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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. To understand the pathogenesis of this pleiotropy, we modeled an allelic series of POLR1A variants in vitro and in vivo. In vitro assessments demonstrate variable effects of individual pathogenic variants on ribosomal RNA synthesis and nucleolar morphology, which supports the possibility of variant-specific phenotypic effects in affected individuals. To further explore variant-specific effects in vivo, we used CRISPR-Cas9 gene editing to recapitulate two human variants in mice. Additionally, spatiotemporal requirements for Polr1a in developmental lineages contributing to congenital anomalies in affected individuals were examined via conditional mutagenesis in neural crest cells (face and heart), the second heart field (cardiac outflow tract and right ventricle), and forebrain precursors in mice. Consistent with its ubiquitous role in the essential function of ribosome biogenesis, we observed that loss of Polr1a in any of these lineages causes cell-autonomous apoptosis resulting in embryonic malformations. Altogether, our work greatly expands the phenotype of human POLR1A-related disorders and demonstrates variant-specific effects that provide insights into the underlying pathogenesis of ribosomopathies., Competing Interests: Declaration of interests A.B., M.J.G.S., K. McWalters, R.P., and R.S. are employees of GeneDx., (Copyright © 2023 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

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. Diagnostic findings and candidate genetic findings in these groups were determined through review of our internal variant database and patient charts., Results: Of the 801 patients analyzed, 147 had insurance prior-authorization denials on record (18.3%). Exome sequencing and microarray were the most frequently denied genetic tests. Private insurance was significantly more likely to deny testing than public insurance (odds ratio = 2.03 [95% CI = 1.38-2.99] P = .0003). Of the 147 patients with insurance denials, 53.7% had at least 1 diagnostic or candidate finding and 10.9% specifically had a clinically diagnostic finding. Fifty percent of patients with clinically diagnostic results had immediate medical management changes (5.4% of all patients experiencing denials)., Conclusion: Many patients face a major barrier to genetic testing in the form of lack of insurance coverage. A number of these patients have clinically diagnostic findings with medical management implications that would not have been identified without access to research testing. These findings support re-evaluation of insurance carriers' coverage policies., Competing Interests: Conflict of Interest The authors declare no conflicts of interest., (Copyright © 2023 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.)

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. Localization diagnostics, laboratory parameters, and the weight of the resected parathyroid glands were evaluated concerning their predictive value of a multiple-gland disease., Results: A number of 1111 (91.7%) had a single-gland disease (SGD), and 100 (8.3%) a multiple-gland disease (MGD). US and MIBI scans were comparable for either negative or positive adenoma localization and suspected MGD. While the PTH level was similar, the calcium level was higher in SGD (2.8 mmol/L versus 2.76 mmol/L, P=0.034). MGD had a significantly lower gland weight (0.78 g versus 0.31 g; P<0.001). A gland weight of 0.418 grams was a predictive factor for MGD with a sensitivity of 72% and a specificity of 66%., Conclusions: Only the weight of the resected parathyroid adenoma was meaningful in predicting MGD. A cut-off value of 0.418 g can differentiate SGD from MGD.

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. Therefore, we examined one of the largest cohorts ever evaluated of a tertiary referral center for endocrine surgery undergoing thyroid surgery for benign thyroid disease., Methods: Overall, 2097 patients who underwent thyroid surgery for benign thyroid disease in 2016 and 2017 were evaluated. RLN was identified by IONM or visualization only. Preoperative and postoperative laryngoscopic examination was used to evaluate RLN paresis. Patients' characteristics and perioperative data were extracted retrospectively., Results: Overall, 1963 patients (2720 nerves at risk [NAR]) were included in this study: 378 surgeries with IONM (560 NAR) and 1585 without IONM (2160 NAR). Transient and permanent RLN pareses were found in 13 (3.4%; NAR=2.3%) and one (0.3%; NAR=0.2%) nerve treated with IONM vs. 37 (2.3%; NAR=1.7%) and five (0.3%; NAR=0.2%) nerves without IONM (P=0.507; NAR P=0.654), respectively., Conclusions: Using intermittent IONM, our retrospective study could not demonstrate a significant decrease of RLN pareses in patients undergoing thyroid surgery for benign thyroid disease. This is probably explained by the very low overall number of RLN pareses in our department. Nevertheless, because of patients' safety to avoid any bilateral RLN pareses, we recommend IONM in bilateral resections.

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. H., Kussmann, J., Ochsenfeld, C., J. Chem. Theory Comput. 1465] and resolution-of-the-identity Coulomb (RI-J) [Kussmann, J., Laqua, H., Ochsenfeld, C., 2020, 16, 1465] and resolution-of-the-identity Coulomb (RI-J) [Kussmann, J., Laqua, H., Ochsenfeld, C., J. Chem. Theory Comput. 2021, 17, 1512], the expensive 4c2e integral evaluation can be avoided entirely, resulting in a highly efficient electronic structure theory method, allowing for fast ab initio molecular dynamics (AIMD) simulations even with large basis sets. Moreover, we propose to combine the final self-consistent field (SCF) step with the subsequent nuclear forces evaluation, providing the forces at virtually no additional cost after a converged SCF calculation, reducing the total runtime of an AIMD simulation by about another 25%. In addition, multiple independent MD trajectories can be computed concurrently on a single node, leading to a greatly increased utilization of the available hardware─especially when combined with graphics processing unit acceleration─improving the overall throughput by up to another 5 times in this way. With all of those optimizations combined, our proposed method provides nearly 3 orders of magnitude faster execution times than traditional 4c2e integral-based methods. To demonstrate the practical utility of the approach, quantum-mechanical/molecular-mechanical dynamics simulations on double-stranded DNA were performed, investigating the relative hydrogen bond strength between adenine-thymine and guanine-cytosine base pairs. In addition, this illustrative application also contains a general accuracy assessment of the introduced approximations (integration grids, resolution-of-the-identity) within AIMD simulations, serving as a protocol on how to apply these new methods to practical problems.

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., Methods: 1089 patients with pHPT who had treatment in one tertiary referral center between 2007 and 2016 were analyzed. Preoperative US and MIBI reports were compared with the parathyroid adenoma's intraoperative localization. All parathyroid glands were confirmed by histological diagnosis., Results: No gland was detectable in 22.5% and 27.7% of all patients, by US or by MIBI, respectively. In relation to the different adenoma locations, the sensitivity of US ranged from 21.3% (upper right) to 68.9% (lower left) and of MIBI ranged from 23.5% (upper right) to 72% (lower left). The specificity for US ranged from 85% (lower right) to 99.2% (upper right) and for MIBI ranged from 86.1% (lower right) to 99.1% (upper right. Positive predictive values for all gland sites were 54% and 59% for MIBI and US, respectively. The value increased for side-only prediction to 73% and 78%, respectively. Neither the parathyroid hormone level nor the calcium value level influenced the sensitivity or specificity of the two test methods., Conclusions: The validity of preoperative US and MIBI depends crucially on the specific localization of adenomas. This should be considered when planning the extent of parathyroid surgery., (© 2022. The Author(s) under exclusive licence to Société Internationale de Chirurgie.)

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. Methods: A total of 545 PTMC patients who underwent thyroidectomy from 2008 to 2020 were retrieved. Univariate and multivariate analyses were performed to evaluate risk factors for bilateral PTMC. Results: 25.1% (n = 137) of all patients had multifocal PTMC, and 13.2% (n = 72) bilateral PTMC, respectively. In contrast to the maximum tumor size, the total tumor size significantly influenced a bilateral tumor manifestation (median total tumor size 5 mm versus 8.5 mm for bilateral PTMC, p < 0.001). A cut-off level for the total tumor size of >10 mm resulted in a sensitivity and specificity of 29.2% and 94.7%, respectively, in predicting a bilateral tumor manifestation, AUC 0.680 (95% CI, 0.611−0.748, p < 0.001). A cut-off of >4 tumors showed a sensitivity of 99.4% and a specificity of 97.5%, AUC 0.897 (95% CI, 0.870−0.924, p < 0.001) in predicting bilaterality. Conclusion: We could demonstrate for the first time that a total tumor size of >10 mm and more than four tumors significantly increased the risk of bilateral PTMC tumor involvement. These findings enable a risk-adjusted patient treatment.

Purpose: This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program., Methods: Extensive analyses of 960 families with suspected genetic disorders included short-read exome sequencing and short-read genome sequencing (srGS); PacBio HiFi long-read genome sequencing (HiFi-GS); variant calling for single nucleotide variants (SNV), structural variant (SV), and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants, and pedigrees were stored in PhenoTips database, with data sharing through controlled access the database of Genotypes and Phenotypes., Results: Diagnostic rates ranged from 11% in patients with prior negative genetic testing to 34.5% in naive patients. Incorporating SVs from genome sequencing added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs compared with srGS. Variants and genes of unknown significance remain the most common finding (58% of nondiagnostic cases)., Conclusion: Computational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated using HiFi-GS sequencing. Importantly, community research is supported by sharing real-time data to accelerate gene validation and by providing HiFi variant (SNV/SV) resources from >1000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses., Competing Interests: Conflict of Interest P. Baybayan, S. Chakraborty, J. Korlach, C. Lambert, W.J. Rowell, and A.M. Wenger are employees and shareholders of Pacific Biosciences. P. Buczkowicz and O. Buske are employees of PhenoTips. N. Miller became an employee of Bionano Genomics after contribution to the work described in this manuscript. All other authors declare no conflicts of interest., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

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- O -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.g., secondary kinetic isotope effect) and reaction exergonicity are largely maintained. Deviations in the free energy profile with different QM region sizes are similar in magnitude to those observed with changes in other simulation protocols, such as different initial enzyme conformations and boundary conditions. Electronic structural properties, such as the covariance matrix of residual charge fluctuations, appear to exhibit rather long-range correlations, especially when the peptide backbone is included in the QM region; this observation holds when a range-separated DFT approach is used as the QM region, suggesting that delocalization error is unlikely the origin. Overall, the analyses suggest that multiple simulation details determine the results of QM/MM enzyme simulations with comparable contributions.

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.=680). Analyzed were demographic data including family history and radiation exposure, preoperative workup including thyroid ultrasound and laboratory test of the TSH value complimented by fine-needle aspiration in case of suspected malignancy, and clinicopathologic features. This study aimed to specify preoperative findings and patients' clinical presentation with cystic lymph node metastasis of PTC., Results: In 0.7% (5/680) of all patients with PTC a cystic cervical lesion was histologically confirmed as cystic lymph node metastasis. Preoperatively, only two of these patients were suspected of lymph node metastasis with unknown origin. In three patients, the resected cystic lymph node metastases were the only lymphatic metastasis. Interestingly 80% (4/5) of the patients suffered from papillary microcarcinoma (MPTC)., Conclusions: Cervical cystic lesions may be challenging in diagnostics and therapy. Although the recommended thyroid ultrasound may detect no pathological findings, a papillary microcarcinoma can be the primary tumor.

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. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

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. Theory Comput. 16, 1456 (2020)] and find that the vast majority of the three-center-one-electron (3c1e) integrals can be computed with reduced numerical precision with virtually no loss in overall accuracy. This leads to a near doubling in performance on central processing units (CPUs) compared to pure fp64 evaluation. Since the cost of evaluating the 3c1e integrals is less significant on graphic processing units (GPUs) compared to CPU, the performance gains from accelerating 3c1e integrals alone is less impressive on GPUs. Therefore, we also investigate the possibility of employing only fp32 operations to evaluate the exchange matrix within the self-consistent-field (SCF) followed by an accurate one-shot evaluation of the exchange energy using mixed fp32/fp64 precision. This still provides very accurate (1.8 µEh maximal error) results while providing a sevenfold speedup on a typical "gaming" GPU (GTX 1080Ti). We also propose the use of incremental exchange-builds to further reduce these errors. The proposed SCF scheme (i-sn-LinK) requires only one mixed-precision exchange matrix calculation, while all other exchange-matrix builds are performed with only fp32 operations. Compared to pure fp64 evaluation, this leads to 4-7× speedups for the whole SCF procedure without any significant deterioration of the results or the convergence behavior.

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, J. Chem. Phys. 1996, 7, 2620], which allows for further optimizations that also provide a significant improvement of the corresponding CPU-based algorithm. Due to the increased performance for the Coulomb evaluation, the calculation of the exchange-correlation potential of density functional theory on CPUs quickly becomes a bottleneck to the overall computational time. Hence, we also present a GPU-based algorithm to evaluate the exchange-correlation terms, which results in an overall high-performance method for density functional calculations. The algorithms to evaluate the potential and nuclear derivative terms are discussed, and their performance on CPUs and GPUs is demonstrated for illustrative calculations.

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., Methods: The study included 442 patients: 125 patients (28.3%) who received a preoperative treatment with KI ("Group KI") and 317 patients (71.7%) without a KI therapy ("Group No-KI"). Indication for KI treatment was a thyroid bruit (82.5%), as well as hyperthyroidism refractive to medical treatment with antithyroid drugs (17.4%)., Results: All patients underwent total thyroidectomy. Permanent vocal cord paresis and permanent hypoparathyroidism were similar in both groups. KI treatment was associated with a significantly longer operative time (142 vs. 128 min, p < 0.001) and a significant higher weight of the thyroid gland. KI treatment did not impact duration of hospital stay or occurrence of secondary hemorrhage., Conclusions: The complication rate of this study population with clinically severe GD was very low-which may be caused by pre-treatment of patients. The complementary option of a potassium iodide treatment before surgery remains a possibility and should be implemented individually.

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 1 -S 0 conical intersections. This is shown for azobenzene, a widely used photoswitch, via single point calculations and NAMD simulations of its cis-trans photoisomerization. We conclude that FS-TDA may be used as an efficient alternative to investigate these processes.

Starting from our recently published implementation of nonadiabatic molecular dynamics (NAMD) on graphics processing units (GPUs), we explore further approaches to accelerate ab initio 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. The resulting scheme delivers an accurate physical picture while virtually eliminating the two computationally most demanding steps of the algorithm. Combined with our GPU-based integral routines for SCF, TDDFT, and TDDFT derivative calculations, NAMD simulations of systems of a few hundreds of atoms at a reasonable time scale become accessible on a single compute node. To demonstrate this and to present a first, illustrative example, we perform TDDFT/MM-NAMD simulations of the rhodopsin protein.

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.; Ochsenfeld, C. J. Chem. Theory Comput . 2018, 14, 3451-3458) by employing our recently developed integral bounds (Thompson, T. H.; Ochsenfeld, C. J. Chem. Phys . 2019, 150, 044101) and high-accuracy numerical integration grid (Laqua, H.; Kussmann, J.; Ochsenfeld, C. J. Chem. Phys . 2018, 149, 204111). The accuracy is assessed for several established test sets, providing errors significantly below 1m E h for the smallest grid. Moreover, a comprehensive performance analysis for large molecules between 62 and 1347 atoms is provided, revealing the outstanding performance of our method, in particular, for large basis sets such as the polarized quadruple-zeta level with diffuse functions.

Nonadiabatic molecular dynamics (NAMD) simulations of molecular systems require the efficient evaluation of excited-state properties, such as energies, gradients, and nonadiabatic coupling vectors. Here, we investigate the use of graphics processing units (GPUs) in addition to central processing units (CPUs) to efficiently calculate these properties at the time-dependent density functional theory (TDDFT) level of theory. Our implementation in the FermiONs++ program package uses the J-engine and a preselective screening procedure for the calculation of Coulomb and exchange kernels, respectively. We observe good speed-ups for small and large molecular systems (comparable to those observed in ground-state calculations) and reduced (down to sublinear) scaling behavior with respect to the system size (depending on the spatial locality of the investigated excitation). As a first illustrative application, we present efficient NAMD simulations of a series of newly designed light-driven rotary molecular motors and compare their S 1 lifetimes. Although all four rotors show different S 1 excitation energies, their ability to rotate upon excitation is conserved, making the series an interesting starting point for rotary molecular motors with tunable excitation energies.

We explore and show the usefulness of the density of states function for computing vibrational free energies and free energy differences between small systems. Therefore, we compare this density of states integration method (DSI) to more established schemes such as Bennett's Acceptance Ratio method (BAR), the Normal Mode Analysis (NMA), and the Quasiharmonic Analysis (QHA). The strengths and shortcomings of all methods are highlighted with three numerical examples. Furthermore, the free energy of the ionization of ammonia and the mutation from serine to cysteine are computed using extensive ab initio molecular dynamics simulations. We conclude that DSI improves upon the other frequency-based methods (NMA and QHA) regarding the treatment of anharmonicity and yielding results comparable to BAR in all cases without the need for alchemical transformations. Low-frequency modes lead to larger errors indicating that long simulation times might be required for larger systems. In addition, we introduce the use of DSI for the localization of the vibrational free energy to specific atoms or residues, leading to insights into the underlying process, a unique feature that is only offered by this method.

The free energy is one of the central quantities in material and natural sciences. While being well-established, e.g., in drug design or catalyst optimization, computational methods lack a straightforward way to gain deeper insights into the calculated free energy, and thus the underlying chemical or physical processes. Here, we present a generally applicable, spectrum-based ansatz that tackles this shortcoming by identifying contributions from specific atoms or groups to the vibrational free energy. We illustrate this in studies of the bromodomain-inhibitor binding and the anomeric effect in glucose providing quantitative evidence in line with chemical intuition in both cases. For the latter example we also report an experimental infrared spectrum and find excellent agreement with our simulated spectra.

We present a modification to Becke's molecular partitioning scheme [A. D. Becke, J. Chem. Phys. 88 , 2547 (1988)] that provides substantially better accuracy for weakly bound complexes and allows for a faster and linear scaling grid generation without introducing a cutoff error. We present the accuracy of our new partitioning scheme for atomization energies of small molecules and for interaction energies of van der Waals complexes. Furthermore, the efficiency and scaling behavior of the grid generation are demonstrated for large molecular systems with up to 1707 atoms.

Thyroid resections represent one of the most common operations with 76,140 interventions in the year 2016 in Germany (source Destatis). These are predominantly benign thyroid gland diseases. Recommendations for the operative treatment of benign thyroid diseases were last published by the CAEK in 2010 as S2k guidelines (Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften e.V. [AWMF] 003/002) against the background of increasingly more radical resection procedures. Hemithyroidectomy and thyroidectomy are routinely performed for benign thyroid disease in practice. The operation-specific risks show a clear increase with the extent of the resection. Therefore, weighing-up of the risk-indications ratio between unilateral lobectomy or thyroidectomy necessitates an independent evaluation of the indications for both sides. This principle in particular has been used to update the guidelines. In addition, the previously published recommendations of the CAEK for correct execution and consequences of intraoperative neuromonitoring were included into the guidelines, which in particular serve the aim to avoid bilateral recurrent laryngeal nerve paralysis. Moreover, the recommendations for the treatment of postoperative complications, such as hypoparathyroidism and postoperative infections were revised. The updated guidelines therefore represent the current state of the science as well as the resulting surgical practice.

Local hybrid functionals, that is, functionals with local dependence on the exact exchange energy density, generalize the popular class of global hybrid functionals and extend the applicability of density functional theory to electronic structures that require an accurate description of static correlation. However, the higher computational cost compared to conventional Kohn-Sham density functional theory restrained their widespread application. Here, we present a low-prefactor, linear-scaling method to evaluate the local hybrid exchange-correlation potential as well as the corresponding nuclear forces by employing a seminumerical integration scheme. In the seminumerical scheme, one integration in the electron repulsion integrals is carried out analytically and the other one is carried out numerically, employing an integration grid. A high computational efficiency is achieved by combining the preLinK method [ J. Kussmann and C. Ochsenfeld, J. Chem. Phys. 2013 138, 134114 ] with explicit screening of integrals for batches of grid points to minimize the screening overhead. This new method, denoted as preLinX, provides an 8-fold performance increase for a DNA fragment containing four base pairs as compared to existing S- and P-junction-based methods. In this way, our method allows for the evaluation of local hybrid functionals at a cost similar to that of global hybrid functionals. The linear-scaling behavior, efficiency, accuracy, and multinode parallelization of the presented method is demonstrated for large systems containing more than 1000 atoms.

The correct description of multi-reference electronic ground states within Kohn-Sham density functional theory (DFT) requires an ensemble-state representation, employing fractionally occupied orbitals. However, the use of fractional orbital occupation leads to non-normalized exact-exchange holes, resulting in large fractional-spin errors for conventional approximative density functionals. In this communication, we present a simple approach to directly include the exact-exchange-hole normalization into DFT. Compared to conventional functionals, our model strongly improves the description for multi-reference systems, while preserving the accuracy in the single-reference case. We analyze the performance of our proposed method at the example of spin-averaged atoms and spin-restricted bond dissociation energy surfaces.

An efficient scheme for the calculation of Born-Oppenheimer molecular dynamics (BOMD) simulations is introduced. It combines the corrected small basis set Hartree-Fock (HF-3c) method by Sure and Grimme [J. Comput. Chem. 2013, 43, 1672], extended Lagrangian BOMD (XL-BOMD) by Niklasson et al. [J. Chem. Phys. 2009, 130, 214109], and the calculation of the two electron integrals on graphics processing units (GPUs) [J. Chem. Phys. 2013, 138, 134114; J. Chem. Theory Comput. 2015, 11, 918]. To explore the parallel performance of our strong scaling implementation of the method, we present timings and extract, as its validation and first illustrative application, high-quality vibrational spectra from simulated trajectories of β-carotene, paclitaxel, and liquid water (up to 500 atoms). We conclude that the presented BOMD scheme may be used as a cost-efficient and reliable tool for computing vibrational spectra and thermodynamics of large molecular systems including explicit solvent molecules containing 500 atoms and more. Simulating 50 ps of maitotoxin (nearly 500 atoms) employing time steps of 0.5 fs requires ∼3 weeks on 12 CPUs (Intel Xeon E5 2620 v3) with 24 GPUs (AMD FirePro 3D W8100).

Histological findings often display an association between papillary thyroid carcinomas (PTC) and autoimmune thyroiditis (AIT) and so differ significantly from follicular thyroid carcinomas (FTC). The aim of this interdisciplinary, retrospective study was to evaluate the association of AIT in patients with PTC and FTC and a control group of benign nodular goiters. One hundred thyroidectomies with histologically confirmed differentiated thyroid carcinomas, 67 with PTC and 33 with FTC, were submitted for examination. The two control groups consisted of 60 patients with euthyroid nodular goiter, displaying no signs for malignancy (no surgery) and 100 patients (second control group) with surgery of a benign nodular goiter. Controls were collected to obtain data about the incidence of significantly increased TPOAbs in the first group and of lymphocytic infiltrates (LI) in the second group. High TPOAbs were found in 35% (23/67) of patients with PTC. LI were detected by histology in 48% (32/67) of PTC. Ten patients (10/32) of this group showed the clinical and histological manifestation of a classic AIT with diffuse dense LI as well as diffuse hypoechogeneity in ultrasonography. In 7/32 cases, the histological report described focal dense LI (fAIT) and in 15/32 cases scant scattered LI. AIT and fAIT, together 25% of all PTC (17/67), showed germinal centers and can therefore be characterized as chronic autoimmune thyroiditis. In this group, high TPOAb could be detected in 94% (16/17). Scan scattered LI without germinal centers (15/32) do not represent a fAIT, although TPOAb are high in 47% (7/15). The younger age group (<45 years) showed significantly more often high TPOAbs (p<0.023) in comparison with the age-group older than 60 years. In contrast to PTC, only 4/33 (12%) patients with FTC had high TPOAb levels. We conclude that in contrast to benign euthyroid goiters and to FTC, different degrees of LI are often associated with high TPOAb levels and seem to be significantly increased in PTC, particularly prominent in younger age. There is a high coincidence between LI and high TPOAb levels. In the presence of hypoechoic thyroid nodule, signs of thyroid autoimmunity such as the presence of high TPOAbs, lymphocytic infiltration in cytology, and/or characteristic ultrasonic features, are arguments that might favor the decision for surgery if a cytologically indeterminate thyroid nodule is found and focal autonomy is excluded by szintiscan., Competing Interests: Conflict of Interest: The authors declare that they have no conflict of interest., (© Georg Thieme Verlag KG Stuttgart · New York.)

We present a parallel integral algorithm for two-electron contributions occurring in Hartree-Fock and hybrid density functional theory that allows for a strong scaling parallelization on inhomogeneous compute clusters. With a particular focus on graphic processing units, we show that our approach allows an efficient use of CPUs and graphics processing units (GPUs) simultaneously, although the different architectures demand conflictive strategies in order to ensure efficient program execution. Furthermore, we present a general strategy to use large basis sets like quadruple-ζ split valence on GPUs and investigate the balance between CPUs and GPUs depending on l-quantum numbers of the corresponding basis functions. Finally, we present first illustrative calculations using a hybrid CPU/GPU environment and demonstrate the strong-scaling performance of our parallelization strategy also for pure CPU-based calculations.

We present an extension of our graphics processing units (GPU)-accelerated quantum chemistry package to employ OpenCL compute kernels, which can be executed on a wide range of computing devices like CPUs, Intel Xeon Phi, and AMD GPUs. Here, we focus on the use of AMD GPUs and discuss differences as compared to CUDA-based calculations on NVIDIA GPUs. First illustrative timings are presented for hybrid density functional theory calculations using serial as well as parallel compute environments. The results show that AMD GPUs are as fast or faster than comparable NVIDIA GPUs and provide a viable alternative for quantum chemical applications.

Nuclear magnetic shieldings have been calculated at the density functional theory (DFT) level for stacks of benzene, hexadehydro[12]annulene, dodecadehydro[18]annulene, and hexabenzocoronene. The magnetic shieldings due to the ring currents in the adjacent molecules have been estimated by calculating nucleus independent molecular shieldings for the monomer in the atomic positions of neighbor molecules. The calculations show that the independent shielding model works reasonably well for the 1 H NMR shieldings of benzene and hexadehydro[12]annulene, whereas for the larger molecules and for the 13 C NMR shieldings the interaction between the molecules leads to shielding effects that are at least of the same size as the ring current contributions from the adjacent molecules. A better agreement is obtained when the nearest neighbors are also considered at full quantum mechanical (QM) level. The calculations suggest that the nearest solvent molecules must be included in the quantum mechanical system, at least when estimating solvent shifts at the molecular mechanics (MM) level. Current density calculations show that the stacking does not significantly affect the ring current strengths of the individual molecules, whereas the shape of the ring current for a single molecule differs from that of the stacked molecules.

We present screening schemes that allow for efficient, linear-scaling short-range exchange calculations employing Gaussian basis sets for both CPU and GPU architectures. They are based on the LinK [C. Ochsenfeld et al., J. Chem. Phys. 109, 1663 (1998)] and PreLinK [J. Kussmann and C. Ochsenfeld, J. Chem. Phys. 138, 134114 (2013)] methods, but account for the decay introduced by the attenuated Coulomb operator in short-range hybrid density functionals. Furthermore, we discuss the implementation of short-range electron repulsion integrals on GPUs. The introduction of our screening methods allows for speedups of up to a factor 7.8 as compared to the underlying linear-scaling algorithm, while retaining full numerical control over the accuracy. With the increasing number of short-range hybrid functionals, our new schemes will allow for significant computational savings on CPU and GPU architectures.

We present a (sub)linear-scaling algorithm to determine indirect nuclear spin-spin coupling constants at the Hartree-Fock and Kohn-Sham density functional levels of theory. Employing efficient integral algorithms and sparse algebra routines, an overall (sub)linear scaling behavior can be obtained for systems with a non-vanishing HOMO-LUMO gap. Calculations on systems with over 1000 atoms and 20 000 basis functions illustrate the performance and accuracy of our reference implementation. Specifically, we demonstrate that linear algebra dominates the runtime of conventional algorithms for 10 000 basis functions and above. Attainable speedups of our method exceed 6 × in total runtime and 10 × in the linear algebra steps for the tested systems. Furthermore, a convergence study of spin-spin couplings of an aminopyrazole peptide upon inclusion of the water environment is presented: using the new method it is shown that large solvent spheres are necessary to converge spin-spin coupling values.

We present an extension of our recently presented PreLinK scheme (J. Chem. Phys. 2013, 138, 134114) for the exact exchange contribution to nuclear forces. The significant contributions to the exchange gradient are determined by preselection based on accurate shell-pair contributions to the SCF exchange energy prior to the calculation. Therefore, our method is highly suitable for massively parallel electronic structure calculations because of an efficient load balancing of the significant contributions only and an unhampered control flow. The efficiency of our method is shown for several illustrative calculations on single GPU servers, as well as for hybrid MPI/CUDA parallel calculations with the largest system comprising 3369 atoms and 26952 basis functions.

An analytical method to calculate the molecular vibrational Hessian matrix at the self-consistent field level is presented. By analysis of the multipole expansions of the relevant derivatives of Coulomb-type two-electron integral contractions, we show that the effect of the perturbation on the electronic structure due to the displacement of nuclei decays at least as r(-2) instead of r(-1). The perturbation is asymptotically local, and the computation of the Hessian matrix can, in principle, be performed with O(N) complexity. Our implementation exhibits linear scaling in all time-determining steps, with some rapid but quadratic-complexity steps remaining. Sample calculations illustrate linear or near-linear scaling in the construction of the complete nuclear Hessian matrix for sparse systems. For more demanding systems, scaling is still considerably sub-quadratic to quadratic, depending on the density of the underlying electronic structure.

We present a simple but accurate preselection method based on Schwarz integral estimates to determine the significant elements of the exact exchange matrix before its evaluation, thus providing an asymptotical linear-scaling behavior for non-metallic systems. Our screening procedure proves to be highly suitable for exchange matrix calculations on massively parallel computing architectures, such as graphical processing units, for which we present a first linear-scaling exchange matrix evaluation algorithm.

Introduction: Over the past years, the incidence of thyroid cancer has surged not only in Germany but also in other countries of the Western hemisphere. This surge was first and foremost due to an increase of prognostically favorable ("low risk") papillary thyroid microcarcinomas, for which limited surgical procedures are often sufficient without loss of oncological benefit. These developments called for an update of the previous practice guideline to detail the surgical treatment options that are available for the various disease entities and tumor stages., Methods: The present German Association of Endocrine Surgeons practice guideline was developed on the basis of clinical evidence considering current national and international treatment recommendations through a formal expert consensus process in collaboration with the German Societies of General and Visceral Surgery, Endocrinology, Nuclear Medicine, Pathology, Radiooncology, Oncological Hematology, and a German thyroid cancer patient support organization., Results: The practice guideline for the surgical management of malignant thyroid tumors includes recommendations regarding preoperative workup; classification of locoregional nodes and terminology of surgical procedures; frequency, clinical, and histopathological features of occult and clinically apparent papillary, follicular, poorly differentiated, undifferentiated, and sporadic and hereditary medullary thyroid cancers, thyroid lymphoma and thyroid metastases from primaries outside the thyroid gland; extent of thyroidectomy; extent of lymph node dissection; aerodigestive tract resection; postoperative follow-up and surgery for recurrence and distant metastases., Conclusion: These evidence-based recommendations for surgical therapy reflect various "treatment corridors" that are best discussed within multidisciplinary teams and the patient considering tumor type, stage, progression, and inherent surgical risk.

Efficient estimates for the preselection of two-electron integrals in atomic-orbital based Møller-Plesset perturbation theory (AO-MP2) theory are presented, which allow for evaluating the AO-MP2 energy with computational effort that scales linear with molecular size for systems with a significant HOMO-LUMO gap. The estimates are based on our recently introduced QQR approach [S. A. Maurer, D. S. Lambrecht, D. Flaig, and C. Ochsenfeld, J. Chem. Phys. 136, 144107 (2012)], which exploits the asympotic decay of the integral values with increasing bra-ket separation as deduced from the multipole expansion and combines this decay behavior with the common Schwarz bound to a tight and simple estimate. We demonstrate on a diverse selection of benchmark systems that our AO-MP2 method in combination with the QQR-type estimates produces reliable results for systems with both localized and delocalized electronic structure, while in the latter case the screening essentially reverts to the common Schwarz screening. For systems with localized electronic structure, our AO-MP2 method shows an early onset of linear scaling as demonstrated on DNA systems. The favorable scaling behavior allows to compute systems with more than 1000 atoms and 10,000 basis functions on a single core that are clearly not accessible with conventional MP2 methods. Furthermore, our AO-MP2 method is particularly suited for parallelization and we present benchmark calculations on a protein-DNA repair complex comprising 2025 atoms and 20,371 basis functions.

Background: Chromosome 15q24 microdeletion syndrome is a rare genomic disorder characterised by intellectual disability, growth retardation, unusual facial morphology and other anomalies. To date, 20 patients have been reported; 18 have had detailed breakpoint analysis., Aim: To further delineate the features of the 15q24 microdeletion syndrome, the clinical and molecular characterisation of fifteen patients with deletions in the 15q24 region was performed, nearly doubling the number of reported patients., Methods: Breakpoints were characterised using a custom, high-density array comparative hybridisation platform, and detailed phenotype information was collected for each patient., Results: Nine distinct deletions with different breakpoints ranging in size from 266 kb to 3.75 Mb were identified. The majority of breakpoints lie within segmental duplication (SD) blocks. Low sequence identity and large intervals of unique sequence between SD blocks likely contribute to the rarity of 15q24 deletions, which occur 8-10 times less frequently than 1q21 or 15q13 microdeletions in our series. Two small, atypical deletions were identified within the region that help delineate the critical region for the core phenotype in the 15q24 microdeletion syndrome., Conclusion: The molecular characterisation of these patients suggests that the core cognitive features of the 15q24 microdeletion syndrome, including developmental delays and severe speech problems, are largely due to deletion of genes in a 1.1-Mb critical region. However, genes just distal to the critical region also play an important role in cognition and in the development of characteristic facial features associated with 15q24 deletions. Clearly, deletions in the 15q24 region are variable in size and extent. Knowledge of the breakpoints and size of deletion combined with the natural history and medical problems of our patients provide insights that will inform management guidelines. Based on common phenotypic features, all patients with 15q24 microdeletions should receive a thorough neurodevelopmental evaluation, physical, occupational and speech therapies, and regular audiologic and ophthalmologic screening.

To understand the genetic heterogeneity underlying developmental delay, we compared copy number variants (CNVs) in 15,767 children with intellectual disability and various congenital defects (cases) to CNVs in 8,329 unaffected adult controls. We estimate that ∼14.2% of disease in these children is caused by CNVs >400 kb. We observed a greater enrichment of CNVs in individuals with craniofacial anomalies and cardiovascular defects compared to those with epilepsy or autism. We identified 59 pathogenic CNVs, including 14 new or previously weakly supported candidates, refined the critical interval for several genomic disorders, such as the 17q21.31 microdeletion syndrome, and identified 940 candidate dosage-sensitive genes. We also developed methods to opportunistically discover small, disruptive CNVs within the large and growing diagnostic array datasets. This evolving CNV morbidity map, combined with exome and genome sequencing, will be critical for deciphering the genetic basis of developmental delay, intellectual disability and autism spectrum disorders.

Introduction: Benign thyroid disorders are among the most common diseases in Germany, affecting around 15 million people and leading to more than 100,000 thyroid surgeries per year. Since the first German guidelines for the surgical treatment of benign goiter were published in 1998, abundant new information has become available, significantly shifting surgical strategy towards more radical interventions. Additionally, minimally invasive techniques have been developed and gained wide usage. These circumstances demanded a revision of the guidelines., Methods: Based on a review of relevant recent guidelines from other groups and additional literature, unpublished data, and clinical experience, the German Association of Endocrine Surgeons formulated new recommendations on the surgical treatment of benign thyroid diseases. These guidelines were developed through a formal expert consensus process and in collaboration with the German societies of Nuclear Medicine, Endocrinology, Pathology, and Phoniatrics & Pedaudiology as well as two patient organizations. Consensus was achieved through several moderated conferences of surgical experts and representatives of the collaborating medical societies and patient organizations., Results: The revised guidelines for the surgical treatment of benign thyroid diseases include recommendations regarding the preoperative assessment necessary to determine when surgery is indicated. Recommendations regarding the extent of resection, surgical techniques, and perioperative management are also given in order to optimize patient outcomes., Conclusions: Evidence-based recommendations for the surgical treatment of benign thyroid diseases have been created to aid the surgeon and to support optimal patient care, based on current knowledge. These recommendations comply with the Association of the Scientific Medical Societies in Germany requirements for S2k guidelines.

An ab initio method for the direct calculation of NMR shieldings for selected nuclei at the Hartree-Fock and density-functional theory level is presented. Our method shows a computational effort scaling only sublinearly with molecular size, as it is motivated by the physical consideration that the chemical shielding is dominated by its local environment. The key feature of our method is to avoid the conventionally performed calculation of all NMR shieldings but instead to solve directly for specific nuclear shieldings. This has important implications not only for the study of large molecules, but also for the simulation of solvent effects and molecular dynamics, since often just a few shieldings are of interest. Our theory relies on two major aspects both necessary to provide a sublinear scaling behavior: First, an alternative expression for the shielding tensor is derived, which involves the response density matrix with respect to the nuclear magnetic moment instead of the response to the external magnetic field. Second, as unphysical long-range contributions occur within the description of distributed gauge origin methods that do not influence the final expectation value, we present a screening procedure to truncate the B-field dependent basis set, which is crucial in order to ensure an early onset of the sublinear scaling. The screening is in line with the r(-2) distance decay of Biot-Savarts law for induced magnetic fields. Our present truncation relies on the introduced concept of "individual gauge shielding contributions" applied to a reformulated shielding tensor, the latter consisting of gauge-invariant terms. The presented method is generally applicable and shows typical speed-ups of about one order of magnitude; moreover, due to the reduced scaling behavior of O(1) as compared to O(N), the wins become larger with increasing system size. We illustrate the validity of our method for several test systems, including ring-current dominated systems and biomolecules with more than 1000 atoms.

Following the discovery of slow fluctuations in the catalytic activity of an enzyme in single-molecule experiments, it has been shown that the classical Michaelis-Menten (MM) equation relating the average enzymatic velocity and the substrate concentration may hold even for slowly fluctuating enzymes. In many cases, the average velocity is that given by the MM equation with time-averaged values of the fluctuating rate constants and the effect of enzyme fluctuations is simply averaged out. The situation is quite different for a sequence of reactions. For colocalization of a pair of enzymes in a sequence to be effective in promoting reaction, the second must be active when the first is active or soon after. If the enzymes are slowly varying and only rarely active, the product of the first reaction may diffuse away before the second enzyme is active, and colocalization may have little value. Even for single-step reactions the interplay of reaction and diffusion with enzyme fluctuations leads to added complexities, but for multistep reactions the interplay of reaction and diffusion, cell size, compartmentalization, enzyme fluctuations, colocalization, and segregation is far more complex than for single-step reactions. In this paper, we report the use of stochastic simulations at the level of whole cells to explore, understand, and predict the behavior of single- and multistep enzyme-catalyzed reaction systems exhibiting some of these complexities. Results for single-step reactions confirm several earlier observations by others. The MM relationship, with altered constants, is found to hold for single-step reactions slowed by diffusion. For single-step reactions, the distribution of enzymes in a regular grid is slightly more effective than a random distribution. Fluctuations of enzyme activity, with average activity fixed, have no observed effects for simple single-step reactions slowed by diffusion. Two-step sequential reactions are seen to be slowed by segregation of the enzymes for each step, and results of the calculations suggest limits for cell size. Colocalization of enzymes for a two-step sequence is seen to promote reaction, and rates fall rapidly with increasing distance between enzymes. Low frequency fluctuations of the activities of colocalized enzymes, with average activities fixed, can greatly reduce reaction rates for sequential reactions.

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls (P = 0.0009, OR = 7.2) and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls (P = 0.028, OR = 2.5). Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents (P = 0.037, OR = 6). Probands were more likely to carry an additional large copy-number variant when compared to matched controls (10 of 42 cases, P = 5.7 x 10(-5), OR = 6.6). The clinical features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease.

A Laplace-transformed second-order Moller-Plesset perturbation theory (MP2) method is presented, which allows to achieve linear scaling of the computational effort with molecular size for electronically local structures. Also for systems with a delocalized electronic structure, a cubic or even quadratic scaling behavior is achieved. Numerically significant contributions to the atomic orbital (AO)-MP2 energy are preselected using the so-called multipole-based integral estimates (MBIE) introduced earlier by us [J. Chem. Phys. 123, 184102 (2005)]. Since MBIE provides rigorous upper bounds, numerical accuracy is fully controlled and the exact MP2 result is attained. While the choice of thresholds for a specific accuracy is only weakly dependent upon the molecular system, our AO-MP2 scheme offers the possibility for incremental thresholding: for only little additional computational expense, the numerical accuracy can be systematically converged. We illustrate this dependence upon numerical thresholds for the calculation of intermolecular interaction energies for the S22 test set. The efficiency and accuracy of our AO-MP2 method is demonstrated for linear alkanes, stacked DNA base pairs, and carbon nanotubes: e.g., for DNA systems the crossover toward conventional MP2 schemes occurs between one and two base pairs. In this way, it is for the first time possible to compute wave function-based correlation energies for systems containing more than 1000 atoms with 10 000 basis functions as illustrated for a 16 base pair DNA system on a single-core computer, where no empirical restrictions are introduced and numerical accuracy is fully preserved.

We present linear-scaling routines for the calculation of the Cholesky decomposition of a symmetric positive-definite matrix and its inverse. As an example, we consider the inversion of the overlap matrix of DNA and amylose fragments as well as of linear alkanes, where the largest system corresponds to a 21,442 x 21,442 matrix. The efficiency and the scaling behavior are discussed and compared to standard LAPACK routines. Our Cholesky routines are publicly available on the web., ((c) 2007 Wiley Periodicals, Inc.)

A reformulation of the fixed-node diffusion quantum Monte Carlo method (FN-DQMC) in terms of the N-particle density matrix is presented, which allows us to reduce the computational effort to linear for the evaluation of the local energy. The reformulation is based on our recently introduced density matrix-based approach for a linear-scaling variational QMC method [J. Kussmann et al., Phys. Rev. B. 75, 165107 (2007)]. However, within the latter approach of using the positive semi-definite N-particle trial density (rhoN T(R)=mid R:Psi(T)(R)mid R:(2)), the nodal information of the trial function is lost. Therefore, a straightforward application to the FN-DQMC method is not possible, in which the sign of the trial function is usually traced in order to confine the random walkers to their nodal pockets. As a solution, we reformulate the FN-DQMC approach in terms of off-diagonal elements of the N-particle density matrix rhoN T(R;R'), so that the nodal information of the trial density matrix is obtained. Besides all-electron moves, a scheme to perform single-electron moves within N-PDM QMC is described in detail. The efficiency of our method is illustrated for exemplary calculations.

A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions.

Quantum-chemical calculations for molecular tweezers systems are presented, where the focus is not only on the recognition process in the host-guest systems, but on the self aggregation of the tweezers host as well. Such intermolecular interactions influence the corresponding NMR spectra strongly by up to 6 ppm for proton chemical shifts, since ring-current effects are particularly important. The quantum-chemical results allow one to reliably assign the spectra and to gain information both on the structure and on the importance of intra- and intermolecular interactions. In addition, we study the accuracy of a variety of density functionals for describing the present host-guest systems, where we observe a considerable underestimation of ring-current effects on (1)H NMR chemical shifts at the density functional theory (DFT) level using smaller basis sets such as 6-31G**, so that larger bases like TZP are required. This stands in contrast to the behavior of the Hartree-Fock scheme, where small basis sets, such as 6-31G**, provide reliable (1)H NMR shieldings for molecular tweezers systems.

Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.

The arrangement of discotic hexa-peri-hexabenzocoronenes (HBCs) into columnar helical superstructures has been investigated in relation to their molecular architecture. The supramolecular structure of two hexaphenyl-substituted HBC derivatives, differing only in the chiral/achiral nature of the attached alkyl side chains, was studied by circular dichroism and temperature-dependent wide-angle X-ray diffraction on oriented filaments. A structural model in agreement with the experimental observations was developed on the basis of accompanying quantum-chemical calculations. The helical organization along the self-assembled columnar structures was induced by the steric requirements of the bulky phenyl rings near the aromatic core, i.e., by their rotation out-of-plane with respect to the aromatic core. On the other hand, a uniform handedness of the twist was generated by chiral alkyl substituents. At higher temperatures the degree of helical organization decreases due to lateral and longitudinal dynamics of the discotic molecules. Annealing at ambient conditions improved the long-range arrangement of the discs along the columnar structures. This reorganization indicated a self-healing of the plastic material which is desirable for application of discotics as active layers in electronic devices. The helical packing resulted in a considerable stability of the mesophase up to 500 degrees C, which has not been reported for a discotic so far.

The structure of supramolecular complexes formed by a naphthalene-spaced tweezer molecule as host and 1,4-dicyanobenzene (DCNB), 1,2,4,5-tetracyanobenzene (TCNB), and 7,7,8,8-tetracyano-p-quinodimethane (TCNQ) as aromatic, electron-deficient guests is investigated by solid-state NMR and X-ray diffraction measurements. Quantum chemical calculations using linear scaling methods are applied to predict and to assign the 1H NMR chemical shifts of the complexes. By combining experiment and theory, insights into intra- and intermolecular effects influencing the proton chemical shifts of the host-guest system are provided in the solid state.