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The small magnitudes of some kinetic isotope effects (KIEs), including those associated with 13C, necessitate a highly precise experimental approach involving the competition of light and heavy substrates. Provided the reaction is first order in the labeled substrate, the product isotopologue ratio converges to the initial reactant isotopologue ratio at completion, but the same is not true for dimerization reactions simply because the product diverges into four distinct isotopologues. The relative populations of these dimers deviate from the statistical distribution under the influence of a KIE. Accordingly, the current study aims to demonstrate this concept by analyzing the relative 13C placement in D-alanine-D-alanine at reaction completion for the dimerization of D-[1-13C]alanine catalyzed by Mycobacterium tuberculosis D-alanine:D-alanine ligase (Ddl). Using 13C NMR spectroscopy and Fourier-transform ion cyclotron mass spectrometry, the relative distributions of the four dimer isotopologues were determined. The ratio of the mono-labeled dimers with 13C at the C-terminus to that with 13C at the N-terminus yielded a relative KIE of 1.011 ± 0.004 for the acyl carbon. This result suggests that the rate-limiting step of the Ddl-catalyzed reaction involves peptide bond formation—either nucleophilic attack by the amino group or collapse of the resulting tetrahedral intermediate. This method of analysis, to the best of our knowledge, is the first of its kind for obtaining competitive KIEs in enzyme-catalyzed dimerization reactions. 

For simulations of strong field ionization using time-dependent configuration with a complex absorbing potential (TDCI-CAP), standard molecular basis set must be augmented by several sets of diffuse functions to support the wavefunction as it is distorted by the strong field and interacts with the absorbing potential. Various sets of diffuse functions used in previous studies have been extended and evaluated for their ability to model the angular dependence of strong field ionization. These sets include diffuse s, p, d and f gaussian functions with selected even-tempered exponents of the form 0.0001×2n placed on each atom. For single-centered test cases, the largest contribution to the ionization rate is from functions with a maximum in the radial distribution close to the onset of the complex absorbing potential, while functions with smaller exponents also contributed to the rate. For molecules, diffuse functions on adjacent centers overlap strongly, leading to linear dependencies. The transformation to remove these linear dependencies mixes functions of different angular momenta making it difficult to assess the importance of individual s, p, d and f functions in simulating the rate for molecules. As an alternative, a hierarchy of diffuse basis sets was constructed starting with a small set and adding one or two functions at a time. These basis sets were evaluated for their ability to reproduce the rate and the shape of the angular dependence of strong field ionization. When combined with the aug-cc-pVTZ molecular basis set and an absorbing potential starting at 3.5 times the van der Waals radius for each atom, the most diffuse s, p, d and f functions need to have exponents of 0.0032, 0.0032, 0.0064 and 0.0064, respectively, or smaller. Strong field ionization from electronegative atoms such as oxygen required additional f functions with tight exponents of 0.0512 and 0.1024. Diffuse basis sets that perform well for the angular dependence of the ionization rate with a static field are equally effective for strong field ionization with a linearly polarized 7 cycle 800 nm pulse. 

While it is widely appreciated that disorder is intricately related to observed sample-to-sample variation in property values, outside of very specialized cases, analysis is often qualitative in nature. One well-understood quantitative approach is based on the 1930s work of Bragg and Williams, who established an order parameter S, which ranges from unity in the case of a perfectly ordered structure to zero in the case of a completely randomized lattice. Here, we demonstrate that this order parameter is directly related to charge carrier mobility in undoped GaN. Extrapolating experimental points yields a value of 1640 cm2/Vs for the maximum room temperature mobility in stoichiometric material, with higher values potentially accessible for Ga-rich material. Additionally, we present a model for observed trends in carrier concentration based on the occurrence of distinct structural motifs, which underpin S. The result is an alternative perspective for the interplay between lattice structure and charge carriers that enables a predictive model for tuning mobility and carrier concentration in undoped material. 

Modeling charge migration resulting from the coherent superposition of cation ground and excited states requires information about the potential energy surfaces of the relevant cation states. Since these states are often of the same electronic symmetry as the ground state of the cation, conventional single reference methods such as coupled cluster cannot be used for the excited states. The EOMCCSD-IP (equation of motion coupled cluster with single and double excitations and ionization) is a convenient and reliable “black-box” method that can be used for the ground and excited states of cations, yielding results of CCSD (coupled cluster with singles and double excitation) quality. Charge migration in haloacetylene cations arises from the superposition of the X and A states of HCCX+ (X = F, Cl, Br and I). The geometries, ionization potentials and vibrational frequencies have been calculated by CCSD/cc-pVTZ for neutral HCCX and the X state of HCCX+ and by EOM CCSD-IP/cc-pVTZ for the X and A states of HCCX+. The results agree very well with each other and with experiment. The very good agreement between CCSD and EOMCCSD-IP for the X states demonstrates that EOMCCSD-IP is a suitable method for calculating the structure and properties of ground and excited states for the HCCX cations. 

ABSTRACT Marine sediments harbour diverse microbial populations, but with increasing depth, these microbes are thought to have low activity due to depleted electron acceptors and lack of new organic matter after burial. However, physiochemical changes in environmental parameters could impact the metabolic activity of microbes in marine sediments. We performed seasonal sampling of shallow sediments to examine changes in population and abundance in relation to physiochemical changes over the year. We used amplicon sequencing, quantitative PCR and geochemistry to assess seasonal abundance of microbial populations at 3 depths (12–14, 38–40 and 48–50 cm) in shallow coastal sediments. 16S rRNA amplicon sequencing showed the sediment microbiome consists of common sediment taxa with minor seasonal variation. However, bacterial gene counts of 16S rRNA genes were highest in summer (2.50 × 10¹² genes/g of sediment) and lowest in spring (1.64 × 10¹¹ genes/g sediment). We observed differences in sediment temperature at depth across seasons (Summer 28°C–25.5°C; Winter 8.7°C–6.3°C) and correlated changes in dissolved organic matter composition that are not typically reported for this environment. We conclude deeper microbial populations in shallow sediments may experience seasonal abundance shifts resulting in a more variable subsurface community than initially presumed in the literature.