Discovery of the archaeal chemical link between glycogen (starch) synthase families using a new mass spectrometry assay

Starch and its analogue glycogen are biosynthesized by enzymes that have been classified by sequence similarities into two families that have no significant sequence overlap: the animal/fungal glycogen synthases and the plant/bacterial glycogen (starch) synthases. Recent gene sequence analysis of putative archaea enzymes implicates them as a third family that links the structural and functional features of the other two classes. Herein, we present the first rapid electrospray ionization mass spectrometry-based assay to quantify any carbohydrate-polymerizing activity, the first cloning and recombinant expression as well as verification of the putative function of a glycogen synthase from the hyperthermophilic archaea Pyrococcus furiosus, and the characterization of a variety of glycogen synthases with the new assay. The new assay allowed the determination of Km and Vmax values for the rabbit, yeast, and P. furiosus glycogen synthases. Most surprisingly, unlike the synthases from rabbit or yeast and in contradiction to what would be expected from structural studies of other nucleotide-sugar binding proteins, the synthase from the archaea source accepts both uridine- and adenine-diphosphate activated glucose competitively and with comparable affinities to form a glucose polymer. This loose substrate specificity implicates this protein as the chemical link between the two branches of glycogen synthases that have evolved to accept primarily one or the other nucleotide as well as a good source enzyme for polymer bioengineering efforts.     

Analog quantum simulation of chemical dynamics

Ultrafast chemical reactions are difficult to simulate because they involve entangled, many-body wavefunctions whose computational complexity grows rapidly with molecular size. In photochemistry, the breakdown of the Born–Oppenheimer approximation further complicates the problem by entangling nuclear and electronic degrees of freedom. Here, we show that analog quantum simulators can efficiently simulate molecular dynamics using commonly available bosonic modes to represent molecular vibrations. Our approach can be implemented in any device with a qudit controllably coupled to bosonic oscillators and with quantum hardware resources that scale linearly with molecular size, and offers significant resource savings compared to digital quantum simulation algorithms. Advantages of our approach include a time resolution orders of magnitude better than ultrafast spectroscopy, the ability to simulate large molecules with limited hardware using a Suzuki–Trotter expansion, and the ability to implement realistic system-bath interactions with only one additional interaction per mode. Our approach can be implemented with current technology; e.g., the conical intersection in pyrazine can be simulated using a single trapped ion. Therefore, we expect our method will enable classically intractable chemical dynamics simulations in the near term.

Dynamics governing ultrafast chemical reactions can be efficiently simulated using analog quantum simulators composed of a coupled system of qudits and bosonic modes.     

Photodissociation Dynamics of Cyclopropenylidene,c‐C3H2

In this joint experimental and theoretical study we characterize the complete dynamical “life cycle” associated with the photoexcitation of the singlet carbene cyclopropenylidene to the lowest lying optically bright excited electronic state: from the initial creation of an excited‐state wavepacket to the ultimate fragmentation of the molecule on the vibrationally hot ground electronic state. Cyclopropenylidene is prepared in this work using an improved synthetic pathway for the preparation of the precursor quadricyclane, thereby greatly simplifying the assignment of the molecular origin of the measured photofragments. The excitation process and subsequent non‐adiabatic dynamics have been previously investigated employing time‐resolved photoelectron spectroscopy and are now complemented with high‐level ab initio trajectory simulations that elucidate the specific vibronic relaxation pathways. Lastly, the fragmentation channels accessed by the molecule following internal conversion are probed using velocity map imaging (VMI) so that the identity of the fragmentation products and their corresponding energy distributions can be definitively assigned.     

Analysis of t-butylphenol acetylene condensed resin with methyl-methine linkages in vulcanized rubber by pyrolysis-gas chromatography/mass spectrometry

Methyl-methine linkages of Novolac, a commercially available t-butylphenol acetylene condensed (TBPA) resin, have been identified by recognition of pyrolysis pathways using pyrolysis-gas chromatography/mass spectrometry (Py-GC/mS) in vulcanized rubber. The diagnostic mass spectrum of t-butylphenol with methyl-methine linkages between phenolic rings was observed at m/z 192, corresponding to 4-t-butyl-2-ethyl-6-methylphenol. Other molecular ions were observed at m/z 178, 164, and 150 in the characteristic pyrolyzates. The ion at m/z 192 in the TBPA resin was observed to be characteristic for methyl-methine linkages between the phenolic groups, and the analytical pyrolysis-GC/mS method was thus able to identify the resin at low levels in vulcanized rubber. Copyright 1999 John Wiley & Sons, Ltd.