personality (Dark Triad traits) in relation to risky decision-making during the COVID-19 crisis. We found that both gain- and loss-framing influenced risk choice in response to COVID-19. People were more risk-averse in the loss condition of the current study compared to the benchmark established by Tversky and Kahneman (1981). Among the Dark Triad traits, psychopathy emerged as the significant predictor of risk taking, suggesting that people who score high in psychopathy are more likely to gamble with other people's lives during the COVID-19 crisis. We suggest that both voters and pandemic-related public awareness campaigns should consider the possibility that decision-makers with psychopathic tendencies may take greater risks with other people's lives during a pandemic. In addition, the framing of public-health messages should be tailored to increase the chances of compliance with government restrictions.

From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis.

Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential.

Pattern-free generation and quantum mechanical scoring of ring-chain tautomers.

In contrast to the computational generation of conventional tautomers, the analogous operation that would produce ring-chain tautomers is rarely available in cheminformatics codes. This is partly due to the perceived unimportance of ring-chain tautomerism and partly because specialized algorithms are required to realize the non-local proton transfers that occur during ring-chain rearrangement. Nevertheless, for some types of organic compounds, including sugars, warfarin analogs, fluorescein dyes and some drug-like compounds, ring-chain tautomerism cannot be ignored. In this work, a novel ring-chain tautomer generation algorithm is presented. It differs from previously proposed solutions in that it does not rely on hard-coded patterns of proton migrations and bond rearrangements, and should therefore be more general and maintainable. We deploy this algorithm as part of a workflow which provides an automated solution for tautomer generation and scoring. The workflow identifies protonatable and deprotonatable sites in the molecule using a previously described approach based on rapid micro-pKa prediction. These data are used to distribute the active protons among the protonatable sites exhaustively, at which point alternate resonance structures are considered to obtain pairs of atoms with opposite formal charge. These pairs are connected with a single bond and a 3D undistorted geometry is generated. The scoring of the generated tautomers is performed with a subsequent density functional theory calculation employing an implicit solvent model. We demonstrate the performance of our workflow on several types of organic molecules known to exist in ring-chain tautomeric equilibria in solution. In particular, we show that some ring-chain tautomers not found using previously published algorithms are successfully located by ours.

Siloxyaluminate and Siloxygallate Complexes as Models for Framework and Partially Hydrolyzed Framework Sites in Zeolites and Zeotypes.

Anionic molecular models for nonhydrolyzed and partially hydrolyzed aluminum and gallium framework sites on silica, M[OSi(OtBu)3 ]4 - and HOM[OSi(OtBu)3 ]3 - (where M=Al or Ga), were synthesized from anionic chlorides Li{M[OSi(OtBu)3 ]3 Cl} in salt metathesis reactions. Sequestration of lithium cations with [12]crown-4 afforded charge-separated ion pairs composed of monomeric anions M[OSi(OtBu)3 ]4 - with outer-sphere [([12]crown-4)2 Li]+ cations, and hydroxides {HOM[OSi(OtBu)3 ]3 } with pendant [([12]crown-4)Li]+ cations. These molecular models were characterized by single-crystal X-ray diffraction, vibrational spectroscopy, mass spectrometry and NMR spectroscopy. Upon treatment of monomeric [([12]crown-4)Li]{HOM[OSi(OtBu)3 ]3 } complexes with benzyl alcohol, benzyloxide complexes were formed, modeling a possible pathway for the formation of active sites for Meerwin-Ponndorf-Verley (MPV) transfer hydrogenations with Al/Ga-doped silica catalysts.

The Ground State Electronic Energy of Benzene.

We report on the findings of a blind challenge devoted to determining the frozen-core, full configuration interaction (FCI) ground-state energy of the benzene molecule in a standard correlation-consistent basis set of double-ζ quality. As a broad international endeavor, our suite of wave function-based correlation methods collectively represents a diverse view of the high-accuracy repertoire offered by modern electronic structure theory. In our assessment, the evaluated high-level methods are all found to qualitatively agree on a final correlation energy, with most methods yielding an estimate of the FCI value around -863 mEH. However, we find the root-mean-square deviation of the energies from the studied methods to be considerable (1.3 mEH), which in light of the acclaimed performance of each of the methods for smaller molecular systems clearly displays the challenges faced in extending reliable, near-exact correlation methods to larger systems. While the discrepancies exposed by our study thus emphasize the fact that the current state-of-the-art approaches leave room for improvement, we still expect the present assessment to provide a valuable community resource for benchmark and calibration purposes going forward.

Clarifying the quantum mechanical origin of the covalent chemical bond.

Lowering of the electron kinetic energy (KE) upon initial encounter of radical fragments has long been cited as the primary origin of the covalent chemical bond based on Ruedenberg's pioneering analysis of H[Formula: see text] and H2 and presumed generalization to other bonds. This work reports KE changes during the initial encounter corresponding to bond formation for a range of different bonds; the results demand a re-evaluation of the role of the KE. Bonds between heavier elements, such as H3C-CH3, F-F, H3C-OH, H3C-SiH3, and F-SiF3 behave in the opposite way to H[Formula: see text] and H2, with KE often increasing on bringing radical fragments together (though the total energy change is substantially stabilizing). The origin of this difference is Pauli repulsion between the electrons forming the bond and core electrons. These results highlight the fundamental role of constructive quantum interference (or resonance) as the origin of chemical bonding. Differences between the interfering states distinguish one type of bond from another.

Probing radical-molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals.

Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical-molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical-molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A "polarize-then-depolarize" (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. These radical extensions are incorporated into the "vertical" and "adiabatic" variants of uALMO-EDA for studies of energy changes and property shifts upon complexation. The EDA is validated on two model complexes, H2O˙F and FH˙OH. It is then applied to several chemically interesting radical-molecule complexes, including the sandwiched and T-shaped benzene dimer radical cation, complexes of pyridine with benzene and naphthalene radical cations, binary and ternary complexes of the hydroxyl radical with water (˙OH(H2O) and ˙OH(H2O)2), and the pre-reactive complexes and transition states in the ˙OH + HCHO and ˙OH + CH3CHO reactions. These examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical-molecule interactions.

Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method.

Recent advances in selected configuration interaction methods have made them competitive with the most accurate techniques available and, hence, creating an increasingly powerful tool for solving quantum Hamiltonians. In this work, we build on recent advances from the adaptive sampling configuration interaction (ASCI) algorithm. We show that a useful paradigm for generating efficient selected CI/exact diagonalization algorithms is driven by fast sorting algorithms, much in the same way iterative diagonalization is based on the paradigm of matrix vector multiplication. We present several new algorithms for all parts of performing a selected CI, which includes new ASCI search, dynamic bit masking, fast orbital rotations, fast diagonal matrix elements, and residue arrays. The ASCI search algorithm can be used in several different modes, which includes an integral driven search and a coefficient driven search. The algorithms presented here are fast and scalable, and we find that because they are built on fast sorting algorithms they are more efficient than all other approaches we considered. After introducing these techniques, we present ASCI results applied to a large range of systems and basis sets to demonstrate the types of simulations that can be practically treated at the full-CI level with modern methods and hardware, presenting double- and triple-ζ benchmark data for the G1 data set. The largest of these calculations is Si2H6 which is a simulation of 34 electrons in 152 orbitals. We also present some preliminary results for fast deterministic perturbation theory simulations that use hash functions to maintain high efficiency for treating large basis sets.

CASSCF with Extremely Large Active Spaces Using the Adaptive Sampling Configuration Interaction Method.

The complete active space self-consistent field (CASSCF) method is the principal approach employed for studying strongly correlated systems. However, exact CASSCF can only be performed on small active spaces of ∼20 electrons in ∼20 orbitals due to exponential growth in the computational cost. We show that employing the Adaptive Sampling Configuration Interaction (ASCI) method as an approximate Full CI solver in the active space allows CASSCF-like calculations within chemical accuracy (<1 kcal/mol for relative energies) in active spaces with more than ∼50 active electrons in ∼50 active orbitals, significantly increasing the sizes of systems amenable to accurate multiconfigurational treatment. The main challenge with using any selected CI-based approximate CASSCF is the orbital optimization problem; they tend to exhibit large numbers of local minima in orbital space due to their lack of invariance to active-active rotations (in addition to the local minima that exist in exact CASSCF). We highlight methods that can avoid spurious local extrema as a practical solution to the orbital optimization problem. We employ ASCI-SCF to demonstrate a lack of polyradical character in moderately sized periacenes with up to 52 correlated electrons and compare against heat-bath CI on an iron porphyrin system with more than 40 correlated electrons.

What Levels of Coupled Cluster Theory Are Appropriate for Transition Metal Systems? A Study Using Near-Exact Quantum Chemical Values for 3d Transition Metal Binary Compounds.

Transition metal compounds are traditionally considered to be challenging for standard quantum chemistry approximations like coupled cluster (CC) theory, which are usually employed to validate lower level methods like density functional theory (DFT). To explore this issue, we present a database of bond dissociation energies (BDEs) for 74 spin states of 69 diatomic species containing a 3d transition metal atom and a main group element, in the moderately sized def2-SVP basis. The presented BDEs appear to have an (estimated) 3σ error less than 1 kJ/mol relative to the exact solutions to the nonrelativistic Born-Oppenheimer Hamiltonian. These benchmark values were used to assess the performance of a wide range of standard single reference CC models, as the results should be beneficial for understanding the limitations of these models for transition metal systems. We find that interactions between metals and monovalent ligands like hydride and fluoride are well described by CCSDT. Similarly, CCSDTQ appears to be adequate for bonds between metals and nominally divalent ligands like oxide and sulfide. However, interactions with polyvalent ligands like nitride and carbide are more challenging, with even CCSDTQ(P)Λ yielding errors on the scale of a few kJ/mol. We also find that many perturbative and iterative approximations to higher order terms either yield disappointing results or actually worsen the performance relative to the baseline low level CC method, indicating that complexity does not always guarantee accuracy.

One or two minds? Neural network modeling of decision making by the unified self.

Ever since the seminal work of Tversky and Kahneman starting in the late 1960s, it has generally been accepted that many characteristic human decision patterns do not follow the norms of economic theories based on rational utility maximization and consistency across frames. Yet people do often make decisions and numerical judgments that are mathematically consistent. In order to account for the range of rational, intuitive, and emotional influences on decision making, prominent psychologists have developed a number of dual-process or dual-system theories of decision processes. Among these theories are System 1 and System 2, Cognitive-Experiential Self-theory, and Fuzzy Trace Theory. Fuzzy Trace Theory (FTT) is the most amenable of these theories to a unified biologically based neural network approach. This article reviews several years of research on a decision theory that integrates the gist and verbatim representations of FTT into a network model. The model is based on several constructs by Grossberg and his colleagues including Adaptive Resonance Theory and Gated Dipole Theory, combined with selective attention and probabilistic distribution of some parameters representing individual differences in decision style. It incorporates data on the functions of several brain regions including sensory cortex, amygdala, orbitofrontal cortex, ventral striatum, thalamus, and anterior cingulate, and premotor cortex.

Expanded Helicenes: A General Synthetic Strategy and Remarkable Supramolecular and Solid-State Behavior.

A divergent synthetic strategy allowed access to several members of a new class of helicenes, the "expanded helicenes", which are composed of alternating linearly and angularly fused rings. The strategy is based on a three-fold, partially intermolecular [2+2+n] (n = 1 or 2) cycloaddition with substrates containing three diyne units. Investigation of aggregation behavior, both in solution and in the solid state, revealed that one of these compounds forms an unusual homochiral, π-stacked dimer via an equilibrium that is slow on the NMR time scale. The versatility of the method was harnessed to access a selenophene-annulated expanded helicene that, in contrast to its benzannulated analogue, exhibits long-range π-stacking in the solid state. The new helicenes possess low racemization barriers, as demonstrated by dynamic 1H NMR spectroscopy.

Energy decomposition analysis of single bonds within Kohn-Sham density functional theory.

An energy decomposition analysis (EDA) for single chemical bonds is presented within the framework of Kohn-Sham density functional theory based on spin projection equations that are exact within wave function theory. Chemical bond energies can then be understood in terms of stabilization caused by spin-coupling augmented by dispersion, polarization, and charge transfer in competition with destabilizing Pauli repulsions. The EDA reveals distinguishing features of chemical bonds ranging across nonpolar, polar, ionic, and charge-shift bonds. The effect of electron correlation is assessed by comparison with Hartree-Fock results. Substituent effects are illustrated by comparing the C-C bond in ethane against that in bis(diamantane), and dispersion stabilization in the latter is quantified. Finally, three metal-metal bonds in experimentally characterized compounds are examined: a [Formula: see text]-[Formula: see text] dimer, the [Formula: see text]-[Formula: see text] bond in dizincocene, and the Mn-Mn bond in dimanganese decacarbonyl.

Efficient and selective catalysis for hydrogenation and hydrosilation of alkenes and alkynes with PNP complexes of scandium and yttrium.

Scandium and yttrium congeneric complexes, supported by a monoanionic PNP ligand, were studied as catalysts for alkene hydrogenation and hydrosilation, and alkyne semihydrogenation and semihydrosilation. The yttrium congener was found to be much more active in all cases, but this greater activity is accompanied by more rapid catalyst decomposition and therefore higher total yields for some of the reactions with the scandium catalyst. Calculations indicate that the reactions may proceed via σ-bond metathesis of the alkyl complexes to form metal hydride intermediates into which alkenes/alkynes insert.

Synthetic control and empirical prediction of redox potentials for Co4O4 cubanes over a 1.4 V range: implications for catalyst design and evaluation of high-valent intermediates in water oxidation.

The oxo-cobalt cubane unit [Co4O4] is of interest as a homogeneous oxygen-evolution reaction (OER) catalyst, and as a functional mimic of heterogeneous cobalt oxide OER catalysts. The synthesis of several new cubanes allows evaluation of redox potentials for the [Co4O4] cluster, which are highly sensitive to the ligand environment and span a remarkable range of 1.42 V. The [CoIII4O4]4+/[CoIII3CoIVO4]5+ and [CoIII3CoIVO4]5+/[CoIII2CoIV2O4]6+ redox potentials are reliably predicted by the pKas of the ligands. Hydrogen bonding is also shown to significantly raise the redox potentials, by ∼500 mV. The potential-pKa correlation is used to evaluate the feasibility of various proposed OER catalytic intermediates, including high-valent Co-oxo species. The synthetic methods and structure-reactivity relationships developed by these studies should better guide the design of new cubane-based OER catalysts.

Preliminary experience on the use of PET/CT in the management of pediatric post-transplant lymphoproliferative disorder.

INTRODUCTION: Post-transplant lymphoproliferative disorder (PTLD) is a well-known complication following prolonged immunosuppression. Contrary to other lymphomas, there is no standardized imaging approach to assess PTLD either at staging or for response to therapy. Positron emission tomography/computed tomography (PET/CT) is an imaging modality that has proven to be useful in lymphoma. However, there is still limited data concerning its use in pediatric PTLD. Our study evaluates the use of PET/CT in pediatric PTLD at our institution. METHODS: To assess the role of PET/CT in pediatric PTLD, we reviewed the pediatric patients with PTLD who had undergone PET/CT at our institution between 2000 and 2016. RESULTS: Nine patients were identified. Six had PET/CT at diagnosis. All lesions seen on CT were identified with PET/CT. Fourteen PET/CTs were done during treatment. Eight PET/CTs were negative, including three where CT showed areas of uncertain significance. In these cases, PET/CT helped us to stop treatment and the patients remain in remission after a long follow-up (mean 74.3 months; range 12.4-180.9 months). PET/CT revealed additional disease in two cases, therefore treatment was intensified. Six biopsies and close follow-up was done to confirm PET/CT results. In one case, PET/CT did not identify central nervous system involvement demonstrated on magnetic resonance imaging. CONCLUSION: PET/CT may have an important role in the staging and follow-up of pediatric PTLD. In our cohort, PET/CT was helpful in staging and assessing treatment response and in clarifying equivocal findings on other imaging modalities.