A Constraint-Based Orbital-Optimized Excited State Method (COOX).

In this work, we present a novel method to directly calculate targeted electronic excited states within a self-consistent field calculation based on constrained density functional theory (cDFT). The constraint is constructed from the static occupied-occupied and virtual-virtual parts of the excited state difference density from (simplified) linear-response time-dependent density functional theory calculations (LR-TDDFT). Our new method shows a stable convergence behavior, provides an accurate excited state density adhering to the Aufbau principle, and can be solved within a restricted SCF for singlet excitations to avoid spin contamination.

Simulation of the non-adiabatic dynamics of an enone-Lewis acid complex in an explicit solvent.

Unlocking the full potential of Lewis acid catalysis for photochemical transformations requires a comprehensive understanding of the ultrafast dynamics of substrate-Lewis acid complexes. In a previous article [Peschel , 2021, , 10155], time-resolved spectroscopy supported by static calculations revealed that the Lewis acid remains attached during the relaxation of the model complex cyclohexenone-BF. In contrast to the experimental observation, surface-hopping dynamics in the gas phase predicted ultrafast heterolytic dissociation.

QM/MM Free Energy Calculations of Long-Range Biological Protonation Dynamics by Adaptive and Focused Sampling.

Water-mediated proton transfer reactions are central for catalytic processes in a wide range of biochemical systems, ranging from biological energy conversion to chemical transformations in the metabolism. Yet, the accurate computational treatment of such complex biochemical reactions is highly challenging and requires the application of multiscale methods, in particular hybrid quantum/classical (QM/MM) approaches combined with free energy simulations. Here, we combine the unique exploration power of new advanced sampling methods with density functional theory (DFT)-based QM/MM free energy methods for multiscale simulations of long-range protonation dynamics in biological systems.

POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies.

Heterozygous pathogenic variants in POLR1A, which encodes the largest subunit of RNA Polymerase I, were previously identified as the cause of acrofacial dysostosis, Cincinnati-type. The predominant phenotypes observed in the cohort of 3 individuals were craniofacial anomalies reminiscent of Treacher Collins syndrome. We subsequently identified 17 additional individuals with 12 unique heterozygous variants in POLR1A and observed numerous additional phenotypes including neurodevelopmental abnormalities and structural cardiac defects, in combination with highly prevalent craniofacial anomalies and variable limb defects.

Adenoma weight: the only predictive factor for multiple gland disease in primary hyperparathyroidism.

Background: Predicting a multiple gland disease (MGD) in primary hyperparathyroidism (pHPT) remains challenging. This study aimed to evaluate predictive factors for MGD.

Methods: A retrospective chart review was performed of 1211 patients with histologically confirmed parathyroid adenoma or hyperplasia between 2007-2016.

Novel blended SNRPE-related spliceosomopathy phenotype characterized by microcephaly and congenital atrichia.

Variants in genes encoding core components of the spliceosomes are associated with craniofacial syndromes, collectively called craniofacial spliceosomopathies. SNRPE encodes a core component of pre-mRNA processing U-rich small nuclear ribonuclear proteins (UsnRNPs). Heterozygous variants in SNRPE have been reported in six families with isolated hypotrichosis simplex in addition to one case of isolated non syndromic congenital microcephaly.

Insurance denials and diagnostic rates in a pediatric genomic research cohort.

Purpose: This study aimed to assess the amount and types of clinical genetic testing denied by insurance and the rate of diagnostic and candidate genetic findings identified through research in patients who faced insurance denials.

Methods: Analysis consisted of review of insurance denials in 801 patients enrolled in a pediatric genomic research repository with either no previous genetic testing or previous negative genetic testing result identified through cross-referencing with insurance prior-authorizations in patient medical records. Patients and denials were also categorized by type of insurance coverage.

Accelerating Hybrid Density Functional Theory Molecular Dynamics Simulations by Seminumerical Integration, Resolution-of-the-Identity Approximation, and Graphics Processing Units.

The computationally very demanding evaluation of the 4-center-2-electron (4c2e) integrals and their respective integral derivatives typically represents the major bottleneck within hybrid Kohn-Sham density functional theory molecular dynamics simulations. Building upon our previous works on seminumerical exact-exchange (sn-LinK) [Laqua, H., Thompsons, T.

Predictive Factors for Bilateral Disease in Papillary Microcarcinoma: A Retrospective Cohort Study.

Background: Based on risk stratification, the therapeutic options in papillary microcarcinoma (PTMC) can be active surveillance or surgery. Multifocal tumor occurrence can be decisive in determining the treatment strategy. The objective of this study was to identify risk factors for bilateral tumor occurrence in PTMC to enable individual therapy planning.

An effective sub-quadratic scaling atomic-orbital reformulation of the scaled opposite-spin RI-CC2 ground-state model using Cholesky-decomposed densities and an attenuated Coulomb metric.

An atomic-orbital reformulation of the Laplace-transformed scaled opposite-spin (SOS) coupled cluster singles and doubles (CC2) model within the resolution of the identity (RI) approximation (SOS-RI-CC2) is presented that extends its applicability to molecules with several hundreds of atoms and triple-zeta basis sets. We exploit sparse linear algebra and an attenuated Coulomb metric to decrease the disk space demands and the computational efforts. In this way, an effective sub-quadratic computational scaling is achieved with our ω-SOS-CDD-RI-CC2 model.

Efficient Integral-Direct Methods for Self-Consistent Reduced Density Matrix Functional Theory Calculations on Central and Graphics Processing Units.

Reduced density matrix functional theory (RDMFT), a promising direction in the problem of describing strongly correlated systems, is currently limited by its explicit dependence on natural orbitals and, by extension, the costly need to construct two-electron integrals in the molecular orbital basis. While a resolution-of-the-identity approach can reduce the asymptotic scaling behavior from () to (), this is still prohibitively expensive for large systems, especially considering the usually slow convergence and the resulting high number of orbital optimization steps. In this work, efficient integral-direct methods are derived and benchmarked for various approximate functionals.

Accuracy of Parathyroid Adenoma Localization by Preoperative Ultrasound and Sestamibi in 1089 Patients with Primary Hyperparathyroidism.

Background: Primary hyperparathyroidism (pHPT) is well treatable surgically. Sonography (US) and sestamibi scintigraphy (MIBI) are used routinely, but it is unclear how valuable they are in determining Parathyroid glands' different locations. This study aimed to evaluate the prognostic value of US and MIBI in relation to the different localization of parathyroid adenomas in one of the largest study populations analyzed to date.

Recurrent laryngeal nerve paresis in benign thyroid surgery with and without intraoperative nerve monitoring.

Background: Recurrent laryngeal nerve (RLN) paresis is a rare but serious complication in thyroid surgery. Intermittent intraoperative nerve monitoring (IONM) was thought to prevent paresis of the RLN, but until today data are not conclusive. Our objective was to confirm the hypothesis that IONM can reduce paresis of RLN compared to nerve visualization alone.

Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition.

To analyze the impact of various technical details on the results of quantum mechanical (QM)/molecular mechanical (MM) enzyme simulations, including the QM region size, catechol--methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The results show that key equilibrium and kinetic properties for methyl transfer in COMT exhibit limited variations with respect to the size of the QM region, which ranges from ∼100 to ∼500 atoms in this study. With extensive sampling, local and global structural characteristics of the enzyme are largely conserved across the studied QM regions, while the nature of the transition state (e.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package.

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods.

Accelerating seminumerical Fock-exchange calculations using mixed single- and double-precision arithmethic.

We investigate the applicability of single-precision (fp32) floating point operations within our linear-scaling, seminumerical exchange method sn-LinK [Laqua et al., J. Chem.

Cystic lymph node metastasis of papillary thyroid cancer: clinical facts.

Background: The therapy planning for cystic cervical lesions is dizzying. Although it is mostly a benign disease, it can also be a cystic lymph node metastasis with the origin of papillary thyroid cancer (PTC).

Methods: Included were all patients with histological confirmed PTC, who underwent a thyroid resection from January 2012 to December 2017 (N.

Management of primary and renal hyperparathyroidism: guidelines from the German Association of Endocrine Surgeons (CAEK).

Background And Aims: The purpose of this review is to provide updated recommendations for the surgical management of primary (pHPT) and renal (rHPT) hyperparathyroidism, formulating a new guideline of the German Association of Endocrine Surgeons (CAEK).

Methods: Evidence-based recommendations for the diagnosis and therapy of pHPT and rHPT were assessed by a multidisciplinary panel using PubMed for a comprehensive literature search together with a structured consensus dialogue (S2k guideline of the Association of the German Scientific Medical Societies, AWMF).

Results: During the last 20 years, a variety of new preoperative localization procedures, such as sestamibi-SPECT, 4D-CT, and various PET/CT procedures, were established for pHPT.

Highly Efficient Resolution-of-Identity Density Functional Theory Calculations on Central and Graphics Processing Units.

We present an efficient method to evaluate Coulomb potential matrices using the resolution of identity approximation and semilocal exchange-correlation potentials on central (CPU) and graphics processing units (GPU). The new GPU-based RI-algorithm shows a high performance and ensures the favorable scaling with increasing basis set size as the conventional CPU-based method. Furthermore, our method is based on the J-engine algorithm [White; , Head-Gordon, 1996, 7, 2620], which allows for further optimizations that also provide a significant improvement of the corresponding CPU-based algorithm.

A Fermi smearing variant of the Tamm-Dancoff approximation for nonadiabatic dynamics involving S-S transitions: Validation and application to azobenzene.

The main shortcoming of time-dependent density functional theory (TDDFT) regarding its use for nonadiabatic molecular dynamics (NAMD) is its incapability to describe conical intersections involving the ground state. To overcome this problem, we combine Fermi smearing (FS) DFT with a fractional-occupation variant of the Tamm-Dancoff approximation (TDA) of TDDFT in the generalized gradient approximation. The resulting method (which we denote as FS-TDA) gives access to ground- and excited-state energies, gradients, and nonadiabatic coupling vectors, which are physically correct even in the vicinity of S-S conical intersections.

Preoperative Potassium Iodide Treatment in Patients Undergoing Thyroidectomy for Graves' Disease-Perspective of a European High-Volume Center.

Background: Potassium iodide (KI) treatment affects the vascularity of the thyroid gland and therefore may improve intraoperative visualization of essential structures. However, clear evidence for its usage is lacking, and its implementation in patients suffering from Graves' disease is becoming rare. The objective of this retrospective study was to assess the impact of KI treatment on the intraoperative course and the outcome of patients undergoing thyroidectomy for Graves' diseases.

Combining Graphics Processing Units, Simplified Time-Dependent Density Functional Theory, and Finite-Difference Couplings to Accelerate Nonadiabatic Molecular Dynamics.

Starting from our recently published implementation of nonadiabatic molecular dynamics (NAMD) on graphics processing units (GPUs), we explore further approaches to accelerate NAMD calculations at the time-dependent density functional theory (TDDFT) level of theory. We employ (1) the simplified TDDFT schemes of Grimme et al. and (2) the Hammes-Schiffer-Tully approach to obtain nonadiabatic couplings from finite-difference calculations.

Highly Efficient, Linear-Scaling Seminumerical Exact-Exchange Method for Graphic Processing Units.

We present a highly efficient and asymptotically linear-scaling graphic processing unit accelerated seminumerical exact-exchange method (sn-LinK). We go beyond our previous central processing unit-based method (Laqua, H.; Kussmann, J.