Prediction of GABARAP interaction with the GABA type A receptor.

We have performed docking simulations on GABARAP interacting with the GABA type A receptor using SwarmDock. We have also used a novel method to study hydration sites on the surface of these two proteins; this method identifies regions around proteins where desolvation is relatively easy, and these are possible locations where proteins can bind each other. There is a high degree of consistency between the predictions of these two methods. Moreover, we have also identified binding sites on GABARAP for other proteins, and listed possible binding sites for as yet unknown proteins on both GABARAP and the GABA type A receptor intracellular domain.

Predicting stability constants for uranyl complexes using density functional theory.

The ability to predict the equilibrium constants for the formation of 1:1 uranyl/ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We use density functional theory (B3LYP) and the integral equation formalism polarizable continuum model (IEF-PCM) to compute aqueous stability constants for UO2(2+) complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root-mean-square deviation from experiment <1.0 for log K1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono- and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelating capability to uranyl.

Ketene reactions with tertiary amines.

Tertiary amines react rapidly and reversibly with arylketenes in acetonitrile forming observable zwitterions, and these undergo amine catalyzed dealkylation forming N,N-disubstituted amides. Reactions of N-methyldialkylamines show a strong preference for methyl group loss by displacement, as predicted by computational studies. Loss of ethyl groups in reactions with triethylamine also occur by displacement, but preferential loss of isopropyl groups in the phenylketene reaction with diisopropylethylamine evidently involves elimination. Quinuclidine rapidly forms long-lived zwitterions with arylketenes, providing a model for catalysis by cinchona and related alkaloids in stereoselective additions to ketenes.

De novo structure-based design of bis-amidoxime uranophiles.

This paper presents a computational approach to the deliberate design of host architectures that recognize and bind specific guests. De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential structures. The efficacy of this computer-aided design methodology is illustrated with a search for bis-amidoxime chelates that are structurally organized for complexation with the uranyl cation.

How amidoximate binds the uranyl cation.

This study identifies how the amidoximate anion, AO, interacts with the uranyl cation, UO(2)(2+). Density functional theory calculations have been used to evaluate possible binding motifs in a series of [UO(2)(AO)(x)(OH(2))(y)](2-x) (x = 1-3) complexes. These motifs include monodentate binding to either the oxygen or the nitrogen atom of the oxime group, bidentate chelation involving the oxime oxygen atom and the amide nitrogen atom, and η(2) binding with the N-O bond. The theoretical results establish the η(2) motif to be the most stable form. This prediction is confirmed by single-crystal X-ray diffraction of UO(2)(2+) complexes with acetamidoxime and benzamidoxime anions.

Effect of relative humidity on hydrogen peroxide production in water droplets.

Mist is generated by ultrasonic cavitation of water (Fisher Biograde, pH 5.5-6.5) at room temperature (20-25 °C) in open air with nearly constant temperature (22-25 °C) but varying relative humidity (RH; 24-52%) over the course of many months. Water droplets in the mist are initially about 7 µm in diameter at about 50% RH. They are collected, and the concentration of hydrogen peroxide (H2O2) is measured using commercial peroxide test strips and by bromothymol blue oxidation. The quantification method is based on the Fenton chemistry of dye degradation to determine the oxidation capacity of water samples that have been treated by ultrasonication. It is found that the hydrogen peroxide concentration varies nearly linearly with RH over the range studied, reaching a low of 2 parts per million (ppm) at 24% RH and a high of 6 ppm at 52% RH. Some possible public health implications concerning the transmission of respiratory viral infections are suggested for this threefold change in H2O2 concentration with RH.

Erratum: Effect of Relative Humidity on Hydrogen Peroxide Production in Water Droplets - CORRIGENDUM.

[This corrects the article DOI: 10.1017/qrd.2021.6.].

Intramolecular competition in the photodissociation of C(3)D(3) radicals at 248 and 193 nm.

Motivated by recent experimental work, a theoretical study of the photodissociation of perdeuterated propargyl (D(2)CCD) and propynyl (D(3)CCC) radicals has been carried out, focusing on the C-C bond cleavage and D(2) loss channels. High-level ab initio calculations were carried out, and RRKM rate constants were calculated for isomerization and dissociation pathways. The resulting reaction barriers, microcanonical rate constants and product branching ratios are consistent with the experimental findings, supporting the overall mechanism of internal conversion followed by statistical dissociation on the ground state surface. We found loose transition states and very low exit barriers for two of the C-C bond cleavage channels and an additional CD(2) + CCD channel, which had not been reported previously. Our results probe the extent of propargyl and propynyl isomerization prior to dissociation at 248 and 193 nm and deliver a comprehensive picture of all ongoing molecular dynamics.

Onset of diradical character in small nanosized graphene patches.

A family of small graphene patches, i.e., rectangular polyaromatic hydrocarbons (PAHs), that have both zigzag and armchair edges is investigated to establish their ground state electronic structure. Broken symmetry density functional theory (DFT) and plane wave DFT were used to characterize the onset of diradical character via relative energies of open-shell and closed-shell singlet states. The perfect pairing (PP) active space approximation of coupled cluster theory was used to characterize diradical character on the basis of promotion of electrons from occupied to unoccupied molecular orbitals. The role of zigzag and armchair edges in the formation of open-shell singlet states is elucidated. In particular, it is found that elongation of the zigzag edge results in an increase of diradical character whereas elongation of the arm chair edge leads to a decrease of diradical character. Analysis of orbitals from PP calculations suggests that diradical states are formally Mobius aromatic multiconfigurational systems.

Edge versus interior in the chemical bonding and magnetism of zigzag edged triangular graphene molecules.

Ab initio density functional theory calculations show that the CC bond lengths fall into three distinct groups: core, apex, and edge, irrespective of whether the molecular center is a single atom or a C(6)-ring. The core, with a geometry that approximates infinite graphene, extends to the penultimate triangular row of carbon atoms, except in the vicinity of an apex. Impressed on the core bonds starting at the center is a small increasing length oscillation. The perimeter CC bonds joined at the apex are the shortest in the molecule. The edge carbon atoms are separated from interior atoms by the longest bonds in the molecule. The spin density localized primarily on edge (not apex) carbons with attached hydrogen (A-sublattice) is likely the highest attainable in any graphene molecule. The CC bonds in the high spin section of the edges are uniform in length and longer than perimeter CC bonds in the zigzag edged linear acenes, hexangulenes, annulenes, and benzene. This is attributed to the large number of edge localized nonbonding molecular orbitals (NBMOs) that sequestered pi-charge making it unavailable for bonding.

Large-Scale Study of Hydration Environments through Hydration Sites.

Hydration sites are locations of interest to water and they can be used to classify the behavior of water around chemical motifs commonly found on the surface of proteins. Inhomogeneous fluid solvation theory (IFST) is a method for calculating hydration free-energy changes from molecular dynamics (MD) trajectories. In this paper, hydration sites are identified from MD simulations of 380 diverse protein structures. The hydration free energies of the hydration sites are calculated using IFST and distributions of these free-energy changes are analyzed. The results show that for some hydration sites near features conventionally regarded as attractive to water, such as hydrogen bond donors, the water molecules are actually relatively weakly bound and are easily displaced. We also construct plots of the spatial density of hydration sites with high, medium, and low hydration free-energy changes which represent weakly and strongly bound hydration sites. It is found that these plots show consistent features around common polar amino acids for all of the proteins studied.

Quantitative metrics for drug-target ligandability.

Ligandability is a prerequisite for druggability and is a much easier concept to understand, model and predict because it does not depend on the complex pharmacodynamic and pharmacokinetic mechanisms in the human body. In this review, we consider a metric for quantifying ligandability from experimental data. We discuss ligandability in terms of the balance between effort and reward. The metric is evaluated for a standard set of well-studied drug targets - some traditionally considered to be ligandable and some regarded as difficult. We suggest that this metric should be used to systematically improve computational predictions of ligandability, which can then be applied to novel drug targets to predict their tractability.

Elution by Le Chatelier's principle for maximum recyclability of adsorbents: applied to polyacrylamidoxime adsorbents for extraction of uranium from seawater.

Amidoxime-based polymer adsorbents have attracted interest within the last decade due to their high adsorption capacities for uranium and other rare earth metals from seawater. The ocean contains an approximated 4-5 billion tons of uranium and even though amidoxime-based adsorbents have demonstrated the highest uranium adsorption capacities to date, they are still economically impractical because of their limited recyclability. Typically, the adsorbed metals are eluted with a dilute acid solution that not only damages the amidoxime groups (metal adsorption sites), but is also not strong enough to remove the strongly bound vanadium, which decreases the adsorption capacity with each cycle. We resolved this challenge by incorporating Le Chatelier's principle to recycle adsorbents indefinitely. We used a solution with a high concentration of amidoxime-like chelating agents, such as hydroxylamine, to desorb nearly a 100% of adsorbed metals, including vanadium, without damaging the metal adsorption sites and preserving the high adsorption capacity. The method takes advantage of knowing the binding mode between the amidoxime ligand and the metal and mimics it with chelating agents that then in a Le Chatelier's manner removes metals by shifting to a new chemical equilibrium. For this reason the method is applicable to any ligand-metal adsorbent and it will make an impact on other extraction technologies.

Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites.

The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

Quantifying the binding strength of U(VI) with phthalimidedioxime in comparison with glutarimidedioxime.

Studies of the complexation of U(vi) with amidoxime-related ligands help in the development of efficient sorbents for the extraction of uranium from seawater. In the present study, the stability constants of the U(vi) complexes with two phthalimidedioxime ligands were determined by potentiometry and spectrophotometry, and compared with glutarimidedioxime previously studied. Density functional theory calculations were performed to identify the most probable protonation sites of the ligand and to help interpret the trend in the binding strength of the ligands. The phthalimidedioxime complexes were found to be 2-3 orders of magnitude weaker than the corresponding glutarimidedioxime complexes, which was attributed to the difference between the ligands in the electronic and structural properties. The incorporation of the aromatic ring into phthalimidedioxime reduces the electron density on the donor atoms of the ligand and makes the imidedioxime moiety less complementary for binding UO2(2+)via its equatorial plane. Though weaker than glutarimidedioxime, phthalimidedioxime still forms fairly strong U(vi) complexes and can still effectively compete with carbonate for the complexation of U(vi) at seawater pH and carbonate concentration. Due to its higher chemical stability in acidic solutions than that of glutarimidedioxime, phthalimidedioxime is a valuable ligand that could have potential use in the extraction of U(vi) from seawater.

N-pyrrolylketene: a nonconjugated heteroarylketene.

N-Pyrrolylketene (5) is calculated to be destabilized and nonconjugated, with a preferred geometry with the pyrrolyl ring orthogonal to the ketenyl group. Ketene 5 is generated from N-pyrrolylacetic acid (7) with use of Mukaiyama's reagent, and reacts with imines forming ß-lactams 10, with a product ratio correlation of log(cis/trans) with σ(+). Photolysis of N-diazoacetylpyrrole (14) in MeOH gives methyl N-pyrrolylacetate (15) from 5 and also ester 17, evidently by trapping of 2-(1-pyrrolylketene) (21), formed by a new vinylogous Wolff rearrangement.

Structural effects on interconversion of oxygen-substituted bisketenes and cyclobutenediones.

Cyclobutenediones 5 disubstituted with HO (a), MeO (b), EtO (c), i-PrO (d), t-BuO (e), PhO (f), 4-MeOC6H4O (g), 4-O2NC6H4O (h), and 3,4-bridging OCH2CH2O (i) substituents upon laser flash photolysis gave the corresponding bisketenes 6a-i, as detected by their distinctive doublet IR absorptions between 2075 and 2106 and 2116 and 2140 cm-1. The reactivities in ring closure back to the cyclobutenediones were greatest for the group 6b-e, with the highest rate constant of 2.95 x 10(7) s-1 at 25 degrees C for 6e (RO = t-BuO) in isooctane, were less for 6a (RO = OH, k = 2.57 x 10(6) s-1 in CH3CN), while 6f-i were the least reactive, with the lowest rate constant of 3.8 x 10(4) s-1 in CH3CN for 6h (RO = 4-O2NC6H4O). The significantly reduced rate constants for 6f-i are attributed to diminution of the electron-donating ability of oxygen to the cyclobutenediones 5f-h by the ArO substituents compared to alkoxy groups and to angle strain in the bridged product cyclobutenedione 5i. The reactivities of the ArO-substituted bisketenes 6f-h in CH3CN varied by a factor of 50 and gave an excellent correlation of the observed rate constants log k with the sigma p constants of the aryl substituents. Computational studies at the B3LYP/6-31G(d) level of ring-closure barriers are consistent with the measured reactivities. Photolysis of squaric acid (5a) in solution provides a convenient preparation of deltic acid (7).

Amino substituted bisketenes: generation, structure, and reactivity.

Hitherto unknown diamino-substituted bisketenes with both free (14) and tethered (16) amino substituents have been generated by using laser flash photolysis for ring opening of the corresponding cyclobutenediones. The time-resolved kinetics of ring closure of the amino bisketenes back to the cyclobutenediones were measured by IR or UV spectroscopy, and give first-order rate constants which vary by a factor of 7.5x10(4), and the bis(Me2N) bisketene 14 is the most reactive in ring closure that has been reported. Rate constants for ring closure of these and previously observed bisketenes vary by a factor of 10(13). The dialkylamino bisketenes 16 (R=Me, n-Bu) with tethered substituents and restricted geometries are less reactive than the bis(Me2N) bisketene 14 by factors of 1700 and 540, respectively. Computational results obtained with DFT methods suggest angle strain in the tethered cyclobutenediones 15 inhibits facile cyclization of bisketenes 16.

Hydration of pyridylketenes: formation of acid enol and dihydropyridine (eneaminone) transients.

2-, 3-, and 4-Pyridylketenes 4 formed in water by photochemical Wolff rearrangements using flash photolysis undergo rapid hydration forming transient intermediates observed by UV spectroscopy. 3-Pyridylketene (3-4) formed the acid enol intermediate 3-10 which was converted to the acid 3-11, and phenylketene gave similar behavior. 4-Pyridylketene (4-4) reacted with a similar initial rate constant of 5.0 x 10(4) s(-1) for decay of an absorption at 275 nm, with concomitant formation of a strong absorption at 370 nm with the same rate constant. The intermediate absorbing at 370 nm decayed with a lifetime 2.4 x 10(3) fold longer than that of the ketene, and is identified as 4-(carboxymethylene)-1,4-dihydropyridine (4-13), resulting from conjugate 1,6-addition of H(2)O to 4-4. 2-Pyridylketene (2-4) underwent hydration with a similar rate constant of 1.1 x 10(4) s(-1) forming a transient with a UV absorption with maxima at 310 and 380 nm that decayed with biexponetial kinetics, with rate constants slower than the rate of formation by factors of 5.2 and 110, respectively. These results are interpreted as indicating the presence of two species, namely Z- and E-2-(carboxymethylene)-1,2-dihydropyridines (2-13), resulting from conjugate 1,4-addition of H(2)O to 2-4. The identifications of the 1,2- and 1,4-(carboxymethylene)dihydropyridines 2- and 4-13 were confirmed by comparison of their UV spectra with those of the corresponding N-methyl derivatives. The amination of 2-pyridylketene in CH(3)CN was reinvestigated, and spectroscopic evidence, computational studies, and preparation of the N-methyl analogue demonstrated formation of the 1,2-dihydropyridine Z-2-8f as the long-lived intermediate.