Photochemical and discharge-driven pathways to aromatic products from 1,3-butadiene

A detailed study of the photochemical and discharge-driven pathways taken by gas-phase 1,3-butadiene has been carried out. Photolysis or discharge excitation was initiated inside a short reaction tube attached to the outlet of a pulsed valve. Bath gas temperatures near 100 K were achieved in the reaction tube by the constrained expansion of the gas mixture into the tube, simulating temperatures of relevance in Titan's atmosphere. Photolysis of 1,3-butadiene was initiated at 218 nm with a laser pulse that counter-propagated the reaction tube. Discharge excitation was carried out using discharge electrodes imbedded in the reaction tube walls, enabling the study of the photochemical and discharge products under similar conditions. Products were detected using either single-photon VUV photoionization (118 nm = 10.5 eV) or resonant two-photon ionization (R(2)PI) spectroscopy in a time-of-flight mass spectrometer. Emphasis was placed on characterization of the aromatic products formed, since these may be of particular relevance to Titan's atmosphere, where benzene has been positively identified and 1,3-butadiene is projected as the principle pathway to its formation. Consistent with previous studies of the photodissociation of 1,3-butadiene, C(3)H(3) + CH(3) is the dominant primary product formed. Under the temperature-pressure conditions present in the reaction tube (T approximately 75-100 K, P = 50 mbar), C(6)H(6) is the dominant secondary photochemical product formed. A 1:1 C(4)H(6):C(4)D(6) mixture was used to prove that the C(6)H(6) product was formed by recombination of two C(3)H(3) radicals; however, a careful search for benzene revealed none, indicating that less than 1% of the C(6)H(6) formed in the reaction tube is benzene. This is consistent with expectations for these temperatures and pressures based on previous modeling of propargyl recombination. Two aromatic products were observed from the photochemistry: ethylbenzene and 3-phenylpropyne. Plausible pathways leading to these products are proposed. In the discharge, C(3)H(3) + CH(3) are also identified as significant primary neutral products and C(6)H(6) as a dominant higher-mass product. In this case, the C(6)H(6) was identified as benzene via its R2PI spectrum, appearing with intensity about 10 times larger than any other aromatic formed in the discharge. R2PI spectra of a total of about 15 aromatic products were recorded from the 1,3-butadiene discharge, among them toluene; styrene; phenylacetylene; o-, m-, and p-xylene; ethylbenzene; indane; indene; beta-methylstyrene; and naphthalene. Previously unidentified spectra in the m/z 142 and 144 mass channels were positively identified as the 1,3- and 1,4-isomers of phenylcyclopentadiene and the analogous 1-phenylcyclopentene.     

Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data

Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called rosettes. The choanoflagellate Monosiga brevicollis contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational software suite, Domain Analysis and Motif Matcher (DAMM), that analyzes peptide-binding cleft sequence identity as compared with human PDZ domains and that can be used in combination with literature searches of known human PDZ-interacting sequences to predict target specificity in choanoflagellate PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a M. brevicollis PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 μM affinity, a value commonly considered the threshold for cellular PDZ–peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contribute to investigations into choanoflagellate signaling and how it informs metazoan evolution.     

Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution

The computation of tautomer ratios of druglike molecules is enormously important in computer-aided drug discovery, as over a quarter of all approved drugs can populate multiple tautomeric species in solution. Unfortunately, accurate calculations of aqueous tautomer ratios—the degree to which these species must be penalized in order to correctly account for tautomers in modeling binding for computer-aided drug discovery—is surprisingly difficult. While quantum chemical approaches to computing aqueous tautomer ratios using continuum solvent models and rigid-rotor harmonic-oscillator thermochemistry are currently state of the art, these methods are still surprisingly inaccurate despite their enormous computational expense. Here, we show that a major source of this inaccuracy lies in the breakdown of the standard approach to accounting for quantum chemical thermochemistry using rigid rotor harmonic oscillator (RRHO) approximations, which are frustrated by the complex conformational landscape introduced by the migration of double bonds, creation of stereocenters, and introduction of multiple conformations separated by low energetic barriers induced by migration of a single proton. Using quantum machine learning (QML) methods that allow us to compute potential energies with quantum chemical accuracy at a fraction of the cost, we show how rigorous relative alchemical free energy calculations can be used to compute tautomer ratios in vacuum free from the limitations introduced by RRHO approximations. Furthermore, since the parameters of QML methods are tunable, we show how we can train these models to correct limitations in the underlying learned quantum chemical potential energy surface using free energies, enabling these methods to learn to generalize tautomer free energies across a broader range of predictions.

We show how alchemical free energies can be calculated with QML potentials to identify deficiencies in RRHO approximations for computing tautomeric free energies, and how these potentials can be learned from experiment to improve prediction accuracy.     

Guises and disguises of quadratic divergences

In this contribution, we present a new perspective on the control of quadratic divergences in quantum field theory, in general, and in the Higgs naturalness problem, in particular. Our discussion is essentially based on an approach where UV divergences are parameterized, after being reduced to basic divergent integrals (BDI) in one internal momentum, as functions of a cutoff and a renormalization group scale λ$\lambda$. We illustrate our proposal with well-known examples, such as the gluon vacuum self energy of QCD and the Higgs decay in two photons within this approach. We also discuss frameworks in effective low-energy QCD models, where quadratic divergences are indeed fundamental.     

A light-front coupled-cluster method for the nonperturbative solution of quantum field theories

We propose a new method for the nonperturbative solution of quantum field theories and illustrate its use in the context of a light-front analog to the Greenberg–Schweber model. The method is based on light-front quantization and uses the exponential-operator technique of the many-body coupled-cluster method. The formulation produces an effective Hamiltonian eigenvalue problem in the valence Fock sector of the system of interest, combined with nonlinear integral equations to be solved for the functions that define the effective Hamiltonian. The method avoids the Fock-space truncations usually used in nonperturbative light-front Hamiltonian methods and, therefore, does not suffer from the spectator dependence, Fock-sector dependence, and uncanceled divergences caused by such truncations.     

A unique approach to accurately measure thickness in thick multilayers

X‐ray optics called multilayer Laue lenses (MLLs) provide a promising path to focusing hard X‐rays with high focusing efficiency at a resolution between 5 nm and 20 nm. MLLs consist of thousands of depth‐graded thin layers. The thickness of each layer obeys the linear zone plate law. X‐ray beamline tests have been performed on magnetron sputter‐deposited WSi₂/Si MLLs at the Advanced Photon Source/Center for Nanoscale Materials 26‐ID nanoprobe beamline. However, it is still very challenging to accurately grow each layer at the designed thickness during deposition; errors introduced during thickness measurements of thousands of layers lead to inaccurate MLL structures. Here, a new metrology approach that can accurately measure thickness by introducing regular marks on the cross section of thousands of layers using a focused ion beam is reported. This new measurement method is compared with a previous method. More accurate results are obtained using the new measurement approach.     

Different rotamer states of cytosine nucleobases in heteronuclear PtPd-, PtPd2, and Pt2Pd2Ag complexes derived from [Pt(2,2'-bpy)(1-MeC-N3)2]2+ (1-MeC = 1-methylcytosine): first examples of species with head-head oriented 1-MeC(-) ligands

[Pt(2,2'-bpy)(1-MeC-N3)(2)](NO(3))(2) (1) (2,2'-bpy = 2,2'-bipyridine; 1-MeC = 1-methylcytosine) exists in water in an equilibrium of head-tail and head-head rotamers, with the former exceeding the latter by a factor of ca. 20 at room temperature. Nevertheless, 1 reacts with (en)Pd(II) (en = ethylenediamine) to give preferentially the dinuclear complex [Pt(2,2'-bpy)(1-MeC(-)-N3,N4)(2)Pd(en)](NO(3))(2)·5H(2)O (2) with head-head arranged 1-methylctosinato (1-MeC(-)) ligands and Pd being coordinated to two exocyclic N4H(-) positions. Addition of AgNO(3) to a solution of 2 leads to formation of a pentanuclear chain compound [{Pt(2,2'-bpy)(1-MeC(-))(2)Pd(en)}(2)Ag](NO(3))(5)·14H(2)O (5) in which Ag(+) cross-links two cations of 2 via the four available O2 sites of the 1-MeC(-) ligands. 2 and 5 appear to be the first X-ray structurally characterized examples of di- and multinuclear complexes derived from a Pt(II) species with two cis-positioned cytosinato ligands adopting a head-head arrangement. (tmeda)Pd(II) (tmeda = N,N,N',N'-tetramethylethylenediamine) and (2,2'-bpy)Pd(II) behave differently toward 1 in that in their derivatives the head-tail orientation of the 1-MeC(-) nucleobases is retained. In [Pt(2,2'-bpy)(1-MeC(-))(2){Pd(2,2'-bpy)}(2)](NO(3))(4)·10H(2)O (4), both (2,2'-bpy)Pd(II) entities are pairwise bonded to N4H(-) and O2 sites of the two 1-MeC(-) rings, whereas in [Pt(2,2'-bpy)(1-MeC(-))(2){Pd(tmeda)}(2)(NO(3))](NO(3))(3)·5H(2)O (3) only one of the two (tmeda)Pd(II) units is chelated to N4H(-) and O2. The second (tmeda)Pd(II) is monofunctionally attached to a single N4H(-) site. On the basis of these established binding patterns, ways to the formation of mixed Pt/Pd complexes and possible intermediates are proposed. The methylene protons of the en ligand in 2 are special in that they display two multiplets separated by 0.64 ppm in the (1)H NMR spectrum.     

Palladium(II)-catalyzed cycloisomerization of substituted 1,5-hexadienes: a combined experimental and computational study on an open and an interrupted hydropalladation/carbopalladation/β-hydride elimination (HCHe) catalytic cycle

The Pd(II)-catalyzed cycloisomerization of 3-alkoxycarbonyl-3-hydroxy-substituted 1,5-hexadienes has been studied experimentally and computationally. Experimentally, the reaction is characterized by a rapid room temperature formation of monomeric as well as dimeric cycloisomerization products using the commercially available precatalyst [(CH(3)CN)(4)Pd](BF(4))(2). In situ NMR measurements indicate the initial kinetic advantage of the desired cycloisomerization pathway to methylene cyclopentanes; however, double bond isomerization, elimination, and dimer formation are competitive undesired pathways. Evaluation of the obtained product structures by NMR spectroscopy and X-ray crystallography indicates that the sole determinant for the monomer/dimer ratio is the regioselectivity of the initial hydropalladation in favor of the allylic (monomer formation) or the homoallylic double bond (dimer formation). In order to account for the experimental results, we propose the coexistence of two product-forming catalytic cycles, an open, monomer generating, as well as an interrupted and redirected, dimer generating, hydropalladation/carbopalladation/β-hydride elimination (HCHe) process. Results from computational studies of the proposed competing catalytic cycles are supportive to our mechanistic hypothesis and pinpoint the pivotal importance of Pd(II)-hydroxo-chelate complexes for the reactivity-stability interplay of on- and off-pathway intermediates.