COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge.

The SAMPL8 blind prediction challenge, which addresses the acid/base dissociation constants (pKa) and the distribution coefficients (logD), was addressed by the Conductor like Screening Model for Realistic Solvation (COSMO-RS). Using the COSMOtherm implementation of COSMO-RS together with a rigorous conformational sampling, yielded logD predictions with a root mean square deviation (RMSD) of 1.36 log units over all 11 compounds and seven bi-phasic systems of the data set, which was the most accurate of all contest submissions (logD).For the SAMPL8 pKa competition, participants were asked to report the standard state free energies of all microstates, which were then used to calculate the macroscopic pKa. We have used COSMO-RS based linear free energy fit models to calculate the requested energies. The assignment of the calculated and experimental pKa values was made on the basis of the popular transitions, i.e. the transition hat was predicted by the majority of the submissions. With this assignment and a model that covers both, pKa and base pKa, we achieved an RMSD of 3.44 log units (18 pKa values of 14 molecules), which is the second place of the six ranked submissions. By changing to an assignment that is based on the experimental transition curves, the RMSD reduces to 1.65. In addition to the ranked contribution, we submitted two more data sets, one for the standard pKa model and one or the standard base pKa model of COSMOtherm. Using the experiment based assignment with the predictions of the two sets we received a RMSD of 1.42 log units (25 pKa values of 20 molecules). The deviation mainly arises from a single outlier compound, the omission of which leads to an RMSD of 0.89 log units.

Blind prediction of toluene/water partition coefficients using COSMO-RS: results from the SAMPL9 challenge.

Accurately predicting partition coefficients log P is crucial for reducing costs and accelerating drug design as it provides valuable information about the bioavailability, pharmacokinetics, and toxicity of different drug candidates. However, the performance of the existing methods is ambiguous, making it unclear whether these methods can be effectively utilized in drug discovery. To assess the performance of these methods, a series of SAMPL challenges have been conducted over the past few years, aiming to enable the development and validation of predictive models. In this study, we present two independent contributions to the SAMPL9 challenge for predicting the toluene/water partition coefficients for 16 molecules. Both submissions, A and B, use the COSMO-RS approach, albeit in slightly different procedures, to compute the transfer free energies from water to toluene of the molecules presented in the challenge, and consequently, their corresponding log P values. Based on the results, COSMO-RS submission A achieves the top position with an R2 value of 0.93 while it ranks second in terms of root-mean-square error (RMSE) with a value of 1.23 log P units. COSMO-RS submission B achieves an R2 value of 0.83 and an RMSE value of 1.48 log P units. Following the challenge, we predict the log P values using a neural network model, which was pre-trained on COSMO-RS data achieving an R2 of 0.92 and RMSE of 1.04 log P units. Compared to previous SAMPL challenges, all contributions displayed large deviations in predicting the toluene/water partition coefficient. These large deviations emphasize that further research is needed to develop accurate and reliable methods for modeling solvent effects on small molecule transfer-free energies.

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations.

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy-cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe-Salpeter methods, second-order Møller-Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE's functionality, including excited-state methods, RPA and Green's function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE's current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE's development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.

Sensorimotor Functional and Structural Networks after Intracerebral Stem Cell Grafts in the Ischemic Mouse Brain.

Past investigations on stem cell-mediated recovery after stroke have limited their focus on the extent and morphological development of the ischemic lesion itself over time or on the integration capacity of the stem cell graft ex vivo However, an assessment of the long-term functional and structural improvement in vivo is essential to reliably quantify the regenerative capacity of cell implantation after stroke. We induced ischemic stroke in nude mice and implanted human neural stem cells (H9 derived) into the ipsilateral cortex in the acute phase. Functional and structural connectivity changes of the sensorimotor network were noninvasively monitored using magnetic resonance imaging for 3 months after stem cell implantation. A sharp decrease of the functional sensorimotor network extended even to the contralateral hemisphere, persisting for the whole 12 weeks of observation. In mice with stem cell implantation, functional networks were stabilized early on, pointing to a paracrine effect as an early supportive mechanism of the graft. This stabilization required the persistent vitality of the stem cells, monitored by bioluminescence imaging. Thus, we also observed deterioration of the early network stabilization upon vitality loss of the graft after a few weeks. Structural connectivity analysis showed fiber-density increases between the cortex and white matter regions occurring predominantly on the ischemic hemisphere. These fiber-density changes were nearly the same for both study groups. This motivated us to hypothesize that the stem cells can influence, via early paracrine effect, the functional networks, while observed structural changes are mainly stimulated by the ischemic event.SIGNIFICANCE STATEMENT In recent years, research on strokes has made a shift away from a focus on immediate ischemic effects and towards an emphasis on the long-range effects of the lesion on the whole brain. Outcome improvements in stem cell therapies also require the understanding of their influence on the whole-brain networks. Here, we have longitudinally and noninvasively monitored the structural and functional network alterations in the mouse model of focal cerebral ischemia. Structural changes of fiber-density increases are stimulated in the endogenous tissue without further modulation by the stem cells, while functional networks are stabilized by the stem cells via a paracrine effect. These results will help decipher the underlying networks of brain plasticity in response to cerebral lesions and offer clues to unravelling the mystery of how stem cells mediate regeneration.

Benchmarking Different QM Levels for Usage with COSMO-RS.

The COSMO-RS method is an established method for the prediction of fluid phase properties such as activity coefficients, liquid-liquid equilibria, and free energy of solvation. It is also frequently used in quantum chemistry-based chemical reaction modeling to predict the solvation contribution to the reactions. The COSMOtherm software, which features the currently most advanced implementation of COSMO-RS, is based on quantum chemical COSMO calculations using the BP functional with the def2-TZVPD basis set. As the accuracy of COSMO-RS depends on the accuracy of the underlying quantum chemical (QC) calculation, it is important to validate the currently used level against other common, presumably superior, approaches such as the more recently developed M06-2x hybrid density functional or wave function methods such as MP2. As compared to other applications where the electronic energy is the most important result of the QC calculation, the COSMO-RS method has a much higher dependence on the molecular polarity and thus the electron density distribution. We find that MP2, PBE0, and M06-2x perform slightly worse in fully reparametrized COSMO-RS with respect to the prediction of experimentally measured properties like pKa or logP. Although MP2 was reported to yield better polarities than most DFT functionals for spin unpolarized molecules, this theoretical advantage does not manifest in a practical benefit for the prediction of thermodynamic properties with a refitted COSMO-RS parameter set. Other pure DFT functionals such as PBE or TPSS can be used instead of BP, but again, no practical advantage is expected as they yield extremely similar polarities to the original BP calculations.

A refined cavity construction algorithm for the conductor-like screening model.

A cavity construction algorithm based on the triangulation of an iso-surface is introduced as a new standard for dielectric continuum solvation calculations with the Conductor-like Screening Model COSMO. It overcomes deficiencies which have become apparent for the original COSMO standard cavity, especially in concave regions of the molecular shaped cavity. The new standard, called FINE Cavity, is described in this article with several application examples. The earlier COSMO cavity construction algorithms are described for comparison. © 2018 Wiley Periodicals, Inc.

Neurogenesis upregulation on the healthy hemisphere after stroke enhances compensation for age-dependent decrease of basal neurogenesis.

Stroke is a leading cause of death and disability worldwide with no treatment for the chronic phase available. Interestingly, an endogenous repair program comprising inflammation and neurogenesis is known to modulate stroke outcome. Several studies have shown that neurogenesis decreases with age but the therapeutic importance of endogenous neurogenesis for recovery from cerebral diseases has been indicated as its ablation leads to stroke aggravation and worsened outcome. A detailed characterization of the neurogenic response after stroke related to ageing would help to develop novel and targeted therapies. In an innovative approach, we used the DCX-Luc mouse, a transgenic model expressing luciferase in doublecortin-positive neuroblasts, to monitor the neurogenic response following middle cerebral artery occlusion over three weeks in three age groups (2, 6, 12months) by optical imaging while the stroke lesion was monitored by quantitative MRI. The individual longitudinal and noninvasive time profiles provided exclusive insight into age-dependent decrease in basal neurogenesis and neurogenic upregulation in response to stroke which are not accessible by conventional BrdU-based measures of cell proliferation. For cortico-striatal strokes the maximal upregulation occurred at 4days post stroke followed by a continuous decrease to basal levels by three weeks post stroke. Older animals effectively compensated for reduced basal neurogenesis by an enhanced sensitivity to the cerebral lesion, resulting in upregulated neurogenesis levels approaching those measured in young mice. In middle aged and older mice, but not in the youngest ones, additional upregulation of neurogenesis was observed in the contralateral healthy hemisphere. This further substantiates the increased propensity of older brains to respond to lesion situation. Our results clearly support the therapeutic relevance of endogenous neurogenesis for stroke recovery and particularly in older brains.

Calculation of solvation free energies with DCOSMO-RS.

The concept of dielectric continuum models has turned out to be very fruitful for the qualitative description of solvation effects in quantum chemical calculations, although from a theoretical perspective its basis is questionable, at least if applied to polar solvents, because the electrostatic nearest neighbor interactions in polar solvents are much too strong to be described by macroscopic dielectric continuum theory. On the basis of this insight, the Conductorlike Screening Model for Realistic Solvation (COSMO-RS) had been developed, which gives a thermodynamically consistent, quantitative description of solvation effects in polar and nonpolar solvents, even in mixtures and at variable temperature, starting from quantum chemical calculations of solute and solvent molecules embedded in a virtual conductor (COSMO). Though COSMO-RS usually only requires quantum chemical calculations in the conductor and thus does not allow for studying of the concrete solvent influence on the solute electron density, the direct COSMO-RS (DCOSMO-RS) has been introduced, which uses the σ-potential, i.e., a solvent specific response function provided by COSMO-RS, as a replacement of the conductor or dielectric response employed in continuum solvation models. In this article we describe the current status of DCOSMO-RS and demonstrate the performance of the DCOSMO-RS approach for the prediction of free energies of solvation.

Brain maturation of the adolescent rat cortex and striatum: changes in volume and myelination.

Longitudinal studies on brain pathology and assessment of therapeutic strategies rely on a fully mature adult brain to exclude confounds of cerebral developmental changes. Thus, knowledge about onset of adulthood is indispensable for discrimination of developmental phase and adulthood. We have performed a high-resolution longitudinal MRI study at 11.7T of male Wistar rats between 21days and six months of age, characterizing cerebral volume changes and tissue-specific myelination as a function of age. Cortical thickness reaches final value at 1month, while volume increases of cortex, striatum and whole brain end only after two months. Myelin accretion is pronounced until the end of the third postnatal month. After this time, continuing myelination increases in cortex are still seen on histological analysis but are no longer reliably detectable with diffusion-weighted MRI due to parallel tissue restructuring processes. In conclusion, cerebral development continues over the first three months of age. This is of relevance for future studies on brain disease models which should not start before the end of month 3 to exclude serious confounds of continuing tissue development.

Complement C3a treatment accelerates recovery after stroke via modulation of astrocyte reactivity and cortical connectivity.

Despite advances in acute care, ischemic stroke remains a major cause of long-term disability. Approaches targeting both neuronal and glial responses are needed to enhance recovery and improve long-term outcome. The complement C3a receptor (C3aR) is a regulator of inflammation with roles in neurodevelopment, neural plasticity, and neurodegeneration. Using mice lacking C3aR (C3aR-/-) and mice overexpressing C3a in the brain, we uncovered 2 opposing effects of C3aR signaling on functional recovery after ischemic stroke: inhibition in the acute phase and facilitation in the later phase. Peri-infarct astrocyte reactivity was increased and density of microglia reduced in C3aR-/- mice; C3a overexpression led to the opposite effects. Pharmacological treatment of wild-type mice with intranasal C3a starting 7 days after stroke accelerated recovery of motor function and attenuated astrocyte reactivity without enhancing microgliosis. C3a treatment stimulated global white matter reorganization, increased peri-infarct structural connectivity, and upregulated Igf1 and Thbs4 in the peri-infarct cortex. Thus, C3a treatment from day 7 after stroke exerts positive effects on astrocytes and neuronal connectivity while avoiding the deleterious consequences of C3aR signaling during the acute phase. Intranasal administration of C3aR agonists within a convenient time window holds translational promise to improve outcome after ischemic stroke.

thermocalc - a poor man's approach to computational thermochemistry.

We present thermocalc, a Perl module to perform the automated calculation of atomization energies and heats of formation for lists of molecules. The methods used are based on density functional theory and second-order perturbation theory to ensure that data sets of medium sized to large molecules can be run at reasonable throughput rates. The quantum chemical calculations are performed using the program package TURBOMOLE in a three-step protocol. In a first step, a pre-optimization of the structure and a zero-point energy calculation are performed. As second step, a geometry optimization is being carried out, and the last step is a single point energy calculation. The level of theory used in the different steps can be modified by the user to allow for customized protocols. The performance of example protocols is investigated on different test sets of molecules. In the course of this work, a simple, but efficient one-parameter correction term based on the shared electron numbers has been developed, which reduces the error of calculated heats of formation significantly.

Prediction of free energies of hydration with COSMO-RS on the SAMPL3 data set.

The COSMO-RS method has been used for the prediction of free energies of hydration on the dataset of 36 chlorinated ethanes, biphenyls and dioxins considered in the SAMPL3 challenge. Straight application of the latest version of the COSMOtherm software yields an overall predictive accuracy of 1.05 kcal/mol (RMSE). The predictions for the chlorinated ethanes and dioxins are much better with 0.40 and 0.49 kcal/mol RMSE, respectively. The predictions for the chlorinated biphenyls show a systematic shift of approximately 1 kcal/mol, but the large RMSE of 1.59 kcal/mol mainly arises from two exceptional outliers. Possible reasons for this observation are discussed.

Polarization charge densities provide a predictive quantification of hydrogen bond energies.

A systematic density functional theory based study of hydrogen bond energies of 2465 single hydrogen bonds has been performed. In order to be closer to liquid phase conditions, different from the usual reference state of individual donor and acceptor molecules in vacuum, the reference state of donors and acceptors embedded in a perfect conductor as simulated by the COSMO solvation model has been used for the calculation of the hydrogen bond energies. The relationship between vacuum and conductor reference hydrogen bond energies is investigated and interpreted in the light of different physical contributions, such as electrostatic energy and dispersion. A very good correlation of the DFT/COSMO hydrogen bond energies with conductor polarization charge densities of separated donor and acceptor atoms was found. This provides a method to predict hydrogen bond strength in solution with a root mean square error of 0.36 kcal mol(-1) relative to the quantum chemical dimer calculations. The observed correlation is broadly applicable and allows for a predictive quantification of hydrogen bonding, which can be of great value in many areas of computational, medicinal and physical chemistry.

The gut microbiota modulates brain network connectivity under physiological conditions and after acute brain ischemia.

The gut microbiome has been implicated as a key regulator of brain function in health and disease. But the impact of gut microbiota on functional brain connectivity is unknown. We used resting-state functional magnetic resonance imaging in germ-free and normally colonized mice under naive conditions and after ischemic stroke. We observed a strong, brain-wide increase of functional connectivity in germ-free animals. Graph theoretical analysis revealed significant higher values in germ-free animals, indicating a stronger and denser global network but with less structural organization. Breakdown of network function after stroke equally affected germ-free and colonized mice. Results from histological analyses showed changes in dendritic spine densities, as well as an immature microglial phenotype, indicating impaired microglia-neuron interaction in germ-free mice as potential cause of this phenomenon. These results demonstrate the substantial impact of bacterial colonization on brain-wide function and extend our so far mainly (sub) cellular understanding of the gut-brain axis.

Some conclusions regarding the predictions of tautomeric equilibria in solution based on the SAMPL2 challenge.

The COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with a COSMO based statistical thermodynamics of surface interactions, has been used in its COSMOtherm implementation for the direct, blind prediction of tautomeric equilibria within the SAMPL2 challenge. Since the quantum chemical level underlying COSMOtherm, i.e. BP/TZVP DFT-calculations, is known to be of limited accuracy with respect to reaction energies, we tested MP2 reaction energy corrections in addition. As expected, the straight application of the latest version of COSMOtherm yielded a poor predictive accuracy of approximately 4 kcal/mol (RMSE) for the eight compounds of the blind prediction data set, and the MP2-corrected predictions reduced the average error considerably to approximately 1.2 kcal/mol. But a more detailed analysis shows that this improvement is not systematic and mostly a lucky coincidence on the small data set. The systematic results of COSMOtherm allow for an efficient empirical correction with an RMSE of 0.61 kcal/mol. This allows for systematic predictions for the most important case of generalized keto-enol tautomerism.

Blind prediction test of free energies of hydration with COSMO-RS.

The COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with COSMO-RS, a statistical thermodynamics treatment of surface interactions, simulations, has been used for the direct, blind prediction of free energies of hydration within the SAMPL challenge. Straight application of the latest version of the COSMOtherm implementation in combination with a rigorous conformational sampling yielded a predictive accuracy of 1.56 kcal/mol (RMSE) for the 23 compounds of the blind prediction dataset. Due to the uncertainties of the extrapolations and assumptions involved in the derivation of the experimental data, the accuracy of the predicted data may be considered to be within the noise level of the experimental data.

Human Neural Stem Cell Induced Functional Network Stabilization After Cortical Stroke: A Longitudinal Resting-State fMRI Study in Mice.

Most stroke studies dealing with functional deficits and assessing stem cell therapy produce extensive hemispheric damage and can be seen as a model for severe clinical strokes. However, mild strokes have a better prospect for functional recovery. Recently, anatomic and behavioral changes have been reported for distal occlusion of the middle cerebral artery (MCA), generating a well-circumscribed and small cortical lesion, which can thus be proposed as mild to moderate cortical stroke. Using this cortical stroke model of moderate severity in the nude mouse, we have studied the functional networks with resting-state functional magnetic resonance imaging (fMRI) for 12 weeks following stroke induction. Further, human neural stem cells (hNSCs) were implanted adjacent to the ischemic lesion, and the stable graft vitality was monitored with bioluminescence imaging (BLI). Differentiation of the grafted neural stem cells was analyzed by immunohistochemistry and by patch-clamp electrophysiology. Following stroke induction, we found a pronounced and continuously rising hypersynchronicity of the sensorimotor networks including both hemispheres, in contrast to the severe stroke filament model where profound reduction of the functional connectivity had been reported by us earlier. The vitality of grafted neural stem cells remained stable throughout the whole 12 weeks observation period. In the stem cell treated animals, functional connectivity did not show hypersynchronicity but was globally slightly reduced below baseline at 2 weeks post-stroke, normalizing thereafter completely. Our resting-state fMRI (rsfMRI) studies on cortical stroke reveal for the first time a hypersynchronicity of the functional brain networks. This hypersynchronicity appears as a hallmark of mild cortical strokes, in contrast to severe strokes with striatal involvement where exclusively hyposynchronicity has been reported. The effect of the stem cell graft was an early and persistent normalization of the functional sensorimotor networks across the whole brain. These novel functional results may help interpret future outcome investigations after stroke and demonstrate the highly promising potential of stem cell treatment for functional outcome improvement after stroke.

Prediction of acidity in acetonitrile solution with COSMO-RS.

The COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with a statistical thermodynamics treatment for realistic solvation simulations, has been used for the prediction of pK(a) values in acetonitrile. For a variety of 93 organic acids, the directly calculated values of the free energies of dissociation in acetonitrile showed a very good correlation with the pK(a) values (r(2) = 0.97) in acetonitrile, corresponding to a standard deviation of 1.38 pK(a) units. Thus, we have a prediction method for acetonitrile pK(a) with the intercept and the slope as the only adjusted parameters. Furthermore, the pK(a) values of CH acids yielding large anions with delocalized charge can be predicted with a rmse of 1.12 pK(a) units using the theoretical values of slope and intercept resulting in truly ab initio pK(a) prediction. In contrast to our previous findings on aqueous acidity predictions the slope of the experimental pK(a) versus theoretical DeltaG(diss) was found to match the theoretical value 1/RT ln (10) very well. The predictivity of the presented method is general and is not restricted to certain compound classes. However, a systematic correction of -7.5 kcal mol(-1) is required for compounds that do not allow electron-delocalization in the dissociated anion. The prediction model was tested on a diverse test set of 129 complex multifunctional compounds from various sources, reaching a root mean square deviation of 2.10 pK(a) units.

Prediction of the free energy of hydration of a challenging set of pesticide-like compounds.

In a blind validation test the COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with a statistical thermodynamics treatment for more realistic solvation (RS) simulations, has been used for the direct prediction of transfer free energies of 55 demanding pesticide-like compounds. Comparison with experimental data yields an rms deviation of approximately 2 kcal/mol, which is in the order of the estimated inaccuracy of the experimental data. A detailed comparison reveals experimental and calculation pitfalls on conformational flexible, multifunctional, polar compounds.

Persistent Quantitative Vitality of Stem Cell Graft Is Necessary for Stabilization of Functional Brain Networks After Stroke.

Stem cell treatment after stroke has demonstrated substantial outcome improvement. However, monitoring of stem cell fate in vivo is still challenging and not routinely performed, yet important to quantify the role of the implanted stem cells on lesion improvement; in several studies even mortality of the graft has been reported. Resting state functional magnetic resonance imaging (rs-fMRI) is a highly sensitive imaging modality to monitor the brain-wide functional network alterations of many brain diseases in vivo. We monitor for 3 months the functional connectivity changes after intracortical stem cell engraftment in large, cortico-striatal (n = 9), and in small, striatal (n = 6) ischemic lesions in the mouse brain with non-invasive rs-fMRI on a 9.4T preclinical MRi scanner with GE-EPI sequence. Graft vitality is continuously recorded by bioluminescence imaging (BLI) roughly every 2 weeks after implantation of 300 k neural stem cells. In cortico-striatal lesions, the lesion extension induces graft vitality loss, in consequence leading to a parallel decrease of functional connectivity strength after a few weeks. In small, striatal lesions, the graft vitality is preserved for the whole observation period and the functional connectivity is stabilized at values as in the pre-stroke situation. But even here, at the end of the observation period of 3 months, the functional connectivity strength is found to decrease despite preserved graft vitality. We conclude that quantitative graft viability is a necessary but not sufficient criterion for functional neuronal network stabilization after stroke. Future studies with even longer time periods after stroke induction will need to identify additional players which have negative influence on the functional brain networks.