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Human glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group is an important target for therapy in neurological disorders and an established tumormarker. However, its physiological functions remain unclear. To better understand general roles, we used the model organism Caenorhabditis elegans to genetically manipulate its three existing orthologous genes and evaluate the impact on worm physiology. The results of gene knockout studies showed that C. elegans GCP2 orthologs affect the pharyngeal physiology, reproduction, and structural integrity of the organism. Promoter-driven GFP expression revealed distinct localization for each of the three gene paralogs, with gcp-2.1 being most abundant in muscles, intestine, and pharyngeal interneurons, gcp-2.2 restricted to the phasmid neurons, and gcp-2.3 located in the excretory cell. The present study provides new insight into the unique phenotypic effects of GCP2 gene knockouts in C. elegans, and the specific tissue localizations. We believe that elucidation of particular roles in a non-mammalian organism can help to explain important questions linked to physiology of this protease group and in extension to human GCP2 involvement in pathophysiological processes. [ABSTRACT FROM AUTHOR]

With the increasing interest in compounds containing heavier elements, the experimental and theoretical community requires computationally efficient approaches capable of simultaneous non-perturbative treatment of relativistic, spin-polarization, and electron correlation effects. The ReSpect program has been designed with this goal in mind and developed to perform relativistic density functional theory (DFT) calculations on molecules and solids at the quasirelativistic two-component (X2C Hamiltonian) and fully relativistic four-component (Dirac–Coulomb Hamiltonian) level of theory, including the effects of spin polarization in open-shell systems at the Kramers-unrestricted self-consistent field level. Through efficient algorithms exploiting time-reversal symmetry, biquaternion algebra, and the locality of atom-centered Gaussian-type orbitals, a significant reduction of the methodological complexity and computational cost has been achieved. This article summarizes the essential theoretical and technical advances made in the program, supplemented by example calculations. ReSpect allows molecules with >100 atoms to be efficiently handled at the four-component level of theory on standard central processing unit-based commodity clusters, at computational costs that rarely exceed a factor of 10 when compared to the non-relativistic realm. In addition to the prediction of band structures in solids, ReSpect offers a growing list of molecular spectroscopic parameters that range from electron paramagnetic resonance parameters (g-tensor, A-tensor, and zero-field splitting), via (p)NMR chemical shifts and nuclear spin–spin couplings, to various linear response properties using either conventional or damped-response time-dependent DFT (TDDFT): excitation energies, frequency-dependent polarizabilities, and natural chiroptical properties (electronic circular dichroism and optical rotatory dispersion). In addition, relativistic real-time TDDFT electron dynamics is another unique feature of the program. Documentation, including user manuals and tutorials, is available at the program's website http://www.respectprogram.org. [ABSTRACT FROM AUTHOR]

We present a detailed theory, implementation, and a benchmark study of a linear damped response time-dependent density functional theory (TDDFT) based on the relativistic four-component (4c) Dirac–Kohn–Sham formalism using the restricted kinetic balance condition for the small-component basis and a noncollinear exchange–correlation kernel. The damped response equations are solved by means of a multifrequency iterative subspace solver utilizing decomposition of the equations according to Hermitian and time-reversal symmetry. This partitioning leads to robust convergence, and the detailed algorithm of the solver for relativistic multicomponent wavefunctions is also presented. The solutions are then used to calculate the linear electric- and magnetic-dipole responses of molecular systems to an electric perturbation, leading to frequency-dependent dipole polarizabilities, electronic absorption, circular dichroism (ECD), and optical rotatory dispersion (ORD) spectra. The methodology has been implemented in the relativistic spectroscopy DFT program ReSpect, and its performance was assessed on a model series of dimethylchalcogeniranes, C4H8X (X = O, S, Se, Te, Po, Lv), and on larger transition metal complexes that had been studied experimentally, [M(phen)3]3+ (M = Fe, Ru, Os). These are the first 4c damped linear response TDDFT calculations of ECD and ORD presented in the literature. [ABSTRACT FROM AUTHOR]

We present an implementation and application of electron dynamics based on real-time time-dependent density functional theory (RT-TDDFT) and relativistic 2-component X2C and 4-component Dirac–Coulomb (4c) Hamiltonians to the calculation of electron circular dichroism and optical rotatory dispersion spectra. In addition, the resolution-of-identity approximation for the Coulomb term (RI-J) is introduced into RT-TDDFT and formulated entirely in terms of complex quaternion algebra. The proposed methodology was assessed on the dimethylchalcogenirane series, C4H8X (X = O, S, Se, Te, Po, Lv), and the spectra obtained by non-relativistic and relativistic methods start to disagree for Se and Te, while dramatic differences are observed for Po and Lv. The X2C approach, even in its simplest one-particle form, reproduces the reference 4c results surprisingly well across the entire series while offering an 8-fold speed-up of the simulations. An overall acceleration of RT-TDDFT by means of X2C and RI-J increases with system size and approaches a factor of almost 25 when compared to the full 4c treatment, without compromising the accuracy of the final spectra. These results suggest that one-particle X2C electron dynamics with RI-J acceleration is an attractive method for the calculation of chiroptical spectra in the valence region. [ABSTRACT FROM AUTHOR]

The solution of the Liouville–von Neumann equation in the relativistic Dirac–Kohn–Sham density matrix formalism is presented and used to calculate X-ray absorption cross sections. Both dynamical relaxation effects and spin–orbit corrections are included, as demonstrated by calculations of the X-ray absorption of SF6 near the sulfur L2,3-edges. We also propose an analysis facilitating the interpretation of spectral transitions from real-time simulations, and a selective perturbation that eliminates nonphysical excitations that are artifacts of the finite basis representation. [ABSTRACT FROM AUTHOR]

The solution of the Liouville-von Neumann equation in the relativistic Dirac-Kohn-Sham density matrix formalism is presented and used to calculate X-ray absorption cross sections. Both dynamical relaxation effects and spin-orbit corrections are included, as demonstrated by calculations of the X-ray absorption of SF6 near the sulfur L2,3-edges. We also propose an analysis facilitating the interpretation of spectral transitions from real-time simulations, and a selective perturbation that eliminates nonphysical excitations that are artifacts of the finite basis representation.