Efficient Spin-Adapted Implementation of Multireference Algebraic Diagrammatic Construction Theory. I. Core-Ionized States and X-ray Photoelectron Spectra.

We present an efficient implementation of multireference algebraic diagrammatic construction theory (MR-ADC) for simulating core-ionized states and X-ray photoelectron spectra (XPS). Taking advantage of spin adaptation, automatic code generation, and density fitting, our implementation can perform calculations for molecules with more than 1500 molecular orbitals, incorporating static and dynamic correlation in the ground and excited electronic states. We demonstrate the capabilities of MR-ADC methods by simulating the XPS spectra of substituted ferrocene complexes and azobenzene isomers. For the ground electronic states of these molecules, the XPS spectra computed using the extended second-order MR-ADC method (MR-ADC(2)-X) are in a very good agreement with available experimental results. We further show that MR-ADC can be used as a tool for interpreting or predicting the results of time-resolved XPS measurements by simulating the core ionization spectra of azobenzene along its photoisomerization, including the XPS signatures of excited states and the minimum energy conical intersection. This work is the first in a series of publications reporting the efficient implementations of MR-ADC methods.

Ebullition dominates methane emissions in stratified coastal waters.

Coastal areas are an important source of methane (CH4). However, the exact origins of CH4 in the surface waters of coastal regions, which in turn drive sea-air emissions, remain uncertain. To gain a comprehensive understanding of the current and future climate change feedbacks, it is crucial to identify these CH4 sources and processes that regulate its formation and oxidation. This study investigated coastal CH4 dynamics by comparing water column data from six stations located in the brackish Tvärminne Archipelago, Baltic Sea. The sediment biogeochemistry and microbiology were further investigated at two stations (i.e., nearshore and offshore). These stations differed in terms of stratification, bottom water redox conditions, and organic matter loading. At the nearshore station, CH4 diffusion from the sediment into the water column was negligible, because nearly all CH4 was oxidized within the upper sediment column before reaching the sediment surface. On the other hand, at the offshore station, there was significant benthic diffusion of CH4, albeit the majority underwent oxidation before reaching the sediment-water interface, due to shoaling of the sulfate methane transition zone (SMTZ). The potential contribution of CH4 production in the water column was evaluated and was found to be negligible. After examining the isotopic signatures of δ13C-CH4 across the sediment and water column, it became apparent that the surface water δ13C-CH4 values observed in areas with thermal stratification could not be explained by diffusion, advective fluxes, nor production in the water column. In fact, these values bore a remarkable resemblance to those detected below the SMTZ. This supports the hypothesis that the source of CH4 in surface waters is more likely to originate from ebullition than diffusion in stratified brackish coastal systems.

Quantifying spin contamination in algebraic diagrammatic construction theory of electronic excitations.

Algebraic diagrammatic construction (ADC) is a computationally efficient approach for simulating excited electronic states, absorption spectra, and electron correlation. Due to their origin in perturbation theory, the single-reference ADC methods may be susceptible to spin contamination when applied to molecules with unpaired electrons. In this work, we develop an approach to quantify spin contamination in the ADC calculations of electronic excitations and apply it to a variety of open-shell molecules starting with either the unrestricted (UHF) or restricted open-shell (ROHF) Hartree-Fock reference wavefunctions. Our results show that the accuracy of low-order ADC approximations [ADC(2) and ADC(3)] significantly decreases when the UHF reference spin contamination exceeds 0.05 a.u. Such strongly spin-contaminated molecules exhibit severe excited-state spin symmetry breaking that contributes to decreasing the quality of computed excitation energies and oscillator strengths. In a case study of phenyl radical, we demonstrate that spin contamination can significantly affect the simulated UV/Vis spectra, altering the relative energies, intensities, and order of electronic transitions. The results presented here motivate the development of spin-adapted ADC methods for open-shell molecules.

Consistent Second-Order Treatment of Spin-Orbit Coupling and Dynamic Correlation in Quasidegenerate N-Electron Valence Perturbation Theory.

We present a formulation and implementation of second-order quasidegenerate N-electron valence perturbation theory (QDNEVPT2) that provides a balanced and accurate description of spin-orbit coupling and dynamic correlation effects in multiconfigurational electronic states. In our approach, the energies and wave functions of electronic states are computed by treating electron repulsion and spin-orbit coupling operators as equal perturbations to the nonrelativistic complete active-space wave functions, and their contributions are incorporated fully up to the second order. The spin-orbit effects are described using the Breit-Pauli (BP) or exact two-component Douglas-Kroll-Hess (DKH) Hamiltonians within spin-orbit mean-field approximation. The resulting second-order methods (BP2- and DKH2-QDNEVPT2) are capable of treating spin-orbit coupling effects in nearly degenerate electronic states by diagonalizing an effective Hamiltonian expanded in a compact non-relativistic basis. For a variety of atoms and small molecules across the entire periodic table, we demonstrate that DKH2-QDNEVPT2 is competitive in accuracy with variational two-component relativistic theories. BP2-QDNEVPT2 shows high accuracy for the second- and third-period elements, but its performance deteriorates for heavier atoms and molecules. We also consider the first-order spin-orbit QDNEVPT2 approximations (BP1- and DKH1-QDNEVPT2), among which DKH1-QDNEVPT2 is reliable but less accurate than DKH2-QDNEVPT2. Both DKH1- and DKH2-QDNEVPT2 hold promise as efficient and accurate electronic structure methods for treating electron correlation and spin-orbit coupling in a variety of applications.

Simulating transient X-ray photoelectron spectra of Fe(CO)5 and its photodissociation products with multireference algebraic diagrammatic construction theory.

Accurate simulations of transient X-ray photoelectron spectra (XPS) provide unique opportunities to bridge the gap between theory and experiment in understanding the photoactivated dynamics in molecules and materials. However, simulating X-ray photoelectron spectra along a photochemical reaction pathway is challenging as it requires accurate description of electronic structure incorporating core-hole screening, orbital relaxation, electron correlation, and spin-orbit coupling in excited states or at nonequilibrium ground-state geometries. In this work, we employ the recently developed multireference algebraic diagrammatic construction theory (MR-ADC) to investigate the core-ionized states and X-ray photoelectron spectra of Fe(CO)5 and its photodissociation products (Fe(CO)4, Fe(CO)3) following excitation with 266 nm light. The simulated transient Fe 3p and CO 3σ XPS spectra incorporating spin-orbit coupling and high-order electron correlation effects are shown to be in a good agreement with the experimental measurements by Leitner et al. [J. Chem. Phys., 2018, 149, 044307]. Our calculations suggest that core-hole screening, spin-orbit coupling, and ligand-field splitting effects are similarly important in reproducing the experimentally observed chemical shifts in transient Fe 3p XPS spectra of iron carbonyl complexes. Our results also demonstrate that the MR-ADC methods can be very useful in interpreting the transient XPS spectra of transition metal compounds.

Dynamic brain communication underwriting face pareidolia.

Face pareidolia is a tendency to seeing faces in nonface images that reflects high tuning to a face scheme. Yet, studies of the brain networks underwriting face pareidolia are scarce. Here, we examined the time course and dynamic topography of gamma oscillatory neuromagnetic activity while administering a task with nonface images resembling a face. Images were presented either with canonical orientation or with display inversion that heavily impedes face pareidolia. At early processing stages, the peaks in gamma activity (40 to 45 Hz) to images either triggering or not face pareidolia originate mainly from the right medioventral and lateral occipital cortices, rostral and caudal cuneus gyri, and medial superior occipital gyrus. Yet, the difference occurred at later processing stages in the high-frequency range of 80 to 85 Hz over a set of the areas constituting the social brain. The findings speak rather for a relatively late neural network playing a key role in face pareidolia. Strikingly, a cutting-edge analysis of brain connectivity unfolding over time reveals mutual feedforward and feedback intra- and interhemispheric communication not only within the social brain but also within the extended large-scale network of down- and upstream regions. In particular, the superior temporal sulcus and insula strongly engage in communication with other brain regions either as signal transmitters or recipients throughout the whole processing of face-pareidolia images.

NIR-II emissive donor-acceptor-donor fluorophores for dual fluorescence bioimaging and photothermal therapy applications.

Fluorescence bioimaging with near-infrared II (NIR-II) emissive organic fluorophores has proven to be a viable noninvasive diagnostic technique. However, there is still the need for the development of fluorophores that possess increased stability as well as functionalities that impart stimuli responsiveness. Through strategic design, we can synthesize fluorophores that possess not only NIR-II optical profiles but also pH-sensitivity and the ability to generate heat upon irradiation. In this work, we employ a donor-acceptor-donor (D-A-D) design to synthesize a series of NIR-II fluorophores. Here we use thienothiadiazole (TTD) as the acceptor, 3-hexylthiophene (HexT) as the π-spacer and vary the alkyl amine donor units: N,N-dimethylaniline (DMA), phenylpiperidine (Pip), and phenylmorpholine (Morp). Spectroscopic analysis shows that all three derivatives exhibit emission in the NIR-II region with λemimax ranging from 1030 to 1075 nm. Upon irradiation, the fluorophores exhibited noticeable heat generation through non-radiative processes. The ability to generate heat indicates that these fluorophores will act as theranostic (combination therapeutic and diagnostic) agents in which simultaneous visualization and treatment can be performed. Additionally, biosensing capabilities were supported by changes in the absorbance properties while under acidic conditions as a result of protonation of the alkyl amine donor units. The fluorophores also show minimal toxicity in a human mammary cell line and with murine red blood cells. Overall, initial results indicate viable NIR-II materials for multiple biomedical applications.

Quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains reveal contradictions in the historical assignments of the strains and indicate the need for species reclassification.

This article reports the results of quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains and a novel endophytic bacterium (SG) isolated from a suspension culture of Arabidopsis thaliana (L.) Heynh in our laboratory. The known strain Rothia sp. ND6WE1A was used as a reference one for SG. Whole-genome sequencing and phylogenetic analysis were based on the 16S rRNA test. Quantitative analysis for the nucleotide identity (ANI) and calculation of evolutionary distances were based on the identified amino acids (AAI) test indicating the generic assignment of the reference strain within and between the identified monophyletic groups of Micrococcaceae. The amino acid data structure of Rothia sp. ND6WE1A was compared against the UniProt database (250 million records) of close lineage of Micrococcaceae, including other Rothia spp. These data presented unique and evolutionary amino acid alignments, eventually expected in the new SG isolate as well. The metagenomic entries of the respective genome and proteome, characterized at the genus and species levels, could be considered for evolutionary taxonomic reclassification of the isolated and the reference strain (SG + Rothia sp. ND6WE1A). Therefore, our results warrant further investigations on the isolated SG strain.

Emotions behind a mask: the value of disgust.

The impact of face masks on social cognition and interaction became a popular topic due to the long-lasting COVID-19 pandemic. This theme persists in the focus of attention beyond the pandemic, since face covering not only reduces the overall amount of face information available but also introduces biases and prejudices affecting social perception at large. Many questions are still open. One of them is whether gender of beholders affects inferring of emotions covered by face masks. Reading covered faces may be particularly challenging for individuals with mental disorders, most of which are gender-specific. Previous findings are not only sparse, but inconclusive because most research had been conducted online with resulting samples heavily dominated by females. Here in a face-to-face study, females and males were presented with a randomized set of faces covered by masks. In a two-alternative forced-choice paradigm, participants had to indicate facial emotions displayed by posers. In general, the outcome dovetails with earlier findings that face masks affect emotion recognition in a dissimilar way: Inferring some emotions suffers more severely than others, with the most pronounced influence of mask wearing on disgust and close to ceiling recognition of fear and neutral expressions. Contrary to our expectations, however, males were on overall more proficient in emotion recognition. In particular, males substantially excelled in inferring disgust. The findings help to understand gender differences in recognition of disgust, the forgotten emotion of psychiatry, that is of substantial value for a wide range of mental disorders including schizophrenia. Watch Prof. Marina Pavlova discussing this her work and this article: https://vimeo.com/860126397/5966610f49?share=copy .

Relationship between journal impact factor and the thoroughness and helpfulness of peer reviews.

The Journal Impact Factor is often used as a proxy measure for journal quality, but the empirical evidence is scarce. In particular, it is unclear how peer review characteristics for a journal relate to its impact factor. We analysed 10,000 peer review reports submitted to 1,644 biomedical journals with impact factors ranging from 0.21 to 74.7. Two researchers hand-coded sentences using categories of content related to the thoroughness of the review (Materials and Methods, Presentation and Reporting, Results and Discussion, Importance and Relevance) and helpfulness (Suggestion and Solution, Examples, Praise, Criticism). We fine-tuned and validated transformer machine learning language models to classify sentences. We then examined the association between the number and percentage of sentences addressing different content categories and 10 groups defined by the Journal Impact Factor. The median length of reviews increased with higher impact factor, from 185 words (group 1) to 387 words (group 10). The percentage of sentences addressing Materials and Methods was greater in the highest Journal Impact Factor journals than in the lowest Journal Impact Factor group. The results for Presentation and Reporting went in the opposite direction, with the highest Journal Impact Factor journals giving less emphasis to such content. For helpfulness, reviews for higher impact factor journals devoted relatively less attention to Suggestion and Solution than lower impact factor journals. In conclusion, peer review in journals with higher impact factors tends to be more thorough, particularly in addressing study methods while giving relatively less emphasis to presentation or suggesting solutions. Differences were modest and variability high, indicating that the Journal Impact Factor is a bad predictor of the quality of peer review of an individual manuscript.

Two-State Hydrogen Atom Transfer Reactivity of Unsymmetric [Cu2(O)(NO)]2+ Complexes.

We report the temperature-dependent spin switching of dicopper oxo nitrosyl [Cu2(O)(NO)]2+ complexes and their influence on hydrogen atom transfer (HAT) reactivity. Electron paramagnetic resonance (EPR) and Evans method analysis suggest that [Cu2(O)(NO)]2+ complexes transition from the S = 1/2 to the S = 3/2 state around ca. 202 K. At low temperatures (198 K) where S = 3/2 dominates, a strong correlation between the rate of HAT (kHAT) and the population of the S = 1/2 state was identified (R2 = 0.988), suggesting that the HAT by [Cu2(O)(NO)]2+ complexes proceeds by the S = 1/2 isomer. Installation of functional groups that introduce an unsymmetric secondary coordination environment accelerates the HAT rates through perturbation of the spin equilibria. Given the often unsymmetric coordination sphere of bimetallic active sites in natural proteins, we anticipate that similar strategies could be employed by metalloenzymes to control HAT reactions.

Core-Excited States and X-ray Absorption Spectra from Multireference Algebraic Diagrammatic Construction Theory.

We report the development and benchmark of multireference algebraic diagrammatic construction theory (MR-ADC) for the simulations of core-excited states and X-ray absorption spectra (XAS). Our work features an implementation that incorporates core-valence separation into the strict and extended second-order MR-ADC approximations (MR-ADC(2) and MR-ADC(2)-X), providing efficient access to high-energy excited states without including inner-shell orbitals in the active space. Benchmark results on a set of small molecules indicate that at equilibrium geometries, the accuracy of MR-ADC is similar to that of single-reference ADC theory when static correlation effects are not important. In this case, MR-ADC(2)-X performs similarly to single- and multireference coupled cluster methods in reproducing the experimental XAS peak spacings. We demonstrate the potential of MR-ADC for chemical systems with multiconfigurational electronic structure by calculating the K-edge XAS spectrum of the ozone molecule with a multireference character in its ground electronic state and the dissociation curve of core-excited molecular nitrogen. For ozone, the MR-ADC results agree well with the data from experimental and previous multireference studies of ozone XAS, in contrast to the results of single-reference methods, which underestimate relative peak energies and intensities. The MR-ADC methods also predict the correct shape of the core-excited nitrogen potential energy curve, and are in good agreement with accurate calculations using driven similarity renormalization group approaches. These findings suggest that MR-ADC(2) and MR-ADC(2)-X are promising methods for the XAS simulations of multireference systems and pave the way for their efficient computer implementation and applications.

Do subtle cultural differences sculpt face pareidolia?

Face tuning to non-face images such as shadows or grilled toasts is termed face pareidolia. Face-pareidolia images represent a valuable tool for investigation of social cognition in mental disorders. Here we examined (i) whether, and, if so, how face pareidolia is affected by subtle cultural differences; and (ii) whether this impact is modulated by gender. With this purpose in mind, females and males from Northern Italy were administered a set of Face-n-Thing images, photographs of objects such as houses or waves to a varying degree resembling a face. Participants were presented with pareidolia images with canonical upright orientation and display inversion that heavily affects face pareidolia. In a two-alternative forced-choice paradigm, beholders had to indicate whether each image resembled a face. The outcome was compared with the findings obtained in the Southwest of Germany. With upright orientation, neither cultural background nor gender affected face pareidolia. As expected, display inversion generally mired face pareidolia. Yet, while display inversion led to a drastic reduction of face impression in German males as compared to females, in Italians, no gender differences were found. In a nutshell, subtle cultural differences do not sculpt face pareidolia, but instead affect face impression in a gender-specific way under unusual viewing conditions. Clarification of the origins of these effects requires tailored brain imaging work. Implications for transcultural psychiatry, in particular, for schizophrenia research, are highlighted and discussed.

Algebraic Diagrammatic Construction Theory for Simulating Charged Excited States and Photoelectron Spectra.

Charged excitations are electronic transitions that involve a change in the total charge of a molecule or material. Understanding the properties and reactivity of charged species requires insights from theoretical calculations that can accurately describe orbital relaxation and electron correlation effects in open-shell electronic states. In this Review, we describe the current state of algebraic diagrammatic construction (ADC) theory for simulating charged excitations and its recent developments. We start with a short overview of ADC formalism for the one-particle Green's function, including its single- and multireference formulations and extension to periodic systems. Next, we focus on the capabilities of ADC methods and discuss recent findings about their accuracy for calculating a wide range of excited-state properties. We conclude our Review by outlining possible directions for future developments of this theoretical approach.

Electronic Structure and Ultrafast Electron Dynamics in CuO Photocatalysts Probed by Surface Sensitive Femtosecond X-ray Absorption Near-Edge Structure Spectroscopy.

CuO is often employed as a photocathode for H2 evolution and CO2 reduction, but observed efficiency is still far below the theoretical limit. To bridge the gap requires understanding the CuO electronic structure; however, computational efforts lack consensus on the orbital character of the photoexcited electron. In this study, we measure the femtosecond XANES spectra of CuO at the Cu M2,3 and O L1 edges to track the element-specific dynamics of electrons and holes. Results show that photoexcitation represents an O 2p to Cu 4s charge transfer state indicating the conduction band electron has primarily Cu 4s character. We also observe ultrafast mixing of Cu 3d and 4s conduction band states mediated by coherent phonons, with Cu 3d character of the photoelectron reaching a maximum of 16%. This is the first observation of the photoexcited redox state in CuO, and results provide a benchmark for theory where electronic structure modeling still relies heavily on model-dependent parametrization.

C(sp3)-H cyanation by a formal copper(iii) cyanide complex.

High-valent metal oxo complexes are prototypical intermediates for the activation and hydroxylation of alkyl C-H bonds. Substituting the oxo ligand with other functional groups offers the opportunity for additional C-H functionalization beyond C-O bond formation. However, few species aside from metal oxo complexes have been reported to both activate and functionalize alkyl C-H bonds. We herein report the first example of an isolated copper(iii) cyanide complex (LCuIIICN) and its C-H cyanation reactivity. We found that the redox potential (E ox) of substrates, instead of C-H bond dissociation energy, is a key determinant of the rate of PCET, suggesting an oxidative asynchronous CPET or ETPT mechanism. Among substrates with the same BDEs, those with low redox potentials transfer H atoms up to a million-fold faster. Capitalizing on this mechanistic insight, we found that LCuIIICN is highly selective for cyanation of amines, which is predisposed to oxidative asynchronous or stepwise transfer of H+/e-. Our study demonstrates that the asynchronous effect of PCET is an appealing tool for controlling the selectivity of C-H functionalization.

Simulating Spin-Orbit Coupling with Quasidegenerate N-Electron Valence Perturbation Theory.

We present the first implementation of spin-orbit coupling effects in fully internally contracted second-order quasidegenerate N-electron valence perturbation theory (SO-QDNEVPT2). The SO-QDNEVPT2 approach enables the computations of ground- and excited-state energies and oscillator strengths combining the description of static electron correlation with an efficient treatment of dynamic correlation and spin-orbit coupling. In addition to SO-QDNEVPT2 with the full description of one- and two-body spin-orbit interactions at the level of two-component Breit-Pauli Hamiltonian, our implementation also features a simplified approach that takes advantage of spin-orbit mean-field approximation (SOMF-QDNEVPT2). The accuracy of these methods is tested for the group 14 and 16 hydrides, 3d and 4d transition metal ions, and two actinide dioxides (neptunyl and plutonyl dications). The zero-field splittings of group 14 and 16 molecules computed using SO-QDNEVPT2 and SOMF-QDNEVPT2 are in good agreement with the available experimental data. For the 3d transition metal ions, the SO-QDNEVPT2 method is significantly more accurate than SOMF-QDNEVPT2, while no substantial difference in the performance of two methods is observed for the 4d ions. Finally, we demonstrate that for the actinide dioxides the results of SO-QDNEVPT2 and SOMF-QDNEVPT2 are in good agreement with the data from previous theoretical studies of these systems. Overall, our results demonstrate that SO-QDNEVPT2 and SOMF-QDNEVPT2 are promising multireference methods for treating spin-orbit coupling with a relatively low computational cost.

Neural circuits underpinning face tuning in male depression.

Reading bodies and faces is essential for efficient social interactions, though it may be thought-provoking for individuals with depression. Yet aberrations in the face sensitivity and underwriting neural circuits are not well understood, in particular, in male depression. Here, we use cutting-edge analyses of time course and dynamic topography of gamma oscillatory neuromagnetic cortical activity during administration of a task with Arcimboldo-like images. No difference in face tuning was found between individuals with depression and their neurotypical peers. Furthermore, this behavioral outcome nicely dovetails with magnetoencephalographic data: at early processing stages, the gamma oscillatory response to images resembling a face was rather similar in patients and controls. These bursts originated primarily from the right medioventral occipital cortex and lateral occipital cortex. At later processing stages, however, its topography altered remarkably in depression with profound engagement of the frontal circuits. Yet the primary difference in depressive individuals as compared with their neurotypical peers occurred over the left middle temporal cortices, a part of the social brain, engaged in feature integration and meaning retrieval. The outcome suggests compensatory recruitment of neural resources in male depression.

Face pareidolia in male schizophrenia.

Faces are valuable signals for efficient social interaction. Yet, social cognition including the sensitivity to a coarse face scheme may be deviant in schizophrenia (SZ). Tuning to faces in non-face images such as shadows, grilled toasts, or ink blots is termed face pareidolia. This phenomenon is poorly investigated in SZ. Here face tuning was assessed in 44 male participants with SZ and person-by-person matched controls by using recently created Face-n-Thing images (photographs of non-face objects to a varying degree resembling a face). The advantage of these images is that single components do not automatically trigger face processing. Participants were administered a set of images with upright and inverted (180° in the image plane) orientation. In a two-alternative forced-choice paradigm, they had to indicate whether an image resembled a face. The findings showed that: (i) With upright orientation, SZ patients exhibited deficits in face tuning: they provided much fewer face responses than controls. (ii) Inversion generally hindered face pareidolia. However, while in neurotypical males, inversion led to a drastic drop in face impression, in SZ, the impact of orientation was reduced. (iii) Finally, in accord with the signal detection theory analysis, the sensitivity index (d-prime) was lower in SZ, whereas no difference occurred in decision criterion. The outcome suggests altered face pareidolia in SZ is caused by lower face sensitivity rather than by alterations in cognitive bias. Comparison of these findings with earlier evidence confirms that tuning to social signals is lower in SZ, and warrants tailored brain imaging research.