Molecular signatures of cortical expansion in the human fetal brain

The third trimester of human gestation is characterised by rapid increases in brain volume and cortical surface area. A growing catalogue of cells in the prenatal brain has revealed remarkable molecular diversity across cortical areas.1,2 Despite this, little is known about how this translates into the patterns of differential cortical expansion observed in humans during the latter stages of gestation. Here we present a new resource, μBrain, to facilitate knowledge translation between molecular and anatomical descriptions of the prenatal developing brain. Built using generative artificial intelligence, μBrain is a three-dimensional cellular-resolution digital atlas combining publicly-available serial sections of the postmortem human brain at 21 weeks gestation3 with bulk tissue microarray data, sampled across 29 cortical regions and 5 transient tissue zones.4 Using μBrain, we evaluate the molecular signatures of preferentially-expanded cortical regions during human gestation, quantified in utero using magnetic resonance imaging (MRI). We find that differences in the rates of expansion across cortical areas during gestation respect anatomical and evolutionary boundaries between cortical types5 and are founded upon extended periods of upper-layer cortical neuron migration that continue beyond mid-gestation. We identify a set of genes that are upregulated from mid-gestation and highly expressed in rapidly expanding neocortex, which are implicated in genetic disorders with cognitive sequelae. Our findings demonstrate a spatial coupling between areal differences in the timing of neurogenesis and rates of expansion across the neocortical sheet during the prenatal epoch. The μBrain atlas is available from: https://garedaba.github.io/micro-brain/ and provides a new tool to comprehensively map early brain development across domains, model systems and resolution scales.

Massively parallel implementation of gradients within the random phase approximation: Application to the polymorphs of benzene

The Random-Phase approximation (RPA) provides an appealing framework for semi-local density functional theory. In its Resolution-of-the-Identity (RI) approach, it is a very accurate and more cost-effective method than most other wavefunction-based correlation methods. For widespread applications, efficient implementations of nuclear gradients for structure optimizations and data sampling of machine learning approaches are required. We report a well scaling implementation of RI-RPA nuclear gradients on massively parallel computers. The approach is applied to two polymorphs of the benzene crystal obtaining very good cohesive and relative energies. Different correction and extrapolation schemes are investigated for further improvement of the results and estimations of error bars.

Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations

Water adsorption and dissociation processes on pristine low-index TiO2 interfaces are important but poorly understood outside the well-studied anatase (101) and rutile (110). To understand these, we construct three sets of machine learning potentials that are simultaneously applicable to various TiO2 surfaces, based on three density-functional-theory approximations. Here we show the water dissociation free energies on seven pristine TiO2 surfaces, and predict that anatase (100), anatase (110), rutile (001), and rutile (011) favor water dissociation, anatase (101) and rutile (100) have mostly molecular adsorption, while the simulations of rutile (110) sensitively depend on the slab thickness and molecular adsorption is preferred with thick slabs. Moreover, using an automated algorithm, we reveal that these surfaces follow different types of atomistic mechanisms for proton transfer and water dissociation: one-step, two-step, or both. These mechanisms can be rationalized based on the arrangements of water molecules on the different surfaces. Our finding thus demonstrates that the different pristine TiO2 surfaces react with water in distinct ways, and cannot be represented using just the low-energy anatase (101) and rutile (110) surfaces.

Radicals in aqueous solution: assessment of density-corrected SCAN functional

We study self-interaction effects in solvated and strongly-correlated cationic molecular clusters, with a focus on the solvated hydroxyl radical. To address the self-interaction issue, we apply the DC-r2SCAN method, with the auxiliary density matrix approach. Validating our method through simulations of bulk liquid water, we demonstrate that DC-r2SCAN maintains the structural accuracy of r2SCAN while effectively addressing spin density localization issues. Extending our analysis to solvated cationic molecular clusters, we find that the hemibonded motif in the [CH3S∴CH3SH]+ cluster is disrupted in the DC-r2SCAN simulation, in contrast to r2SCAN that preserves the (three-electron-two-center)-bonded motif. Similarly, for the [SH∴SH2]+ cluster, r2SCAN restores the hemibonded motif through spin leakage, while DC-r2SCAN predicts a weaker hemibond formation influenced by solvent-solute interactions. Our findings demonstrate the potential of DC-r2SCAN combined with the auxiliary density matrix method to improve electronic structure calculations, providing insights into the properties of solvated cationic molecular clusters. This work contributes to the advancement of self-interaction corrected electronic structure theory and offers a computational framework for modeling condensed phase systems with intricate correlation effects.

Sparse tensor based nuclear gradients for periodic Hartree-Fock and low-scaling correlated wave function methods in the CP2K software package: A massively parallel and GPU accelerated implementation

The development of novel double-hybrid density functionals offers new levels of accuracy and is leading to fresh insights into the fundamental properties of matter. Hartree-Fock exact exchange and correlated wave function methods, such as second-order Møller-Plesset (MP2) and direct random phase approximation (dRPA), are usually required to build such functionals. Their high computational cost is a concern, and their application to large and periodic systems is, therefore, limited. In this work, low-scaling methods for Hartree-Fock exchange (HFX), SOS-MP2, and direct RPA energy gradients are developed and implemented in the CP2K software package. The use of the resolution-of-the-identity approximation with a short range metric and atom-centered basis functions leads to sparsity, allowing for sparse tensor contractions to take place. These operations are efficiently performed with the newly developed Distributed Block-sparse Tensors (DBT) and Distributed Block-sparse Matrices (DBM) libraries, which scale to hundreds of graphics processing unit (GPU) nodes. The resulting methods, resolution-of-the-identity (RI)-HFX, SOS-MP2, and dRPA, were benchmarked on large supercomputers. They exhibit favorable sub-cubic scaling with system size, good strong scaling performance, and GPU acceleration up to a factor of 3. These developments will allow for double-hybrid level calculations of large and periodic condensed phase systems to take place on a more regular basis.

Can AI Help Improve Water Quality? Towards the Prediction of Degradation of Micropollutants in Wastewater

Micropollutants have become a serious environmental problem by threatening ecosystems and the quality of drinking water. This account investigates if advanced AI can be used to find solutions for this problem. We review background, the challenges involved, and the current state-of-the-art of quantitative structure-biodegradation relationships (QSBR). We report on recent progress combining experiment, quantum chemistry (QC) and chemoinformatics, and provide a perspective on potential future uses of AI technology to help improve water quality.

A variational formulation of the Harris functional as a correction to approximate Kohn-Sham density functional theory

Accurate descriptions of intermolecular interactions are of great importance in simulations of molecular liquids. We present an electronic structure method that combines the accuracy of the Harris functional approach with the computational efficiency of approximately linear-scaling density functional theory (DFT). The non-variational nature of the Harris functional has been addressed by constructing a Lagrangian energy functional, which restores the variational condition by imposing stationarity with respect to the reference density. The associated linear response equations may be treated with linear-scaling efficiency in an atomic orbital based scheme. Key ingredients to describe the structural and dynamical properties of molecular systems are the forces acting on the atoms and the stress tensor. These first-order derivatives of the Harris Lagrangian have been derived and implemented in consistence with the energy correction. The proposed method allows for simulations with accuracies close to the Kohn-Sham DFT reference. Embedded in the CP2K program package, the method is designed to enable ab initio molecular dynamics simulations of molecular solutions for system sizes of several thousand atoms. Available subsystem DFT methods may be used to provide the reference density required for the energy correction at near linear-scaling efficiency. As an example of production applications, we applied the method to molecular dynamics simulations of the binary mixtures cyclohexane-methanol and toluene-methanol, performed within the isobaric-isothermal ensemble, to investigate the hydrogen bonding network in these non-ideal mixtures.

Excited-State Properties for Extended Systems: Efficient Hybrid Density Functional Methods

Time-dependent density functional theory has become state-of-the-art for describing photophysical and photochemical processes in extended materials because of its affordable cost. The inclusion of exact exchange was shown to be essential for the correct description of the long-range asymptotics of electronic interactions and thus a well-balanced description of valence, Rydberg, and charge-transfer excitations. Several approaches for an efficient treatment of exact exchange have been established for the ground state, while implementations for excited-state properties are rare. Furthermore, the high computational costs required for excited-state properties in comparison to ground-state computations often hinder large-scale applications on periodic systems with hybrid functional accuracy. We therefore propose two approximate schemes for improving computational efficiency for the treatment of exact exchange. Within the auxiliary density matrix method (ADMM), exact exchange is estimated using a relatively small auxiliary basis and the introduced basis set incompleteness error is compensated by an exchange density functional correction term. Benchmark results for a test set of 35 molecules demonstrate that the mean absolute error introduced by ADMM is smaller than 0.3 pm for excited-state bond lengths and in the range of 0.02-0.04 eV for vertical excitation, adiabatic excitation, and fluorescence energies. Computational timings for a series of covalent-organic frameworks demonstrate that a speed-up of at least 1 order of magnitude can be achieved for excited-state geometry optimizations in comparison to conventional hybrid functionals. The second method is to use a semiempirical tight binding approximation for both Coulomb and exchange contributions to the excited-state kernel. This simplified Tamm-Dancoff approximation (sTDA) achieves an accuracy comparable to approximated hybrid density functional theory when referring to highly accurate coupled-cluster reference data. We find that excited-state bond lengths deviate by 1.1 pm on average and mean absolute errors in vertical excitation, adiabatic excitation, and fluorescence energies are in the range of 0.2-0.5 eV. In comparison to ADMM-approximated hybrid functional theory, sTDA accelerates the computation of broad-band excitation spectra by 1 order of magnitude, suggesting its potential use for large-scale screening purposes.

Impact of comorbidities and ablation strategy on outcome after pulmonary vein isolation with cryo-balloon in patients with non- paroxysmal atrial fibrillation

Background

Presence of several comorbidities in patients with atrial fibrillation is well known, but impact of them on outcome after pulmonary vein isolation with cryo-balloon is not enough investigated. First aim of the study was analysis of the impact of comorbidities on long term outcome after PVI with cryo-balloon new generation (CBA) and secondary goal was evaluation of the impact of additional posterior roof ablation (PRA) in these patients.

Methods

Patients with non-paroxysmal AF ablated with CBA in our institution since May 2012 and completed follow up >3 months were enrolled in the study. The history of AF, cardiac comorbidities (CAD, Non ischemic-cardiomyopathy, heart insufficiency, right ventricular dysfunction) diabetes mellitus, and renal failure were assessed at admission, all patients received echocardiographic examination and blood test.

After a single trans-septal access and PV angiography PVI was performed using a 28-mm CBA. Mapping of PV signals before, during, and after each cryo application was performed with a 3F lasso catheter. The procedural endpoint after PVI was defined as complete elimination of all fragmented signals at the PV antrum with verification of entrance and exit block. In some patients PRA was performed additionally to PVI at discretion of physician. The primary endpoint of this study was the first documented recurrence of atrial tachyarrhythmia (>30 sec.), hospitalization due to cardio-vascular cause, re-do procedure or re-administration of anti-arrhythmic drugs.

Results

Among 560 patients 78 (13.9%) had no comorbidity and 299 (53.4%) were lasted with >1 comorbidity. A total of 260 (46.4%) recurrences were obtained within median follow up of 28 (12–57) months. Female gender, long time from first diagnosis >12 months and cardiac comorbidity were revealed to be independent predictors for long term recurrences whereas additional PRA performed in 176 pts independently improved outcome (61.9% vs 49.7%).

Conclusion

Cardiac comorbidities increased probability of post ablation recurrences, but performing of additional posterior roof ablation improved outcome in our cohort. These results should be confirmed in multi-center randomized study

Funding Acknowledgement

Type of funding sources: None.

First-principles correction scheme for linear-response time-dependent density functional theory calculations of core electronic states

Linear-response time-dependent density functional theory (LR-TDDFT) for core level spectroscopy using standard local functionals suffers from self-interaction error and a lack of orbital relaxation upon creation of the core hole. As a result, LR-TDDFT calculated x-ray absorption near edge structure spectra needed to be shifted along the energy axis to match experimental data. We propose a correction scheme based on many-body perturbation theory to calculate the shift from first-principles. The ionization potential of the core donor state is first computed and then substituted for the corresponding Kohn-Sham orbital energy, thus emulating Koopmans's condition. Both self-interaction error and orbital relaxation are taken into account. The method exploits the localized nature of core states for efficiency and integrates seamlessly in our previous implementation of core level LR-TDDFT, yielding corrected spectra in a single calculation. We benchmark the correction scheme on molecules at the K- and L-edges as well as for core binding energies and report accuracies comparable to higher order methods. We also demonstrate applicability in large and extended systems and discuss efficient approximations.

Efficient and low-scaling linear-response time-dependent density functional theory implementation for core-level spectroscopy of large and periodic systems

We discuss our implementation of linear-response time-dependent density functional theory (LR-TDDFT) for core level near-edge absorption spectroscopy. The method is based on established LR-TDDFT approaches to X-ray absorption spectroscopy (XAS) with additional accurate approximations for increased efficiency. We validate our implementation by reproducing benchmark results at the K-edge and showing that spin-orbit coupling effects at the L_2,3-edge are well described. We also demonstrate that the method is suitable for extended systems in periodic boundary conditions and measure a favorable sub-cubic scaling of the calculation cost with system size. We finally show that GPUs can be efficiently exploited and report speedups of up to a factor 2.

Double-Hybrid DFT Functionals for the Condensed Phase: Gaussian and Plane Waves Implementation and Evaluation

Intermolecular interactions play an important role for the understanding of catalysis, biochemistry and pharmacy. Double-hybrid density functionals (DHDFs) combine the proper treatment of short-range interactions of common density functionals with the correct description of long-range interactions of wave-function correlation methods. Up to now, there are only a few benchmark studies available examining the performance of DHDFs in condensed phase. We studied the performance of a small but diverse selection of DHDFs implemented within Gaussian and plane waves formalism on cohesive energies of four representative dispersion interaction dominated crystal structures. We found that the PWRB95 and ωB97X-2 functionals provide an excellent description of long-ranged interactions in solids. In addition, we identified numerical issues due to the extreme grid dependence of the underlying density functional for PWRB95. The basis set superposition error (BSSE) and convergence with respect to the super cell size are discussed for two different large basis sets.

P1006Cryo-balloon ablation in elderly; Outcome and prediction of recurrence

Background

It is well known that prevalence of atrial fibrillation correlates with age, however the data on ablation of atrial fibrillation in elderly patients is poor. Aim of this study was analysis of outcome and prediction of recurrence after cryo-balloon ablation (CBA) in elderly patients based on available data in our registry.

Methods

The history of AF was assessed at admission. Additionally, all patients received echocardiographic examination and blood test. After a single trans-septal access and PV angiography PVI was performed using a 28-mm CBA. Mapping of PV signals before, during, and after each cryo application was performed with a 3F lasso catheter. The procedural endpoint after PVI was defined as complete elimination of all fragmented signals at the PV antrum with verification of entrance and exit block. Primary endpoint was first documented recurrence of AF, atrial tachycardia or atrial flutter (>30 sec.). All patients received a follow-up every 3 month within 1st year, once yearly thereafter and in case of symptoms. Seven days Holter ECG was recorded by every follow up.

Results

A total of 44 (39%) of enrolled patients were male, 48 (43%) suffered non- paroxysmal AF(nPAF), 93 (82%) had hypertension, CAD was diagnosed by 27 (24%), 28 (25%) had DM (Hb1AC > 6), Stroke/TIA was observed in 11 (10%). Median Age in elderly was 76 (75-78) y, BMI 25.77 (23.51-28.69), time since 1st diagnosis 40 (6-50) month, LA area index 11.36 (9.77-13.20), TAPSE 23 (19-26), GFR 74 (66-83) mL/min, LVEF 60 (57-62). A total of 44 patients (39%) reached endpoint within follow up of 20 (12-38) months. Univariate association with outcome was found by follows parameter: Time from 1st diagnosis > 3 y (HR = 3.22 (1.66-6.27), p=.001); LA area index (HR = 1.17 (1.03-1.32), p=.013); DM (HR = 1.89 (1.02-3.55), p=.042); nPAF (HR = 1.90 (1.04-3.47), p=.036). After multivariate analysis only time from 1st diagnosis > 3 y, (HR= 3.17 (1.62-6.16), p=.001 and nPAF (HR = 1.84 (1.01-3.36)), p=.048 were revealed to be predictive. The area under probability score calculated for these predictors was .731 (.638-8.25), p=.001. Follows complications were observed: 2 (2%) - pericard tamponades, 4 (4%) phrenicus nerve injury. Conclusion. PVI with cryo-balloon is effective for elderly patients providing freedom of arrhythmic events in 61% of patients. Longer history of AF over 3 years since 1st diagnosis was main predictor for post ablation recurrence. In elderly patients with shorter history of AF efficiency and safety of CBA is comparable with general population.

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

Quantifying the hydration structure of sodium and potassium ions: taking additional steps on Jacob's Ladder

The ability to reproduce the experimental structure of water around the sodium and potassium ions is a key test of the quality of interaction potentials due to the central importance of these ions in a wide range of important phenomena.

Coupling of Surface Chemistry and Electric Double Layer at TiO2 Electrochemical Interfaces

Surfaces of metal oxides at working conditions are usually electrified because of the acid-base chemistry. The charged interface compensated with counterions forms the so-called electric double layer. The coupling of surface chemistry and the electric double layer is considered to be crucial but is poorly understood because of the lack of information at the atomistic scale. Here, we used the latest development in density functional theory-based finite-field molecular dynamics simulation to investigate the pH dependence of the Helmholtz capacitance at electrified rutile TiO₂(110)-NaCl electrolyte interfaces. It is found that, because of competing forces from surface adsorption and from the electric double layer, water molecules have a stronger structural fluctuation at high pH, and this leads to a much larger capacitance. It is also seen that interfacial proton transfers at low pH increase significantly the capacitance value. These findings elucidate the microscopic origin of the same trend observed in titration experiments.

Respiration resolved imaging with continuous stable state 2D acquisition using linear frequency SWEEP

Purpose

To investigate the potential of continuous radiofrequency (RF) shifting (SWEEP) as a technique for creating densely sampled data while maintaining a stable signal state for dynamic imaging.

Methods

We present a method where a continuous stable state of magnetization is swept smoothly across the anatomy of interest, creating an efficient approach to dense multiple 2D slice imaging. This is achieved by introducing a linear frequency offset to successive RF pulses shifting the excited slice by a fraction of the slice thickness with each successive repeat times (TR). Simulations and in vivo imaging were performed to assess how this affects the measured signal. Free breathing, respiration resolved 4D volumes in fetal/placental imaging is explored as potential application of this method.

Results

The SWEEP method maintained a stable signal state over a full acquisition reducing artifacts from unstable magnetization. Simulations demonstrated that the effects of SWEEP on slice profiles was of the same order as that produced by physiological motion observed with conventional methods. Respiration resolved 4D data acquired with this method shows reduced respiration artifacts and resilience to non‐rigid and non‐cyclic motion.

Conclusions

The SWEEP method is presented as a technique for improved acquisition efficiency of densely sampled short‐TR 2D sequences. Using conventional slice excitation the number of RF pulses required to enter a true steady state is excessively high when using short‐TR 2D acquisitions, SWEEP circumvents this limitation by creating a stable signal state that is preserved between slices.

Toward GW Calculations on Thousands of Atoms

The GW approximation of many-body perturbation theory is an accurate method for computing electron addition and removal energies of molecules and solids. In a canonical implementation, however, its computational cost is [Formula: see text] in the system size N, which prohibits its application to many systems of interest. We present a full-frequency GW algorithm in a Gaussian-type basis, whose computational cost scales with N² to N³. The implementation is optimized for massively parallel execution on state-of-the-art supercomputers and is suitable for nanostructures and molecules in the gas, liquid or condensed phase, using either pseudopotentials or all electrons. We validate the accuracy of the algorithm on the GW100 molecular test set, finding mean absolute deviations of 35 meV for ionization potentials and 27 meV for electron affinities. Furthermore, we study the length-dependence of quasiparticle energies in armchair graphene nanoribbons of up to 1734 atoms in size, and compute the local density of states across a nanoscale heterojunction.

Mapping the Free Energy of Lithium Solvation in the Protic Ionic Liquid Ethylammonuim Nitrate: A Metadynamics Study

Understanding lithium solvation and transport in ionic liquids is important due to their possible application in electrochemical devices. Using first-principles simulations aided by a metadynamics approach we study the free-energy landscape for lithium ions at infinite dilution in ethylammonium nitrate, a protic ionic liquid. We analyze the local structure of the liquid around the lithium cation and obtain a quantitative picture in agreement with experimental findings. Our simulations show that the lowest two free energy minima correspond to conformations with the lithium ion being solvated either by three or four nitrate ions with a transition barrier between them of 0.2 eV. Other less probable conformations having different solvation pattern are also investigated.

The impact of metalation on adsorption geometry, electronic level alignment and UV-stability of organic macrocycles on TiO2(110)

Metal complexes of the tetradentate bipyridine based macrocycle pyrphyrin (Pyr) have recently shown promise as water reduction catalysts in homogeneous photochemical water splitting reactions. In this study, the adsorption and metalation of pyrphyrin on stoichiometric TiO₂(110) is investigated in ultrahigh vacuum by means of scanning tunneling microscopy, photoelectron spectroscopy, low-energy electron diffraction, and density functional theory. In a joint experimental and computational effort, the local adsorption geometry at low coverage, the long-range molecular ordering at higher coverage and the electronic structure have been determined for both the bare ligand and the cobalt-metalated Pyr molecule on TiO₂. The energy level alignment of CoPyr/TiO₂ supports electron injection into TiO₂ upon photoexcitation of the CoPyr complex and thus renders it a potential sensitizer dye. Importantly, Co-incorporation is found to stabilize the Pyr molecule against photo-induced degradation, while the bare ligand is decomposed rapidly under continuous UV-irradiation. This interesting phenomenon is discussed in terms of additional de-excitation channels for electronically highly excited molecular states.

Computing the Kirkwood g-Factor by Combining Constant Maxwell Electric Field and Electric Displacement Simulations: Application to the Dielectric Constant of Liquid Water

In his classic 1939 paper, Kirkwood linked the macroscopic dielectric constant of polar liquids to the local orientational order as measured by the g-factor (later named after him) and suggested that the corresponding dielectric constant at short-range is effectively equal to the macroscopic value just after "a distance of molecular magnitude" [ Kirkwood, J. Chem. Phys., 1939, 7, 911 ]. Here, we show a simple approach to extract the short-ranged Kirkwood g-factor from molecular dynamics (MD) simulation by superposing the outcomes of constant electric field E and constant electric displacement D simulations [ Zhang and Sprik, Phys. Rev. B: Condens. Matter Mater. Phys., 2016, 93, 144201 ]. Rather than from the notoriously slow fluctuations of the dipole moment of the full MD cell, the dielectric constant can now be estimated from dipole fluctuations at short-range, accelerating the convergence. Exploiting this feature, we computed the bulk dielectric constant of liquid water modeled in the generalized gradient approximation (PBE) to density functional theory and found it to be at least 40% larger than the experimental value.

From porphyrins to pyrphyrins: adsorption study and metalation of a molecular catalyst on Au(111)

The molecular ligand pyrphyrin, a tetradentate bipyridine based macrocycle, represents an interesting but widely unexplored class of molecules. It resembles the well-known porphyrin, but consists of pyridyl subunits instead of pyrroles. Metal complexes based on pyrphyrin ligands have recently shown promise as water reduction catalysts in homogeneous photochemical water splitting reactions. In this study, the adsorption and metalation of pyrphyrin on a single crystalline Au(111) surface is investigated in an ultrahigh vacuum by means of scanning tunneling microscopy, low-energy electron diffraction, X-ray photoelectron spectroscopy and density functional theory. Pyrphyrin coverages of approximately one monolayer and less are obtained by sublimation of the molecules on the substrate kept at room temperature. The molecules self-assemble in two distinct phases of long-range molecular ordering depending on the surface coverage. The deposition of cobalt metal and subsequent annealing lead to the formation of Co-ligated pyrphyrin molecules accompanied by a pronounced change of the molecular self-assembly. Electronic structure calculations taking the herringbone reconstruction of Au(111) into account show that the molecules are physisorbed, but preferred adsorption sites are identified where Co and the N atoms of the two terminal cyano groups are optimally coordinated to the surface Au atoms. An intermediate state of the metalation reaction is observed and the reaction steps for the Co metalation of pyrphyrin molecules on Au(111) are established in a joint experimental and computational effort.

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Wetting of water on hexagonal boron nitride@Rh(111): a QM/MM model based on atomic charges derived for nano-structured substrates

The wetting of water on corrugated and flat hexagonal boron nitride (h-BN) monolayers on Rh(111) is studied within a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. Water is treated by QM methods, whereas the interactions between liquid and substrate are described at the MM level. The electrostatic properties of the substrate are reproduced by assigning specifically generated partial charges to each MM atom. We propose a method to determine restrained electrostatic potential (RESP) charges that can be applied to periodic systems. Our approach is based on the Gaussian and plane waves algorithm and allows an easy tuning of charges for nano-structured substrates. We have successfully applied it to reproduce the electrostatic potential of the corrugated and flat h-BN/Rh(111) known as nanomesh. Molecular dynamics simulations of water films in contact with these substrates are performed and structural and dynamic properties of the interfaces are analyzed. Based on this analysis and on the interaction energies between water film and substrate, we found that the corrugated nanomesh is slightly more hydrophilic. On a macroscopic scale, we expect a smaller contact angle for a droplet on the corrugated surface.

Dividing a complex reaction involving a hypervalent iodine reagent into three limiting mechanisms by ab initio molecular dynamics

The electrophilic N-trifluoromethylation of MeCN with a hypervalent iodine reagent to form a nitrilium ion, that is rapidly trapped by an azole nucleophile, is thought to occur via reductive elimination (RE). A recent study showed that, depending on the solvent representation, the S(N)2 is favoured to a different extent over the RE. However, there is a discriminative solvent effect present, which calls for a statistical mechanics approach to fully account for the entropic contributions. In this study, we perform metadynamic simulations for two trifluoromethylation reactions (with N- and S-nucleophiles), showing that the RE mechanism is always favoured in MeCN solution. These computations also indicate that a radical mechanism (single electron transfer) may play an important role. The computational protocol based on accelerated molecular dynamics for the exploration of the free energy surface is transferable and will be applied to similar reactions to investigate other electrophiles on the reagent. Based on the activation parameters determined, this approach also gives insight into the mechanistic details of the trifluoromethylation and shows that these commonly known mechanisms mark the limits within which the reaction proceeds.

Non-innocent adsorption of Co-pyrphyrin on rutile(110)

Co-pyrphyrin adsorbed on rutile(110) as a supported catalyst for water reduction.

Dehalogenation and coupling of a polycyclic hydrocarbon on an atomically thin insulator

Catalytic activity is of pivotal relevance in enabling efficient and selective synthesis processes. Recently, covalent coupling reactions catalyzed by solid metal surfaces opened the rapidly evolving field of on-surface chemical synthesis. Tailored molecular precursors in conjunction with the catalytic activity of the metal substrate allow the synthesis of novel, technologically highly relevant materials such as atomically precise graphene nanoribbons. However, the reaction path on the metal substrate remains unclear in most cases, and the intriguing question is how a specific atomic configuration between reactant and catalyst controls the reaction processes. In this study, we cover the metal substrate with a monolayer of hexagonal boron nitride (h-BN), reducing the reactivity of the metal, and gain unique access to atomistic details during the activation of a polyphenylene precursor by sequential dehalogenation and the subsequent coupling to extended oligomers. We use scanning tunneling microscopy and density functional theory to reveal a reaction site anisotropy, induced by the registry mismatch between the precursor and the nanostructured h-BN monolayer.

Control of molecular organization and energy level alignment by an electronically nanopatterned boron nitride template

Suitable templates to steer the formation of nanostructure arrays on surfaces are indispensable in nanoscience. Recently, atomically thin sp(2)-bonded layers such as graphene or boron nitride (BN) grown on metal supports have attracted considerable interest due to their potential geometric corrugation guiding the positioning of atoms, metallic clusters or molecules. Here, we demonstrate three specific functions of a geometrically smooth, but electronically corrugated, sp(2)/metal interface, namely, BN/Cu(111), qualifying it as a unique nanoscale template. As functional adsorbates we employed free-base porphine (2H-P), a prototype tetrapyrrole compound, and tetracyanoquinodimethane (TCNQ), a well-known electron acceptor. (i) The electronic moirons of the BN/Cu(111) interface trap both 2H-P and TCNQ, steering self-organized growth of arrays with extended molecular assemblies. (ii) We report an effective decoupling of the trapped molecules from the underlying metal support by the BN, which allows for a direct visualization of frontier orbitals by scanning tunneling microscopy (STM). (iii) The lateral molecular positioning in the superstructured surface determines the energetic level alignment; i.e., the energy of the frontier orbitals, and the electronic gap are tunable.