Search

Tree structure and diversity of a secondary Atlantic Forest resulting from the abandonment (ca. 70 years) of a shaded coffee (Coffea arabica) plantation was studied in southeastern Brazil. All trees with DBH ≥ 5 cm (alive and dead) were measured in 25 plots of 20 × 20 m. Out of the 1926 sampled trees, 1837 were living trees belonging to 116 species. The most important species (importance value - IV) in the community were Euterpe edulis (22.9% - present in all plots) and Piptadenia gonoacantha (16.5%). Euterpe edulis is a typical palm tree of high importance value in mature forests, comprising 41.2% of individuals. The results show a more mature tree community in relation to other secondary forests with the same abandonment period in the region, with high richness and diversity of species, high basal area, and low dead tree density. In addition, several endangered species were recorded with high conservation value for the regional flora. The results also showed many typical characteristics of “novel ecosystems” discussed here in order to value these environments, still neglected due to strong environmental human alterations.

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

The Chronus Quantum (ChronusQ) software package is an open source (under the GNU General Public License v2) software infrastructure which targets the solution of challenging problems that arise in ab initio electronic structure theory. Special emphasis is placed on the consistent treatment of time dependence and spin in the electronic wave function, as well as the inclusion of relativistic effects in said treatments. In addition, ChronusQ provides support for the inclusion of uniform finite magnetic fields as external perturbations through the use of gauge-including atomic orbitals. ChronusQ is a parallel electronic structure code written in modern C++ which utilizes both message passing implementation and shared memory (OpenMP) parallelism. In addition to the examination of the current state of code base itself, a discussion regarding ongoing developments and developer contributions will also be provided. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Ab Initio Electronic Structure Methods Electronic Structure Theory > Density Functional Theory.

Eruption cysts are soft tissue analogs of dentigerous cysts and are frequently observed in children under 10 years of age, coinciding with the eruption of deciduous teeth. It is rare to encounter eruption cysts in neonates, as tooth eruption is typically uncommon at such an early age. We present a unique case of a 26-hour-old twin male infant referred to the pediatric oral and maxillofacial surgeon at the Riley Hospital for Children at Indiana University Health for assessment of a pink-colored cystic swelling on the anterior mandibular alveolar ridge. Given the increasing challenges with latching and feeding, the decision was made to opt for surgical excision of the lesion. A radiograph of the area could not be obtained due to the inaccessibility associated with the neonate. During the excisional surgical procedure, two mandibular incisors, identified as natal teeth, were noted, and subsequently extracted due to excessive mobility and aspiration risk. The excised tissue was submitted to the Oral Pathology Group at Indiana University School of Dentistry. Microscopic examination of the submitted tissue confirmed the diagnosis of a congenital eruption cyst. Regular follow-ups are scheduled to monitor the progression of teeth eruption. Here, we present the first report of a congenital eruption cyst with histopathological features. Surgical excision was opted for in our case due to the feeding challenges; however, these cysts could be monitored clinically as they may regress spontaneously in most cases. [ABSTRACT FROM AUTHOR]

The Melissa officinalisL. (Lamiaceae) presents high levels of phenolic compounds that have a serie of biological effects, as anti-inflammatory that inhibits the activity of cyclooxygenase and inhibition of Cytochromes P450. Due to his biological effects, it is in evidence in diverse studies. They are present in vegetables and in diverse forms in our food, like tea and herbal capsules. The objective this study was to compare the difference in availability of active molecules from medicinal plants in two different forms of use, capsules and tea. After simulation in vitro of gastric digestion, the total phenolic compounds were determined employing a spectrophotometric method Folin-Ciocalteau. We obtained higher values of total phenols in the digestion of capsules than in Melissa officinalis. It indicates that probably the capsules presents more availability of active ingredients that infusions. It is worth mentioning the need for further studies to compare the total phenol content of Melissa officinalisinfusions, as well as the use of other plants to verify the best use of medicinal plants.

Metallo dithiolene complexes with biological and catalytic relevance are well-known for having strong metal-ligand covalency, which dictates their valence electronic structures. We present the resonant sulfur Kβ (1s3p) X-ray emission spectroscopy (XES) for a series of Ni and Cu bis(dithiolene) complexes to reveal the ligand sulfur contributions to both the occupied and unoccupied valence orbitals. While S K-edge X-ray absorption spectroscopy played a critical role in identifying the covalency of the unoccupied orbitals of metal dithiolenes, the present focus on XES explores the occupied density of states. For a series of [Cu(mnt) 2 ] n - and [Ni(mnt) 2 ] n - anions and dianions, a comparison of the nonresonant and resonant S Kβ XES spectra highlights the dramatic improvement in spectral resolution and corresponding ability to differentiate subtle changes in occupied electronic structure across the series. Furthermore, the use of resonant inelastic X-ray scattering (RIXS) probes the valence excited states and the core-valence couplings of the complexes. By employing a theoretical approach based on time-dependent density functional theory to interpret the RIXS spectra, we reveal how metal-ligand covalency influences the excited state energies and covalencies. We identify the low energy excited states as having the same symmetry as the nominal "ligand field" or "d-d" states that typically dominate the photophysics of 3d metal complexes but with significant metal-ligand charge transfer character dictated by their covalency. These results suggest that strong metal-ligand covalency can be used to influence the charge-transfer photochemistry of first row transition metal complexes.

Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain on π π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained by n π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of the π π * state leading to a wrong π π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers., (© 2024 American Society for Photobiology.)

This study aims to investigate the effects of melatonin on follicular growth, viability and ultrastructure, as well as on the levels of mRNA for antioxidant enzymes, reactive oxygen species (ROS) and meiotic progression in oocytes from in vitro cultured bovine early antral follicles. To this end, isolated early antral follicles (500-600 μm) were cultured in TCM-199 + alone or supplemented with 10 -6 , 10 -7 or 10 -8  M melatonin at 38.5°C with 5% CO 2 for 8 days. Follicle diameters were evaluated at days 0, 4 and 8 of culture. At the end of culture, ultrastructure, chromatin configuration, viability (calcein-AM and ethidium homodimer-1 staining), and the levels of ROS and mRNA for catalase (CAT), superoxide dismutase (SOD) and peroxiredoxin 6 (PRDX6) and glutathione peroxidase (GPx) were investigated in oocyte-granulosa cell complexes (OGCs). The results showed that early antral follicles cultured with 10 -6 and 10 -8  M melatonin had a progressive and significant increase in their diameters throughout the culture period (p < .05). Additionally, oocytes from follicles cultured with 10 -7 or 10 -8  M melatonin had increased fluorescence for calcein-AM, while those cultured with 10 -6 or 10 -7  M had reduced fluorescence for ethidium homodimer-1. Different from follicles cultured in other treatments, those cultured with 10 -8  M melatonin had well-preserved ultrastructure of oocyte and granulosa cells. Melatonin, however, did not influence the levels of ROS, the mitochondrial activity, oocyte meiotic resumption and expression mRNA for SOD, CAT, GPX1 and PRDX6. In conclusion, the presence of 10 -8  M melatonin in culture medium improves viability and preserves the ultrastructure of oocyte and granulosa cells of early antral follicles cultured in vitro., (© 2024 Wiley-VCH GmbH. Published by John Wiley & Sons Ltd.)

This study investigated the effects of cyclic adenosine monophosphate modulating during cumulus-oocyte complexes (COCs) pre-maturation and the role of melatonin on in vitro maturation (IVM) of bovine COCs. In experiment one, COCs were pre-matured for 8 h in control medium or with 3-isobutyl-1-methylxanthine (IBMX) and forskolin, IBMX and C-type natriuretic peptide, c-type natriuretic peptide and forskolin or IBMX, forskolin and c-type natriuretic peptide. Then, meiotic progression was evaluated. In experiment two, COCs were pre-matured, followed by IVM in control medium alone or with 10 -6 , 10 -7 or 10 -8 M melatonin. After IVM, chromatin configuration, transzonal projections (TZPs), reactive oxygen species, mitochondrial distribution, ultrastructure and mRNA expression for antioxidant enzymes were evaluated. In experiment 1, COCs pre-matured with both C-type natriuretic peptide and forskolin or C-type natriuretic peptide, forskolin and IBMX had lower meiotic resumption rate when compared to control. Considering that IBMX had not an additional effect to potentiate inhibition of meiotic resumption, a combination of C-type natriuretic peptide and forskolin was chosen. In experiment 2, COCs matured with 10 -8 M melatonin had greater rates of meiotic resumption when compared to the other treatments (P < 0.05). The COCs matured with 10 -7 or 10 -8 M melatonin had greater mitochondrial activity (P < 0.05), while those matured with 10 -6 or 10 -8 M of melatonin had greater levels of TZPs. Ultrastructure of oocyte and cumulus cells after IVM with melatonin was relatively well preserved. COCs matured with 10 -8 M melatonin increased mRNA expression for superoxide dismutase (SOD) and catalase (CAT) (P < 0.05), when compared to non-cultured and pre-matured COCs, respectively. In conclusion, bovine COC pre-maturation with C-type natriuretic peptide and forskolin, followed by IVM with 10 -8 M melatonin improves meiotic resumption rates, TZPs, mitochondrial distribution and mRNA expression for SOD and CAT., Competing Interests: Declaration of Competing Interest The authors declare that they have no competing interests., (Copyright © 2023 Elsevier B.V. All rights reserved.)

One of the prominent peculiarities of nanoparticles (NPs) is their ability to cross biological barriers. Therefore, the development of NPs with different properties has great therapeutic potential in the area of reproduction because the association of drugs, hormones and other compounds with NPs represents an alternative for delivering substances directly at a specific site and for treatment of reproductive problems. Additionally, lipid-based NPs can be taken up by the tissues of patients with ovarian failure, deep endometriosis, testicular dysfunctions, etc., opening up new perspectives for the treatment of these diseases. The development of nanomaterials with specific size, shape, ligand density and charge certainly will contribute to the next generation of therapies to solve fertility problems in humans. Therefore, this review discusses the potential of NPs to treat reproductive disorders, as well as to regulate the levels of the associated hormones. The possible limitations of the clinical use of NPs are also highlighted.

BACKGROUND: TB is an infectious disease with a worldwide impact. TB is closely associated with social and housing conditions, exerting a significant impact on the prison population, which is particularly susceptible to the disease. Evidence suggests that the COVID-19 pandemic has exacerbated social vulnerability. This study therefore aimed to analyse the impact of the pandemic on the diagnosis of new cases of TB in the Brazilian prison population in the years 2020 and 2021. METHODS: This is an ecological study involving cases of TB recorded in the prison population of Brazil from 2015 to 2021. Data were collected from the Brazil's Information System for Notifiable Diseases. RESULTS: The incidence of TB in the prison population in Brazil fell from 1,005.9/100,000 population between 2015 and 2019 to 852.3/100,000 population between 2020 and 2021. In 2021, there was a deficit of 539 cases (-7.6%) compared to what was expected for the year. In 2020, there was a 10% reduction in TB diagnoses in January and February, reaching 3.8% in March. A negative percentage was observed in most of the subsequent months. In 2021, the year began with a 21.6% decline in January, returning to positive values only in August and September. CONCLUSION: The first years of the COVID-19 pandemic resulted in underdiagnosis of TB in the Brazilian prison population.

Preantral to early antral follicles transition is a complex process regulated by endocrine and paracrine factors, as well as by a precise interaction among oocyte, granulosa cells and theca cells. Understanding the mechanisms that regulate this step of folliculogenesis is important to improve in vitro culture systems, and opens new perspectives to use oocytes from preantral follicles for assisted reproductive technologies. Therefore, this review aims to discuss the endocrine and paracrine mechanisms that control granulosa cell proliferation and differentiation, formation of the antral cavity, estradiol production, atresia, and follicular fluid production during the transition from preantral to early antral follicles. The strategies that promote in vitro growth of preantral follicles are also discussed.

This study aims to evaluate the effects of N -acetylcysteine (NAC) on bovine oocyte maturation, mitochondrial activity and transzonal projections (TZP), as well as on the levels of reactive oxygen species (ROS) and messenger RNA (mRNA) for catalase ( CAT ) superoxide dismutase ( SOD ), periredoxin-6 ( Prdx6 ), glutathione peroxidase ( GPx ), growth and differentiation factor-9 ( GDF9 ), histone H1Foo , cyclin B1 ( CCNB1 ) and c- Mos . Bovine cumulus-oocyte complexes (COC) of medium-sized antral follicles (3.0-6.0 mm) were prematured in TCM-199 for 8 h at 38.5°C in 5% CO 2 . After prematuration in the presence of forskolin and C-type natriuretic peptide, COCs were matured in TCM-199 alone or with 0.1, 0.5 or 2.5 mM NAC. Then, oocytes were classified according to the stage of chromatin. Furthermore, mitochondrial activity and intracellular levels of ROS and TZP were also evaluated. The levels of mRNAs for CAT , SOD , Prdx6 , GPx , GDF9 , H1Foo , CCNB1 and c- Mos were evaluated using real-time polymerase chain reaction (RT-PCR). The results showed that NAC significantly increased the percentages of oocytes with resumption of meiosis when compared with those oocytes matured in control medium. Oocytes had homogeneous mitochondrial distribution, and those cultured with 0.1 and 0.5 mM NAC had lower levels of ROS when compared with the control. In addition, 0.5 mM NAC reduced TZP and the levels of mRNA for CCNB1 . In contrast, NAC did not influence the expression of CAT , GPx , Prdx6 , SOD , GDF9 , H1Foo , and c -Mos . In conclusion, 0.5 mM NAC reduced the levels of ROS, TZP and mRNA for CCNB1 , and improved in vitro resumption of meiosis in oocytes from medium-sized bovine antral follicles.

This study aimed to investigate the effects of different concentrations of N-acetylcysteine (NAC) on the growth, antrum formation, viability, and ultrastructure of bovine secondary follicles cultured in vitro for 18 days. To this end, the follicles were cultured in TCM-199+ medium alone or supplemented with 1.0, 5.0, or 25.0 mM NAC. Follicular growth, antrum formation, viability (calcein-AM and ethidium homodimer-1) and ultrastructure were evaluated at the end of culture period. The results showed that 1.0 mM NAC increased the percentage of growing follicles and the fluorescence intensity for calcein-AM when compared to other treatments (p < 0.05). On the other hand, follicles cultured with 25.0 mM NAC had higher fluorescence intensity for ethidium homodimer-1, which is a sign of degeneration. Ultrastructural analysis showed that oocytes from follicles cultured in control medium alone or with 1 mM NAC had intact zonae pellucidae in close association with oolemmae, but the ooplasm showed mitochondria with a reduced number of cristae. On the other hand, oocytes from follicles cultured with 5 or 25 mM NAC had extremely vacuolated cytoplasm and no recognizable organelles. In conclusion, 1 mM NAC increases cytoplasmic calcein staining and the growth rate in bovine secondary follicles cultured in vitro, but the presence of 5 or 25 mM NAC causes damage in cellular membranes and organelles, as well as reducing the percentages of growing follicles.

This study aimed to describe the development process, content validation, and usability of a COVID-19 screening system incorporated into a chatbot-type intelligent virtual assistant (CoronaBot). This is a methodological research carried out in three phases. The first corresponded to the development of the flowchart and content of the virtual assistant, the second phase consisted of the implementation of the content in chatbot, and the third phase consisted of content validation. Data analysis was performed by agreement rate, content validity index, and kappa statistical test. Finally, in the third phase, the chatbot's usability was analyzed using the System Usability Scale, by 10 users. The CoronaBot content presented domains with agreement rate above 87.5%, and its items referring to symptomatological scores and interface screens had values of content validity index with a mean of 0.96, kappa test with values from 0.70 to 0.76, and interspecialist agreement of 1.00, demonstrating excellence of prototype content. The global usability score was 80.1. The script developed and incorporated into the chatbot prototype achieved a satisfactory level of content validity. The usability of the chatbot was considered good, adding to the credibility of the device., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

The emergence of state-of-the-art X-ray light sources has paved the way for novel spectroscopies that take advantage of their atomic specificity to shed light on fundamental physical, chemical, and biological processes both in the static and time domains. The success of these experiments hinges on the ability to interpret and predict core-level spectra, which has opened avenues for theory to play a key role. Over the last two decades, linear-response time-dependent density functional theory (LR-TDDFT), despite various theoretical challenges, has become a computationally attractive and versatile framework to study excited-state spectra including X-ray spectroscopies. In this context, we focus our discussion on LR-TDDFT approaches for the computation of X-ray Near-Edge Structure (XANES), Valence-to-Core X-ray Emission (VtC-XES), and Resonant Inelastic X-ray Scattering (RIXS) spectroscopies in molecular systems with an emphasis on Gaussian basis set implementations. We illustrate these approaches with applications and provide a brief outlook of possible new directions.

Spectroscopy simulations are of paramount importance for the interpretation of experimental electronic spectra, the disentangling of overlapping spectral features, and the tracing of the microscopic origin of the observed signals. Linear and nonlinear simulations are based on the results drawn from electronic structure calculations that provide the necessary parameterization of the molecular systems probed by light. Here, we investigate the applicability of excited-state properties obtained from linear-response time-dependent density functional theory (TDDFT) in the description of nonlinear spectra by employing the pseudowavefunction approach and compare them with benchmarks from highly accurate RASSCF/RASPT2 calculations and with high temporal resolution experimental results. As a test case, we consider the prediction of femtosecond transient absorption and two-dimensional electronic spectroscopy of a perylene bisimide dye in solution. We find that experimental signals are well reproduced by both theoretical approaches, showing that the computationally cheaper TDDFT can be a suitable option for the simulation of nonlinear spectroscopy of molecular systems that are too large to be treated with higher-level RASSCF/RASPT2 methods.

Assisted reproductive technology (ART) have contributed to preserve fertility in humans and to increase multiplication of genetically superior animals. Despite being highly practiced worldwide, ART presents some challenges, especially because gametes and embryos are kept in vitro for a variable period of time, and the oxidative stress in vitro can have negative impact on oocyte competence and embryo development. Nanotechnology needs to be considered to help overcome some of those impairments, since it can provide strategies to deliver antioxidants and hormones to gametes and embryos in vitro. The application of nanotechnology to ART can allow the development of new protocols using nanomaterials to improve in vitro oocyte competence and embryo production. This review discusses the applicability of nanomaterials to improve sperm selection, to deliver antioxidants and hormones to preantral follicles, oocytes, and embryos in vitro, as well as the concerns about using nanotechnology in ART., (© 2021 Wiley Periodicals LLC.)

Fibrodysplasia Ossificans Progressiva (FOP) is a rare congenital intractable disease associated with a mutation in ACVR1 gene, characterized by skeleton malformations. Ascorbic acid (AA) and propranolol (PP) in combination is reported to minimize flare-ups in patients. FOP leukocyte phenotype may possibly be modulated by AA and PP treatment. In this study, expression of 22 potential target genes was analyzed by RT-PCR in peripheral blood mononuclear cells culture (PBMC) from FOP patients and controls to determine effectiveness of the combination therapy. PBMC were treated with AA, PP and AA+PP combination. Basal expression of 12 of the 22 genes in FOP PBMC was statistically different from controls. ACVR1 , ADCY2 , ADCY9 and COL3 were downregulated while COL1 was upregulated. ADRB1 , ADRB2 , RUNX2 , TNF-α and ACTB , were all overexpressed in FOP PBMC. In control, AA upregulated COL1, SVCT1, ACTB, AGTR2 and downregulated ADCY2 . In FOP cells, AA upregulated ACVR1, BMP4, COL1, COL3, TNF-α , ADCY2, ADCY9, AGTR2 and MAS , while downregulated ADBR2, RUNX2, ADCY1, SVCT1 and ACTB . PP increased ADBR1 and decreased RUNX2, TNF-α, AGTR1, ACTB and CHRNA7 genes in treated control PBMC compared to untreated. PP upregulated ADBR1, ADBR2 and MAS , and downregulated TNF-α and ACTB in treated FOP PBMC versus untreated. AA+PP augmented ADRB1 and ADRB2 expressions in control PBMC. In FOP PBMC, AA+PP augmented ACVR1, COL1, COL3, ADBR1, AGTR2 and MAS expression and downregulated ADBR2, RUNX2, ACTB and MRGD . These data show distinct gene expression modulation in leukocytes from FOP patients when treated with AA and or PP., Competing Interests: The authors have no conflicts of interest to disclose., (2021, International Research and Cooperation Association for Bio & Socio - Sciences Advancement.)

Oxidative stress is generated by an imbalance between reactive oxygen species (ROS) formation and cellular defense mechanisms. To reduce cellular damage caused by ROS in vivo or in vitro, N-acetyl-cysteine (NAC) is converted into metabolites that have the capacity of stimulating synthesis of glutathione (GSH) which functions directly as free radical scavengers. The NAC antioxidant potential evaluated to the greatest extent is the indirect action of NAC, as a precursor of GSH, with glutathione being the primary antioxidant in cells. During long-term preantral follicle culture, NAC has a synergic action with FSH and an important function in sustaining preantral follicle growth and follicle-cell viability in vitro. The NAC inclusion in in vitro maturation medium for cumulus-oocyte complexes (COC) leads to protection of oocytes from damage induced by heat stress, reductions in ROS, and increases in cumulus cell expansion. Developing embryos are susceptable to oxidative stress because of susceptability to cellular structure damage and not having well-developed defense mechanisms. Results from various indicate there are beneficial effects of NAC on embryonic development by increasing GSH biosynthesis and regulating cell proliferation. In addition, NAC is also an effective antioxidant during cryopreservation of ovarian follicles, oocytes and embryos, because inclusion of NAC in preservation medium leads to improvements in mitochondrial function and cell viability, and reductions in ROS and cellular apoptosis. In this review, there is evaluation of mechanisms of action of NAC and beneficial effects during in vitro culture of preantral follicles, as well as oocyte maturation, embryonic development and cryopreservation., (Copyright © 2021. Published by Elsevier B.V.)

Resonant stimulated X-ray Raman spectroscopy of the bimetallic [Mn III Mn IV (μ-O) 2 (μ-OAC)(tacn) 2 ] 2+ manganese complex is investigated in a simulation study. Essential biological processes, including water oxidation in photosynthesis, involve charge transfer between manganese sites of different oxidation states. We study a prototypical binuclear mixed-valence transition-metal complex with two Mn atoms in different oxidation states surrounded by ligand structures and employ a pump-probe sequence of resonant X-ray Raman excitations to follow the charge transfer occurring in the molecule. This allows us to generate and monitor valence-electron wave packets at selected regions in the molecule by exploiting element-specific core-excited states. A two-color protocol is presented, with pump and probe pulses tuned to the Mn and N K-edges. A natural orbital decomposition allows the visualization of the electron dynamics underlying the signal.

A time-dependent (TD) formulation of equation-of-motion coupled-cluster (EOM-CC) theory can provide excited-state information over an arbitrarily wide energy window with a reduced memory footprint relative to conventional, frequency-domain EOM-CC theory. However, the floating-point costs of the time-integration required by TD-EOM-CC are generally far larger than those of the frequency-domain form of the approach. This work considers the potential of the short iterative Lanczos (SIL) integration scheme [ J. Chem. Phys. 1986 , 85 , 5870-5876] to reduce the floating-point costs of TD-EOM-CC simulations. Low-energy and K-edge absorption features for small molecules are evaluated using TD-EOM-CC with single and double excitations, with the time-integrations carried out via SIL and fourth-order Runge-Kutta (RK4) schemes. Spectra derived from SIL- and RK4-driven simulations are nearly indistinguishable, and with an appropriately chosen subspace dimension, the SIL requires far fewer floating-point operations than are required by RK4. For K-edge spectra, SIL is the more efficient scheme by an average factor of 7.2.

Computation of intermolecular interactions is a challenge in drug discovery because accurate ab initio techniques are too computationally expensive to be routinely applied to drug-protein models. Classical force fields are more computationally feasible, and force fields designed to match symmetry adapted perturbation theory (SAPT) interaction energies can remain accurate in this context. Unfortunately, the application of such force fields is complicated by the laborious parameterization required for computations on new molecules. Here, we introduce the component-based machine-learned intermolecular force field (CLIFF), which combines accurate, physics-based equations for intermolecular interaction energies with machine-learning models to enable automatic parameterization. The CLIFF uses functional forms corresponding to electrostatic, exchange-repulsion, induction/polarization, and London dispersion components in SAPT. Molecule-independent parameters are fit with respect to SAPT2+(3)δMP2/aug-cc-pVTZ, and molecule-dependent atomic parameters (atomic widths, atomic multipoles, and Hirshfeld ratios) are obtained from machine learning models developed for C, N, O, H, S, F, Cl, and Br. The CLIFF achieves mean absolute errors (MAEs) no worse than 0.70 kcal mol -1 in both total and component energies across a diverse dimer test set. For the side chain-side chain interaction database derived from protein fragments, the CLIFF produces total interaction energies with an MAE of 0.27 kcal mol -1 with respect to reference data, outperforming similar and even more expensive methods. In applications to a set of model drug-protein interactions, the CLIFF is able to accurately rank-order ligand binding strengths and achieves less than 10% error with respect to SAPT reference values for most complexes.

We present a time-dependent density functional theory (TDDFT) approach to compute the light-matter couplings between two different manifolds of excited states relative to a common ground state in the context of 4d transition metal systems. These quantities are the necessary ingredients to solve the Kramers-Heisenberg (KH) equation for resonant inelastic X-ray scattering (RIXS) and several other types of two-photon spectroscopies. The procedure is based on the pseudo-wavefunction approach, where the solutions of a TDDFT calculation can be used to construct excited-state wavefunctions, and on the restricted energy window approach, where a manifold of excited states can be rigorously defined based on the energies of the occupied molecular orbitals involved in the excitation process. Thus, the present approach bypasses the need to solve the costly TDDFT quadratic-response equations. We illustrate the applicability of the method to 4d transition metal molecular complexes by calculating the 2p4d RIXS maps of three representative ruthenium complexes and comparing them to experimental results. The method can capture all the experimental features in all three complexes to allow the assignment of the experimental peaks, with relative energies correct to within ∼0.6 eV at the cost of two independent TDDFT calculations.

We demonstrate how optical cavities can be exploited to control both valence- and core-excitations in a prototypical model transition metal complex, ferricyanide ([Fe(iii)(CN) 6 ] 3- ), in an aqueous environment. The spectroscopic signatures of hybrid light-matter polariton states are revealed in UV/Vis and X-ray absorption, and stimulated X-ray Raman signals. In an UV/Vis cavity, the absorption spectrum exhibits the single-polariton states arising from the cavity photon mode coupling to both resonant and off-resonant valence-excited states. We further show that nonlinear stimulated X-ray Raman signals can selectively probe the bipolariton states via cavity-modified Fe core-excited states. This unveils the correlation between valence polaritons and dressed core-excitations. In an X-ray cavity, core-polaritons are generated and their correlations with the bare valence-excitations appear in the linear and nonlinear X-ray spectra., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained from quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The program capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Calculations at two levels of electronic structure theory, time-dependent density functional theory (with NWChem) and RASSCF/RASPT2 (with OpenMolcas) are presented and compared where possible. The iSPECTRON program is available online at https://github.com/ispectrongit/iSPECTRON/ and distributed open source under the terms of the Educational Community License version 2.0 (ECL 2.0)., (© 2021 Wiley Periodicals LLC.)

Ru-complexes are widely studied because of their use in biological applications and photoconversion technologies. We reveal novel insights into the chemical bonding of a series of Ru(ii)- and Ru(iii)-complexes by leveraging recent advances in high-energy-resolution tender X-ray spectroscopy and theoretical calculations. We perform Ru 2p4d resonant inelastic X-ray scattering (RIXS) to probe the valence excitations in dilute solvated Ru-complexes. Combining these experiments with a newly developed theoretical approach based on time-dependent density functional theory, we assign the spectral features and quantify the metal-ligand bonding interactions. The valence-to-core RIXS features uniquely identify the metal-centered and charge transfer states and allow extracting the ligand-field splitting for all the complexes. The combined experimental and theoretical approach described here is shown to reliably characterize the ground and excited valence states of Ru complexes, and serve as a basis for future investigations of ruthenium, or other 4d metals active sites, in biological and chemical applications., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

We demonstrate how the near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of single and double core-hole states created by the ionization of a heteroatom can be used to probe subtle changes in intramolecular chemical environments that are nearly indistinguishable by conventional NEXAFS spectroscopy. Using prototypical organic molecules (2/3-pentanone and pentanal), we show how new spectral features emerge in the C K-edge NEXAFS spectra, when creating single and double core-holes at the oxygen heteroatom site. The effect on the lowest unoccupied molecular orbitals is analyzed by studying the double-core-hole-induced ultrafast valence electron dynamics of the three molecules. The predicted changes from our simulations should be observable with state-of-the-art experiments at X-ray free-electron lasers.

We present a relativistic time-dependent equation-of-motion coupled-cluster with single and double excitations (TD-EOM-CCSD) formalism. Unlike other explicitly time-dependent quantum chemical methods, the present approach considers the time correlation function of the dipole operator, as opposed to the expectation value of the time-dependent dipole moment. We include both scalar relativistic effects and spin-orbit coupling variationally in this scheme via the use of the exact two-component (X2C) wave function as the reference that enters the coupled-cluster formalism. In order to evaluate the accuracy of X2C-TD-EOM-CCSD, we compare zero-field splitting in atomic absorption spectra of open-shell systems (Na, K, Mg + , and Ca + ) with values obtained from experiment. In closed-shell species (Na + , K + , Mg 2+ , and Ca 2+ ), we observe singlet-triplet mixing in the X2C-TD-EOM-CC calculations, which results from the use of the X2C reference. The effects of the X2C reference are evaluated by comparing spectra derived from X2C-TD-EOM-CC calculations to those from TD-EOM-CC calculations using a complex generalized Hartree-Fock ([Formula: see text]-GHF) reference.

A time-dependent (TD) formulation of equation-of-motion (EOM) coupled-cluster (CC) theory is developed, which, unlike other similar TD-EOM-CC approaches [D. R. Nascimento and A. E. DePrince III, J. Chem. Theory Comput. 12, 5834-5840 (2016)], can be applied to any type of linear electronic spectroscopy. The TD-EOM-CC method is formally equivalent to the standard frequency-domain formulation of EOM-CC theory, with a potential computational advantage of a comparatively low memory footprint. This general TD-EOM-CC framework is applied to the linear absorption and electric circular dichroism spectra of several small oxirane derivatives.

Ligand substitution reactions are common in solvated transition metal complexes, and harnessing them through initiation with light promises interesting practical applications, driving interest in new means of probing their mechanisms. Using a combination of time-resolved x-ray absorption spectroscopy and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations and x-ray absorption near-edge spectroscopy calculations, we elucidate the mechanism of photoaquation in the model system iron(ii) hexacyanide, where UV excitation results in the exchange of a CN - ligand with a water molecule from the solvent. We take advantage of the high flux and stability of synchrotron x-rays to capture high precision x-ray absorption spectra that allow us to overcome the usual limitation of the relatively long x-ray pulses and extract the spectrum of the short-lived intermediate pentacoordinated species. Additionally, we determine its lifetime to be 19 (±5) ps. The QM/MM simulations support our experimental findings and explain the ∼20 ps time scale for aquation as involving interconversion between the square pyramidal (SP) and trigonal bipyramidal pentacoordinated geometries, with aquation being only active in the SP configuration.

Objectives: Calorie restriction (CR) is an important intervention for reducing adiposity and improving glucose homeostasis. Recently we found that in rats, a severe calorie restriction (SCR) beginning at birth up to adult age promotes positive effects on cardiometabolic risk factors and heart. The aim of this study was to investigate the effects of this new model of SCR on adipose tissue and glucose homeostasis of rats and to evaluate the effects of refeeding., Methods: From birth to 90 d of age, rats were divided into an ad libitum (AL) group, which had free access to food, and a CR50 group, which had food limited to 50% of that consumed by the AL group. From this moment, half of the CR50 animals had free access to food (the refeeding group [CR50-R]), and the other half continued 50% restricted for an additional 90-d period. Food intake was assessed daily and body weight weekly. In the final week of the SCR/refeeding protocol, oral glucose and intraperitoneal insulin tolerance tests were performed. Thereafter, rats were sacrificed and visceral fat was collected and used for histologic and Western blot analysis., Results: Findings from this study revealed that SCR beginning at birth and up to adult life promoted a large decrease in visceral adiposity; improvement in glucose/insulin tolerance; and upregulation of adipose proliferating cell nuclear antigen, sirtuin 1, peroxisome proliferator-activated receptor-γ, and adiponectin. Refeeding abolished all of these effects. SCR from birth to adult age promoted beneficial effects on adipose tissue and glucose homeostasis; whereas refeeding abolished these effects., (Copyright © 2019 Elsevier Inc. All rights reserved.)

The nematicidal effect of different organic materials was evaluated in order to develop a non-chemical alternative soil treatment for control of the free-living stages of small ruminant gastrointestinal nematodes. The selected organic materials were residues from the juice industry of acerola, cashew, grape, guava, papaya and pineapple, as well as castor residue from the biodiesel industry. LC90 results showed that pineapple residue was the most efficient inhibitor of larval development, followed by castor, grape, cashew, acerola, guava and papaya. Castor residue was also a good source of nitrogen and was used in a greenhouse experiment to prevent larval development in contaminated goat faeces that was deposited in pots containing the grasses Brachiaria brizantha (var. Paiaguás) or Megathyrsus maximus x M. infestum (var. Massai). Castor residue caused a significant (P < 0.05) reduction (85.04%) in Paiaguás grass contamination (L3.dry mass-1) and a reduction of 17.35% in Massai grass contamination (P > 0.05), with an increase in the biomass production of Massai (251.43%, P < 0.05) and Paiaguás (109.19%, P > 0.05) grasses. This strategy, called Econemat®, with good results in vitro shows to be promising on pasture increasing phytomass production.

Fibrodysplasia ossificans progressiva (FOP) is a rare, intractable and devastating genetic connective tissue disorder characterized by progressive ectopic ossification in the soft tissues and skeleton. Three patients, one teenage girl (P1), one male adult (P2) and one male child (P3), were studied and treated with FOPCON (combined formulation of 14 mg of propranolol and 250 mg of ascorbic acid), given three times per day. P1 started treatment in March 2012, P2 in October 2012 and P3 in July 2015. The clinical follow-up of these three patients, before initiating treatment with FOPCON, showed that FOP flare-ups used to occur frequently and that under FOPCON therapy, none of these patients had flare-ups. The striking feature of this treatment with FOPCON, is that, all three cases suffered accidental falls with documented injures until complete healing and that where major flare-ups should occur, injures or sequels, there was none. The present clinical observation shows that ascorbic acid plus the nonspecific beta blocker propranolol can be effectively useful, when administered previously and continually, in the prophylaxis of FOP flare-ups, especially for accidental falls. In this regard, FOPCON could be a prophylactic aid in cases of surgery of patients with FOP, hoping that it may benefit patients from having the severe sequels, characteristic of heterotopic bone formation. All three patients reported, to date, they no longer had flare-ups nor heterotopic ossification and showed normal scar healing.

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

The Hartree-Fock problem was recently recast as a semidefinite optimization over the space of rank-constrained two-body reduced-density matrices (RDMs) [ Phys. Rev. A 2014 , 89 , 010502(R) ]. This formulation of the problem transfers the nonconvexity of the Hartree-Fock energy functional to the rank constraint on the two-body RDM. We consider an equivalent optimization over the space of positive semidefinite one-electron RDMs (1-RDMs) that retains the nonconvexity of the Hartree-Fock energy expression. The optimized 1-RDM satisfies ensemble N-representability conditions, and ensemble spin-state conditions may be imposed as well. The spin-state conditions place additional linear and nonlinear constraints on the 1-RDM. We apply this RDM-based approach to several molecular systems and explore its spatial (point group) and spin ( Ŝ 2 and Ŝ 3 ) symmetry breaking properties. When imposing Ŝ 2 and Ŝ 3 symmetry but relaxing point group symmetry, the procedure often locates spatial-symmetry-broken solutions that are difficult to identify using standard algorithms. For example, the RDM-based approach yields a smooth, spatial-symmetry-broken potential energy curve for the well-known Be-H 2 insertion pathway. We also demonstrate numerically that, upon relaxation of Ŝ 2 and Ŝ 3 symmetry constraints, the RDM-based approach is equivalent to real-valued generalized Hartree-Fock theory.