Multireference Methods are Realistic and Useful Tools for Modeling Catalysis

Highly correlated systems, in particular those that include transition metals, are ubiquitous in catalysis. The significant static correlation found in such systems is often poorly accounted for using Kohn Sham density functional theory methods, as they are single determinantal in nature. Applications to catalysis of more rigorous and appropriate multiconfigurational methods have been reported in select instances, but their use remains rare. We discuss obstacles that hinder the routine application of multireference (MR) wave function theoretical calculations to catalytic systems and the current state of the art with respect to removing those obstacles

Comparative growth and static allometry in the genus Chlorocebus

Characterizing variation in growth across populations is critical to understanding multiple aspects of development in primates, including within-taxon developmental plasticity and the evolution of life history patterns. Growth in wild primates has often been reported and directly compared across larger taxonomic groups and within social groups, but comparisons are rarely investigated across widely dispersed populations of a single taxon. With the Vervet Phenome-Genome Project and the International Vervet Research Consortium, we trapped 936 vervet monkeys of all ages representing three populations (Kenyan pygerythrus, South African pygerythrus, and sabaeus from St. Kitts & Nevis). We gathered 10 different body measurements from each including mass, body breadth and length, segmental limb lengths, and chest circumference. To gain a better understanding of how ontogenetic patterns vary in these populations, we calculated bivariate allometry coefficients, derived using PCA on log-transformed and z-standardized trait values, and compared them to isometric vector coefficients. Within all population samples, around weaning age most traits showed a negative allometric relationship to body length. As each population ages, however, distinct patterns emerge, showing population differences in onset and intensity of growth among traits. In concordance with other analyses on growth in these populations, our results suggest that there exist relative differences in patterns of growth between Chlorocebus populations, further suggesting selection for unique developmental pathways in each

The static allometry of sexual and non-sexual traits in vervet monkeys

Sexual traits vary tremendously in static allometry. This variation may be explained in part by body size-related differences in the strength of selection. We tested this hypothesis in two populations of vervet monkeys, using estimates of the level of condition dependence for different morphological traits as a proxy for body size-related variation in the strength of selection. In support of the hypothesis, we found that the steepness of allometric slopes increased with the level of condition dependence. One trait of particular interest, the penis, had shallow allometric slopes and low levels of condition dependence, in agreement with one of the most consistent patterns yet detected in the study of allometry, namely that of genitalia exhibiting shallow allometries.This research was supported by NIH grant R01RR0163009

Beyond Density Functional Theory: the Multiconfigurational Approach to Model Heterogeneous Catalysis

Catalytic processes are crucially important for many practical chemical applications. Heterogeneous catalysts are especially appealing because of their high stability and the relative ease with which they may be recovered and reused. Computational modeling can play an important role in the design of more catalytically active materials through the identification of reaction mechanisms and the opportunity to assess hypothetical catalysts in silico prior to experimental verification. Kohn-Sham density functional theory (KS-DFT) is the most used method in computational catalysis because it is affordable and it gives results of reasonable accuracy in many instances. Furthermore, it can be employed in a “black-box” mode that does not require significant a priori knowledge of the system. However, KS-DFT has some limitations: it suffers from self-interaction error (sometime referred to as delocalization error), but a greater concern is that it provides an intrinsically single-reference description of the electronic structure, and this can be especially problematic for modeling catalysis when transition metals are involved. In this perspective, we highlight some noteworthy applications of KS-DFT to heterogeneous computational catalysis, as well as cases where KS-DFT fails accurately to describe electronic structures and intermediate spin states in open-shell transition metal systems. We next provide an introduction to state-of-the-art multiconfigurational (MC; also referred to as multireference (MR)) methods and their advantages and limitations for modeling heterogeneous catalysis. We focus on specific examples to which MC methods have 2 been applied and discuss the challenges associated with these calculations. We conclude by offering our vision for how the community can make further progress in the development of MC methods for application to heterogeneous catalysis

Accelerated process development for integrated end-to-end biologics manufacturing

With the exception of monoclonal antibodies, biologics typically require bespoke manufacturing processes that vary widely in the type of and number of unit operations. This constraint leads to custom facility designs and unique strategies for process development for every new molecule. To enable flexible, multi-product manufacturing facilities and to reduce the speed to clinic for new molecules, streamlined manufacturing processes and associated strategies for process development are needed. We have developed a bench-scale, integrated and automated manufacturing platform capable of rapidly producing a variety of recombinant proteins with phase-appropriate quality for early development1. The system comprises three modules for fermentation via perfusion, straight-through chromatographic purification, and formulation. To facilitate the production of multiple products on the same system, we have also developed a holistic strategy for process design to manufacture new products in as few as twelve weeks after obtaining the product sequence. While upstream process development in our host (Pichia pastoris) has been relatively straightforward, there are not many tools currently available for developing fully integrated straight-through chromatographic processes. Therefore, we developed an in silico tool for the prediction of fully integrated purification processes based on a one-time collection of host-related data combined with conventional high-throughput chromatographic screening data for each new target molecule2. We used this tool to develop fully integrated, end-to-end production processes for three molecules (hGH, IFNα-2b, and G-CSF) with at least 45% fewer steps than traditional processes. While our in silico tool allows for rapid resin selection, it may not predict the optimal process for each individual molecule since it is based on conventional high-throughput screening techniques which seek to optimize each chromatographic step independently rather than optimizing a fully integrated, multi-column process. To address this limitation, we have also developed a DoE-like framework for the optimization of fully integrated purification processes once the resins have been selected. First, a series of range finding experiments are carried out on each individual column, similar to conventional screening but with limited analytics. Next, we carry out fully integrated (multi-column) testing of the proposed operational area with more extensive analytics, including host cell protein, DNA, and yield measurements. We use this methodology to develop optimized processes for the end-to-end production of a variety of single domain antibodies with high yield and purity. Further, we present a method for predicting the optimal operating conditions for a new molecule within the same class based only on its biophysical characteristics, reducing the timeline from sequence to early stage, phase-appropriate product to only six weeks. Using these holistic strategies for process development, we have produced over ten different recombinant proteins on our manufacturing platform including enzymes, cytokines, singe domain antibodies, and vaccine subunits. We believe that such integrated strategies for process design could enable the rapid translation from sequence to early stage clinical development of products for a variety of molecules and potentially allow clinical testing of a greater number of high quality molecules for vaccines and biopharmaceuticals. 1. Crowell, L. E. et al. On-demand manufacturing of clinical-quality biopharmaceuticals. Nat. Biotechnol. (2018). doi:10.1038/nbt.4262 2. Timmick, S. M. et al. An impurity characterization based approach for the rapid development of integrated downstream purification processes. Biotechnol. Bioeng. 1–13 (2018). doi:10.1002/bit.2671

Motor cortex organization after stroke is related to side of stroke and level of recovery.

The present study hypothesized that side of stroke and level of recovery influence motor system organization after stroke.Functional MRI was performed on 14 control subjects and 21 patients with chronic stroke during index finger tapping (control subjects, right; patients, recovered side).On functional MRI, stroke patients with right arm involvement showed (1) significantly smaller activation in contralateral motor cortexes compared with control subjects; (2) smaller ipsilateral (nonstroke) premotor and larger contralateral (stroke-side) sensorimotor activation compared with patients with left arm involvement, although electromyogram across groups was similar; and (3) 2.7-fold-larger contralateral sensorimotor cortex activation, ventrally, in those with full recovery compared with those with partial recovery, despite similar tapping force, frequency, range of motion, and electromyogram between groups. Supplementary motor area activation was unrelated to level of recovery.After stroke that causes mild to moderate initial impairment and mild residual hand weakness, cortical organization varies with side of injury and with final motor status. The findings may have implications for treatment after stroke

Performance of SM8 on a Test To Predict Small-Molecule Solvation Free Energies

The SM8 quantum mechanical aqueous continuum solvation model is applied to a 17-molecule test set proposed by Nicholls et al. (J. Med. Chem.2008, 51, 769) to predict free energies of solvation. With the M06-2X density functional, the 6-31G(d) basis set, and CM4M charge model, the root-mean-square error (RMSE) of SM8 is 1.08 kcal mol−1 for aqueous geometries and 1.14 kcal mol−1 for gas-phase geometries. These errors compare favorably with optimal explicit and continuum models reported by Nicholls et al., having RMSEs of 1.33 and 1.87 kcal mol−1, respectively. Other models examined by these workers had RMSEs of 1.5−2.6 kcal mol−1. We also explore the use of other density functionals and charge models with SM8 and the RMSE increases to 1.21 kcal mol−1 for mPW1/CM4 with gas-phase geometries, to 1.50 kcal mol−1 for M06-2X/CM4 with gas-phase geometries, and to 1.27−1.64 kcal mol−1 with three different models at B3LYP gas-phase geometries

Liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry adds enhanced functionalities to MALDI MS profiling for disease diagnostics

A liquid matrix-assisted laser desorption/ionization (liquid MALDI) method has been developed for high-throughput atmospheric pressure (AP) mass spectrometry (MS) analysis of the molecular content of crude bioliquids for disease diagnostics. The presented method is rapid and highly robust, enabling its application in environments where speed and low-cost high-throughput analyses are required. Importantly, because of the creation of multiply charged analyte ions, it provides additional functionalities that conventional solid MALDI MS profiling is lacking, including the use of high-performance mass analyzers with limited m/z range. The concomitant superior MS/MS performance that is achieved similar to ESI MS/MS adds greater analytical power and specificity to MALDI MS profiling while retaining the advantages of a fast laser-based analysis system and off-line large-scale sample preparation. The potential of this MALDI MS profiling method is demonstrated on the detection of dairy cow mastitis, which is a substantial economic burden on the dairy industry with losses of hundreds of dollars per diseased cow per year, equating to a total annual loss of billions of dollars, as well as leading to the use of large quantities of antibiotics, adding to the proliferation of antimicrobial resistance. Only small amounts of aliquots obtained from the daily farm milking process were prepared for liquid MALDI MS profiling using a simple one-pot/two-step analyte extraction. Automated analysis was performed using a custom-built AP-MALDI ion source, enabling the simultaneous detection of lipids, peptides, and proteins. Diagnostic, multiply charged, proteinaceous ions were easily sequenced and identified by MS/MS experiments. Samples were classified according to mastitis status using multivariate analysis, achieving 98.5% accuracy (100% specificity) determined by “leave 20% out” cross-validation. The methodology is generally applicable to AP-MALDI MS profiling on most commercial high-resolution mass spectrometers, with the potential for expansion into hospitals for rapid assessment of human and other biofluids

Pyrene-edged Fe(II)4L6 cages adaptively reconfigure during guest binding.

Differential guest-binding behavior was observed between two pyrene-edged Fe4L6 cages, prepared from isomeric bis(4-aminophenyl)pyrene derivatives, 2-formylpyridine and iron(II). The cage based on a 1,6-pyrene scaffold possesses an enclosed cavity suitable for the encapsulation of large hydrophobic guests including fullerenes, polycyclic aromatic hydrocarbons, and large, structurally complex natural products such as steroids. Addition of the fullerenes C60 and C70 to the cage brought about a re-equilibration among the different cage diastereomers in order to maximize the binding affinity of the system. Density functional theory was employed to rationalize the experimentally observed energy differences for C60 binding within the cage diastereomers. In contrast, the cage isomer based on a 2,7-pyrene scaffold has a more porous cavity and did not show affinity for neutral hydrophobic guests.This work was supported by the UK Engineering and Physical Sciences Research Council (EPSRC) and the US National Science Foundation (NSF CHE-1124244)This is the final version of the article. It was first published by ACS at http://pubs.acs.org/doi/abs/10.1021/ja507617

Facile Conversion of syn-[Fe-IV(O)(TMC)](2+) into the anti Isomer via Meunier's Oxo-Hydroxo Tautomerism Mechanism

The syn and anti isomers of [Fe-IV(O)(TMC)](2+) (TMC=tetramethylcyclam) represent the first isolated pair of synthetic non-heme oxoiron(IV) complexes with identical ligand topology, differing only in the position of the oxo unit bound to the iron center. Both isomers have previously been characterized. Reported here is that the syn isomer [Fe-IV(O-syn)(TMC)(NCMe)](2+) (2) converts into its anti form [Fe-IV(O-anti)(TMC)(NCMe)](2+) (1) in MeCN, an isomerization facilitated by water and monitored most readily by (HNMR)-H-1 and Raman spectroscopy. Indeed, when (H2O)-O-18 is introduced to 2, the nascent 1 becomes O-18-labeled. These results provide compelling evidence for a mechanism involving direct binding of a water molecule trans to the oxo atom in 2 with subsequent oxo-hydroxo tautomerism for its incorporation as the oxo atom of 1. The nonplanar nature of the TMC supporting ligand makes this isomerization an irreversible transformation, unlike for their planar heme counterparts