Evaluation of a large set of patients with Autoimmune Polyglandular Syndrome from a single reference centre in context of different classifications

PURPOSE

To characterize patients with APS and to propose a new approach for their follow-up. Query ID="Q1" Text="Please check the given names and familynames."

METHODS

Monocentric observational retrospective study enrolling patients referred to the Outpatients clinic of the Units of Endocrinology, Diabetology, Gastroenterology, Rheumatology and Clinical Immunology of our Hospital for Autoimmune diseases.

RESULTS

Among 9852 patients, 1174 (11.9%) [869 (73.9%) female] were diagnosed with APS. In 254 subjects, the diagnosis was made at first clinical evaluation (Group 1), all the other patients were diagnosed with a mean latency of 11.3 ± 10.6 years (Group 2). Group 1 and 2 were comparable for age at diagnosis (35.7 ± 16.3 vs. 40.4 ± 16.6 yrs, p = .698), but different in male/female ratio (81/173 vs 226/696, p = .019). In Group 2, 50% of patients developed the syndrome within 8 years of follow-up. A significant difference was found after subdividing the first clinical manifestation into the different outpatient clinic to which they referred (8.7 ± 8.0 vs. 13.4 ± 11.6 vs. 19.8 ± 8.7 vs. 7.4 ± 8.1 for endocrine, diabetic, rheumatologic, and gastroenterological diseases, respectively, p < .001).

CONCLUSIONS

We described a large series of patients affected by APS according to splitters and lumpers. We propose a flowchart tailored for each specialist outpatient clinic taking care of the patients. Finally, we recommend regular reproductive system assessment due to the non-negligible risk of developing premature ovarian failure.

Cardiovascular and metabolic comorbidities in patients with thyroid nodules: the impact of incidental diagnosis

PURPOSE

The prevalence of thyroid nodules (TN) in the general population has increased as screening procedures are implemented and an association with metabolic and cardiovascular disorders has been reported. The aim of this study was to investigate the reason leading to the diagnosis of TN and to compare the clinical characteristics of patients diagnosed incidentally with those of patients diagnosed for thyroid-related reasons.

METHODS

We designed a retrospective cross-sectional study including consecutive patients with TN from two high-volume hospital-based centers for thyroid diseases (Pavia and Messina) in Italy. Data regarding reason leading to TN diagnosis, age, sex, BMI, presence of cardio-metabolic comorbidities were collected.

RESULTS

Among the 623 enrolled subjects, the US diagnosis of TN was prompted by thyroid-related reasons in 421 (67.6%, TD group) and incidental in 202 (32.4%, ID group) with a similar distribution in the two centers (p = 0.960). The ID group patients were more frequently males (38.6% vs 22.1%, p < 0.001) and significantly older (58.9 ± 13.7 vs 50.6 ± 15.5 years, p < 0.001) than the TD group ones, and had a higher rate of cardiovascular comorbidities (73.8% vs 47.5%, p < 0.001), despite having a similar BMI (27.9 ± 5.2 vs 27.8 ± 13.5, p = 0.893).

CONCLUSIONS

Stratification of patients with TN according to the diagnostic procedure leading to diagnosis allows a better epidemiological characterization of this inhomogeneous and large population.

Close-Up Look at Electronic Spectroscopic Signatures of Common Pharmaceuticals in Solution

Simulating electronic properties and spectral signals requires robust computational approaches that need tuning with the system's peculiarities. In this paper, we test implicit and fully atomistic solvation models for the calculation of UV-vis and electronic circular dichroism (ECD) spectra of two pharmaceutically relevant molecules, namely, (2S)-captopril and (S)-naproxen, dissolved in aqueous solution. Room temperature molecular dynamics simulations reveal that these two drugs establish strong contacts with the surrounding solvent molecules via hydrogen bonds. Such specific interactions, which play a major role in the spectral response and are neglected in implicit approaches, are further characterized and quantified with natural bond orbital methods. Our calculations show that simulated spectra, and especially ECD, are in good agreement with experiments solely when conformational and configurational dynamics, mutual polarization, and solute-solvent repulsion effects are considered.

Bone health and body composition in transgender adults before gender-affirming hormonal therapy: data from the COMET study

PURPOSE

Preliminary data suggested that bone mineral density (BMD) in transgender adults before initiating gender-affirming hormone therapy (GAHT) is lower when compared to cisgender controls. In this study, we analyzed bone metabolism in a sample of transgender adults before GAHT, and its possible correlation with biochemical profile, body composition and lifestyle habits (i.e., tobacco smoke and physical activity).

METHODS

Medical data, smoking habits, phospho-calcic and hormonal blood tests and densitometric parameters were collected in a sample of 125 transgender adults, 78 Assigned Females At Birth (AFAB) and 47 Assigned Males At Birth (AMAB) before GAHT initiation and 146 cisgender controls (57 females and 89 males) matched by sex assigned at birth and age. 55 transgender and 46 cisgender controls also underwent a complete body composition evaluation and assessment of physical activity using the International Physical Activity Questionnaire (IPAQ).

RESULTS

14.3% of transgender and 6.2% of cisgender sample, respectively, had z-score values < -2 (p = 0.04). We observed only lower vitamin D values in transgender sample regarding biochemical/hormonal profile. AFAB transgender people had more total fat mass, while AMAB transgender individuals had reduced total lean mass as compared to cisgender people (53.94 ± 7.74 vs 58.38 ± 6.91, p < 0.05). AFAB transgender adults were more likely to be active smokers and tend to spend more time indoor. Fat Mass Index (FMI) was correlated with lumbar and femur BMD both in transgender individuals, while no correlations were found between lean mass parameters and BMD in AMAB transgender people.

CONCLUSIONS

Body composition and lifestyle factors could contribute to low BMD in transgender adults before GAHT.

Prognostic role and characteristics of the indeterminate response in differentiated thyroid cancer: a systematic review

PURPOSE

The management of differentiated thyroid cancer (DTC) is actually based on a dynamic risk stratification based on classes of response to the therapy. Indeterminate response (IR) includes a heterogeneous group of patients with different characteristics, particularly different Tg and AbTg levels and/or imaging findings. The aim of systematic review (SR) is to evaluate the prognosis, diagnostic findings and other characteristics of patients in the IR class.

METHODS

A wide literature search in the Scopus, PubMed/MEDLINE and Web of Science databases was performed to find published articles on patients with DTC and IR after treatment. The quality assessment of studies was carried out using QUADAS-2 evaluation.

RESULTS

Eight articles were included in the systematic review. Six studies evaluated the prognosis and the prognostic factor in patients with IR, one study evaluated the role of 2-[18F]FDG PET-CT in the management of patients with IR and biochemical incomplete response and one study the risk factors for IR.

CONCLUSION

Patients with DTC and IR to therapy have a probability of disease relapse < 15%. Tg value could be a predictor of disease progression. The role of 2-[18F]FDG PET-CT needs to be further investigated.

Interactions and reactivity in crystalline intermediates of mechanochemical cyclorhodation reactions

There is experimental evidence that solid mixtures of the rhodium dimer [Cp*RhCl2]2 and benzo[h] quinoline (BHQ) produce two different polymorphic molecular cocrystals called 4α and 4β under ball milling conditions. The addition of NaOAc to the mixture leads to the formation of the rhodacycle [Cp*Rh-(BHQ)Cl], where the central Rh atom retains its tetracoordinate character. Isolate 4β reacts with NaOAc leading to the same rhodacycle while isolate 4α does not under the same conditions. We show that the puzzling difference in reactivity between the two cocrystals can be traced back to fundamental aspects of the intermolecular interactions between the BHQ and [Cp*RhCl2]2 fragments in the crystalline environment. To support this view, we report a number of descriptors of the nature and strength of chemical bonds and intermolecular interactions in the extended solids and in a cluster model. We calculate formal quantum mechanical descriptors based on electronic structure, electron density, and binding and interaction energies including an energy decomposition analysis. Without exception, all descriptors point to 4β being a transient structure higher in energy than 4α with larger local and global electrophilic and nucleophilic powers, a more favorable spatial and energetic distribution of the frontier orbitals, and a more fragile crystal structure.

Effective fully polarizable QM/MM approaches to compute Raman and Raman Optical Activity spectra in aqueous solution

Raman and Raman Optical Activity (ROA) signals are amply affected by solvent effects, especially in the presence of strongly solute-solvent interactions such as Hydrogen Bonding (HB). In this work, we extend the fully atomistic polarizable Quantum Mechanics/Molecular Mechanics approach, based on the Fluctuating Charges and Fluctuating Dipoles force field to the calculation of Raman and ROA spectra. Such an approach is able to accurately describe specific HB interactions, by also accounting for anisotropic contributions due to the inclusion of fluctuating dipoles. To highlight the potentiality of the novel approach, Raman and ROA spectra of L-Serine and L-Cysteine dissolved in aqueous solution are computed and compared both with alternative theoretical approaches and experimental measurements.

Multiscale Frozen Density Embedding/Molecular Mechanics Approach for Simulating Magnetic Response Properties of Solvated Systems

We present a three-layer hybrid quantum mechanical/quantum embedding/molecular mechanics approach for calculating nuclear magnetic resonance (NMR) shieldings and J-couplings of molecular systems in solution. The model is based on the frozen density embedding (FDE) and polarizable fluctuating charges (FQ) and fluctuating dipoles (FQFμ) force fields and permits the accurate ab initio description of short-range nonelectrostatic interactions by means of the FDE shell and cost-effective treatment of long-range electrostatic interactions through the polarizable force field FQ(Fμ). Our approach's accuracy and potential are demonstrated by studying NMR spectra of Brooker's merocyanine in aqueous and nonaqueous solutions.

Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces

We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.

Testing the Influence of Laser Pulse Energy and Rate in the Atom Probe Tomography Analysis of Minerals

The use of atom probe tomography (APT) for mineral analysis is contributing to fundamental studies in Earth Sciences. Meanwhile, the need for standardization of this technique is becoming evident. Pending the use of mineral standards, the optimization of analysis parameters is needed to facilitate the study of different mineral groups in terms of data collection and quality. The laser pulse rate and energy are variables that highly affect the atom evaporation process occurring during APT analysis, and their testing is important to forecast mineral behavior and obtain the best possible data. In this study, five minerals representative of major groups (albite, As-pyrite, barite, olivine, and monazite) were analyzed over a range of laser pulse energies (10-50 pJ) and rates (100-250 kHz) to assess output parameter quality and evaluate compositional estimate stoichiometry. Among the studied minerals, As-pyrite, with the higher thermal conductivity and lower band gap, was the most affected by the laser pulse variation. Chemical composition estimates equal or close to the general chemical formula were achieved for monazite and As-pyrite. The analysis of multihit events has proved to be the best strategy to verify the efficacy of the evaporation process and to evaluate the best laser pulse setting for minerals.

QM/Classical Modeling of Surface Enhanced Raman Scattering Based on Atomistic Electromagnetic Models

We present quantum mechanics (QM)/frequency dependent fluctuating charge (QM/ωFQ) and fluctuating dipoles (QM/ωFQFμ) multiscale approaches to model surface-enhanced Raman scattering spectra of molecular systems adsorbed on plasmonic nanostructures. The methods are based on a QM/classical partitioning of the system, where the plasmonic substrate is treated by means of the atomistic electromagnetic models ωFQ and ωFQFμ, which are able to describe in a unique fashion and at the same level of accuracy the plasmonic properties of noble metal nanostructures and graphene-based materials. Such methods are based on classical physics, i.e. Drude conduction theory, classical electrodynamics, and atomistic polarizability to account for interband transitions, by also including an ad-hoc phenomenological correction to describe quantum tunneling. QM/ωFQ and QM/ωFQFμ are thus applied to selected test cases, for which computed results are compared with available experiments, showing the robustness and reliability of both approaches.

Continuum vs. atomistic approaches to computational spectroscopy of solvated systems

Molecular spectral signals can be significantly altered by solvent effects. Among the many theoretical approaches to this problem, continuum and atomistic solvation models have emerged as the most effective for properly describing solvent effects on the spectroscopic signal. In this feature article, we review the continuum and atomistic descriptions as applied to the calculation of molecular spectra, by detailing the similarities and differences between the two approaches from the formal point of view and by analyzing their advantages and disadvantages from the computational point of view. Various spectral signals, of increasing complexity, are considered and illustrative examples, selected to exacerbate the differences between the two approaches, are discussed.

Correction to "Going Beyond the Limits of Classical Atomistic Modeling of Plasmonic Nanostructures"

[This corrects the article DOI: 10.1021/acs.jpcc.1c04716.].

Water Maintains the UV-Vis Spectral Features During the Insertion of Anionic Naproxen and Ibuprofen into Model Cell Membranes

UV-vis spectra of anionic ibuprofen and naproxen in a model lipid bilayer of the cell membrane are investigated using computational techniques in combination with a comparative analysis of drug spectra in purely aqueous environments. The simulations aim at elucidating the intricacies behind the negligible changes in the maximum absorption wavelength in the experimental spectra. A set of configurations of the systems constituted by lipid, water, and drugs or just water and drugs are obtained from classical Molecular Dynamics simulations. UV-vis spectra are computed in the framework of atomistic Quantum Mechanical/Molecular Mechanics (QM/MM) approaches together with Time-Dependent Density Functional Theory (TD-DFT). Our results suggest that the molecular orbitals involved in the electronic transitions are the same, regardless of the chemical environment. A thorough analysis of the contacts between the drug and water molecules reveals that no significant changes in UV-vis spectra are a consequence of ibuprofen and naproxen molecules being permanently microsolvated by water molecules, despite the presence of lipid molecules. Water molecules microsolvate the charged carboxylate group as expected but also microsolvate the aromatic regions of the drugs.

Integrated Multiscale Multilevel Approach to Open Shell Molecular Systems

We present a novel multiscale approach to study the electronic structure of open shell molecular systems embedded in an external environment. The method is based on the coupling of multilevel Hartree-Fock (MLHF) and Density Functional Theory (MLDFT), suitably extended to the unrestricted formalism, to Molecular Mechanics (MM) force fields (FF). Within the ML region, the system is divided into active and inactive parts, thus describing the most relevant interactions (electrostatic, polarization, and Pauli repulsion) at the quantum level. The surrounding MM part, which is formulated in terms of nonpolarizable or polarizable FFs, permits a physically consistent treatment of long-range electrostatics and polarization effects. The approach is extended to the calculation of hyperfine coupling constants and applied to selected nitroxyl radicals in an aqueous solution.

Strain-Induced Plasmon Confinement in Polycrystalline Graphene

Terahertz spectroscopy is a perfect tool to investigate the electronic intraband conductivity of graphene, but a phenomenological model (Drude-Smith) is often needed to describe disorder. By studying the THz response of isotropically strained polycrystalline graphene and using a fully atomistic computational approach to fit the results, we demonstrate here the connection between the Drude-Smith parameters and the microscopic behavior. Importantly, we clearly show that the strain-induced changes in the conductivity originate mainly from the increased separation between the single-crystal grains, leading to enchanced localization of the plasmon excitations. Only at the lowest strain values explored, a behavior consistent with the deformation of the individual grains can instead be observed.

UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA

UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomolecular receptors. The extraction of information at the molecular level from experimental RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramolecular system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/molecular mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with experimental data, thus confirming the reliability of the computational protocol.

Body composition, trabecular bone score and vertebral fractures in subjects with Klinefelter syndrome

BACKGROUND

Klinefelter syndrome (KS) frequently causes skeletal fragility characterized by profound alterations in bone microstructure with increased risk of fractures. Increased body fat mass associated with decreased body lean mass are frequent features of KS with possible detrimental effects on skeletal health. In this cross-sectional study, we evaluated the associations between body composition parameters, vertebral fractures (VFs) and trabecular bone score (TBS) in adult subjects with KS.

METHODS

Seventy-one adult males (median age 41 years, range 18-64) with 47, XXY KS were consecutively enrolled by two Endocrinology and Andrology Units (IRCCS Humanitas Research Hospital in Milan and ASST Spedali Civili in Brescia). Dual-energy X-ray absorptiometry (DXA) was performed to assess bone mineral density (BMD) at lumbar spine, femoral neck and total hip, TBS and body composition. Prevalence of VFs was assessed by quantitative morphometry on lateral spine X-rays.

RESULTS

VFs were detected in 14 patients (19.7%), without significant association with low BMD (p = 0.912). In univariate logistic regression analysis, VFs were significantly associated with truncal/leg fat ratio (OR 2.32 per tertile; 95% CI 1.05-5.15; p = 0.038), whereas impaired TBS (detected in 23.4% of subjects) was associated with older age at study entry (p = 0.001) and at diagnosis of disease (p = 0.015), body mass index (BMI; p = 0.001), waist circumference (p = 0.007), fat mass index (FMI; p < 0.001), FMI/lean mass index (LMI) ratio (p = 0.001). Prevalence of VFs was not significantly different between subjects with impaired TBS as compared to those with normal TBS (26.7 vs. 18.4%; p = 0.485). Skeletal end-points were not significantly associated with duration of testosterone replacement therapy and serum testosterone and 25hydroxyvitamin D values.

CONCLUSION

Body composition might influence bone quality and risk of VFs in subjects with KS.

SIMULTANEOUS INTAKE OF LIQUID L-T4 FORMULATION AND IRON SALT: FACT OR FICTION?

Context

Hypothyroidism and iron deficiency are among the most common pathologies in population. Therefore, there are a lot of patients assuming both iron salt supplements and levothyroxine therapy.

Objective

To evaluate the effect of iron salt intake on L-T4 absorption among different L-T4 formulations.

Materials and methods

A PubMed/MEDLINE, Web of Science, and Scopus research was performed. Original studies and reviews written in English and published online up to 21 December 2022 were selected and reviewed. The final reference list was defined based on the relevance of each paper to the scope of this review.

Results

The data show an impaired absorption of L-T4 in tablets formulation when taken concomitantly with iron salt supplements. These phenomena seem to be circumvented by new L-T4 formulations.

Conclusion

Liquid L-T4 formulations can be ingested with iron salts, with no impairment of absorption. More studies are necessary to confirm these data for soft-gel capsules L-T4.

Dissecting Bonding Interactions in Cysteine Dimers

Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions.

Assessing the quality of QM/MM approaches to describe vacuo-to-water solvatochromic shifts

The performance of different quantum mechanics/molecular mechanics embedding models to compute vacuo-to-water solvatochromic shifts is investigated. In particular, both nonpolarizable and polarizable approaches are analyzed and computed results are compared to reference experimental data. We show that none of the approaches outperform the others and that errors strongly depend on the nature of the molecular transition to be described. Thus, we prove that the best choice of embedding model highly depends on the molecular system and that the use of a specific approach as a black box can lead to significant errors and, sometimes, totally wrong predictions.

Multiple Facets of Modeling Electronic Absorption Spectra of Systems in Solution

In this Perspective, we outline the essential physicochemical aspects that need to be considered when building a reliable approach to describe absorption properties of solvated systems. In particular, we focus on how to properly model the complexity of the solvation phenomenon, arising from dynamical aspects and specific, strong solute-solvent interactions. To this end, conformational and configurational sampling techniques, such as Molecular Dynamics, have to be coupled to accurate fully atomistic Quantum Mechanical/Molecular Mechanics (QM/MM) methodologies. By exploiting different illustrative applications, we show that an effective reproduction of experimental spectral signals can be achieved by delicately balancing exhaustive sampling, hydrogen bonding, mutual polarization, and nonelectrostatic effects.

Vitamin D and interferon-γ co-operate to increase the ACE-2 receptor expression in primary cultures of human thyroid cells

BACKGROUND

A more severe course of COVID-19 was associated with low levels of Vitamin D (VitD). Moreover in vitro data showed that VitD up-regulates the mRNA of the Angiotensin Converting Enzyme 2 (ACE-2), the SARS-COV-2 receptor in different type of cells. ACE-2 is expressed in several type of tissues including thyroid cells, on which its mRNA was shown to be up-regulated by interferon-gamma (IFN-γ). The aim of the present study was to investigate if treatment with VitD alone or in combination with IFN-γ would increase ACE-2 both at mRNA and protein levels in primary cultures of human thyrocytes.

MATERIALS AND METHODS

Primary thyroid cell cultures were treated with VitD and IFN-γ alone or in combination for 24 h. ACE-2 mRNA levels were measured by Real-time Polymerase Chain Reaction (RT-PCR). The presence of ACE-2 on thyroid cell membrane was assessed by immunocytochemistry basally and after the previous mentioned treatments.

RESULTS

ACE-2 mRNA levels increased after treatment with VitD and IFN-γ alone. The combination treatment (VitD + IFN-γ) showed an additive increase of ACE-2-mRNA. Immunocytochemistry experiments showed ACE-2 protein on thyroid cells membrane. ACE-2 expression increased after treatment with VitD and IFN-γ alone and further increased by the combination treatment with VitD + IFN-γ.

CONCLUSIONS

VitD would defend the body by SARS-COV2 both by regulating the host immune defense and by up-regulating of the expression of the ACE-2 receptor. The existence of a co-operation between VitD and IFN-γ demonstrated in other systems is supported also for ACE-2 up-regulation. These observations lead to an increased interest for the potential therapeutic benefits of VitD supplementation in COVID-19.

Formation and evolution of C-C, C-O, C[double bond, length as m-dash]O and C-N bonds in chemical reactions of prebiotic interest

A series of prebiotic chemical reactions yielding the precursor building blocks of amino acids, proteins and carbohydrates, starting solely from HCN and water is studied here. We closely follow the formation and evolution of the pivotal C-C, C-O, C[double bond, length as m-dash]O, and C-N bonds, which dictate the chemistry of the molecules of life. In many cases, formation of these bonds is set in motion by proton transfers in which individual water molecules act as catalysts so that water atoms end up in the products. Our results indicate that the prebiotic formation of carbon dioxide, formaldehyde, formic acid, formaldimine, glycolaldehyde, glycine, glycolonitrile, and oxazole derivatives, among others, are best described as highly nonsynchronous concerted single step processes. Nonetheless, for all reactions involving double proton transfer, the formation and breaking of O-H bonds around a particular O atom occur in a synchronous fashion, apparently independently from other primitive processes. For the most part, the first process to initiate seems to be the double proton transfer in the reactions where they are present, then bond breaking/formation around the reactive carbon in the carbonyl group and finally rupture of the C-N bonds in the appropriate cases, which are the most reluctant to break. Remarkably, within the limitations of our non-dynamical computational model, the wide ranges of temperature and pressure in which these reactions occur, downplay the problematic determination of the exact constraints on the early Earth.

Do We Really Need Quantum Mechanics to Describe Plasmonic Properties of Metal Nanostructures?

Optical properties of metal nanostructures are the basis of several scientific and technological applications. When the nanostructure characteristic size is of the order of few nm or less, it is generally accepted that only a description that explicitly describes electrons by quantum mechanics can reproduce faithfully its optical response. For example, the plasmon resonance shift upon shrinking the nanostructure size (red-shift for simple metals, blue-shift for d-metals such as gold and silver) is universally accepted to originate from the quantum nature of the system. Here we show instead that an atomistic approach based on classical physics, ωFQFμ (frequency dependent fluctuating charges and fluctuating dipoles), is able to reproduce all the typical "quantum" size effects, such as the sign and the magnitude of the plasmon shift, the progressive loss of the plasmon resonance for gold, the atomistically detailed features in the induced electron density, and the non local effects in the nanoparticle response. To support our findings, we compare the ωFQFμ results for Ag and Au with literature time-dependent DFT simulations, showing the capability of fully classical physics to reproduce these TDDFT results. Only electron tunneling between nanostructures emerges as a genuine quantum mechanical effect, that we had to include in the model by an ad hoc term.

Amide Spectral Fingerprints are Hydrogen Bonding-Mediated

The origin of the peculiar amide spectral features of proteins in aqueous solution is investigated, by exploiting a combined theoretical and experimental approach to study UV Resonance Raman (RR) spectra of peptide molecular models, namely N-acetylglycine-N-methylamide (NAGMA) and N-acetylalanine-N-methylamide (NALMA). UVRR spectra are recorded by tuning Synchrotron Radiation at several excitation wavelengths and modeled by using a recently developed multiscale protocol based on a polarizable QM/MM approach. Thanks to the unparalleled agreement between theory and experiment, we demonstrate that specific hydrogen bond interactions, which dominate hydration dynamics around these solutes, play a crucial role in the selective enhancement of amide signals. These results further argue the capability of vibrational spectroscopy methods as valuable tools for refined structural analysis of peptides and proteins in aqueous solution.

In silico design of graphene plasmonic hot-spots

We propose a route for the rational design of engineered graphene-based nanostructures, which feature enormously enhanced electric fields in their proximity. Geometrical arrangements are inspired by nanopatterns allowing single molecule detection on noble metal substrates, and are conceived to take into account experimental feasibility and ease in fabrication processes. The attention is especially focused on enhancement effects occurring close to edge defects and grain boundaries, which are usually present in graphene samples. There, very localized hot-spots are created, with enhancement factors comparable to noble metal substrates, thus potentially paving the way for single molecule detection from graphene-based substrates.

Cardiac involvement in athletes infected by SARS COV-2 disease

Objectives

The aim of the present study was to conduct a review of the current literature evaluating the available evidence to date in terms of epidemiology, pathophysiology and clinical presentation of COVID-19 in relation to cardiovascular involvement, with a special focus on the myocarditis model, in the population of athletes (professional and recreational) who are preparing to return to competitions, with the ultimate aim of guaranteeing maximum safety for resuming sports activities.

News

The COVID-19 pandemic has resulted in the inevitable cancellation of most sports activities, practiced at both a professional and amateur level, in order to minimize the risk of spreading the infection. Since the number of athletes who tested positive was rather high, the potential cardiac involvement in this peculiar population of subjects contracting the disease in a mild (asymptomatic, slightly symptomatic) or moderate form, has recently raised concerns following the observation of cases of recorded myocardial damage, myocarditis, arrhythmias and a first reported case of Sudden Cardiac Death (SCD) in a 27-year-old professional basketball player. Several studies even seem to confirm the possibility of permanent impairment of the cardiorespiratory system following the infection. Medical history, biomarkers, electrocardiographical and cardiac imaging features appear to be crucial in distinguishing cardiovascular alterations related to COVID-19 infection from typical adaptations to exercise related to athletes' heart.

Prospects and Projects

Clarifications and prospective data based on long-term follow-ups on larger populations of athletes are still needed to exclude the development of myocardial damage capable of negatively affecting prognosis and increasing cardiovascular risk in athletes recovered from COVID-19 in asymptomatic (simple positivity to SARS-COV-2) or in a mild form.

Conclusion

From a clinical point of view extreme caution is necessary when planning the return to sport (Return To Play-RTP) of athletes recovered from a mild or asymptomatic form of COVID-19: a careful preliminary medical-sports evaluation should be carried out in order to assess the potential development of myocardial damage that would increase their cardiovascular risk.

The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective

Specific S477N, N501Y, K417N, K417T, E484K mutations in the receptor binding domain (RBD) of the spike protein in the wild type SARS-COV-2 virus have resulted, among others, in the following variants: B.1.160 (20A or EU2, first reported in continental Europe), B1.1.7 (α or 20I501Y.V1, first reported in the United Kingdom), B.1.351 (β or 20H/501Y.V2, first reported in South Africa), B.1.1.28.1 (γ or P.1 or 20J/501Y.V3, first reported in Brazil), and B.1.1.28.2 (ζ, or P.2 or 20B/S484K, also first reported in Brazil). From the analysis of a set of bonding descriptors firmly rooted in the formalism of quantum mechanics, including Natural Bond Orbitals (NBO), Quantum Theory of Atoms In Molecules (QTAIM) and highly correlated energies within the Domain Based Local Pair Natural Orbital Coupled Cluster Method (DLPNO-CCSD(T)), and from a set of computed electronic spectral patterns with environmental effects, we show that the new variants improve their ability to recognize available sites to either hydrogen bond or to form salt bridges with residues in the ACE2 receptor of the host cells. This results in significantly improved initial virus⋅⋅⋅cell molecular recognition and attachment at the microscopic level, which trigger the infectious cycle.

Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach

We report on the first formulation of a novel polarizable QM/MM approach, where the density functional tight binding (DFTB) is coupled to the fluctuating charge (FQ) force field. The resulting method (DFTB/FQ) is then extended to the linear response within the TD-DFTB framework and challenged to study absorption spectra of large condensed-phase systems.

Impact of hypogonadism on bone mineral density and vertebral fractures in HIV-infected men

PURPOSE

Hypogonadism and osteoporosis are frequently reported in HIV-infected men and, besides multifactorial pathogenesis, they might be directly linked because of testicular involvement in bone health. We evaluated the prevalence of osteoporosis and vertebral fractures (VFs) in HIV-infected men, and assessed their relationship with gonadal function.

METHODS

We enrolled 168 HIV-infected men (median age 53). Osteoporosis and osteopenia were defined with T-score ≤  - 2.5SD and T-score between  - 1 and  - 2.5SD, respectively. VFs were assessed by quantitative morphometric analysis. Total testosterone (TT), calculated free testosterone (cFT), Sex Hormone Binding Globulin (SHBG), Luteinizing Hormone (LH) and Follicle Stimulating Hormone (FSH) were obtained; overt hypogonadism was defined on symptoms and low TT or cFT, and classified into primary and secondary according to gonadotropins; compensated hypogonadism was defined as normal TT and cFT with high LH levels.

RESULTS

Overall, osteoporosis and osteopenia were found in 87.5% of patients, and VFs were detected in 25% of them; hypogonadism was identified in 26.2% of cases. Osteoporotic patients had higher SHBG vs those with normal bone mineral density (BMD). Fractured patients were more frequently hypogonadal and with higher SHBG. SHBG showed negative correlation with both spine and femoral BMD, and positive correlation with VFs. In multivariate models, FSH showed negative impact only on femoral BMD, whereas older age and higher SHBG predicted VFs.

CONCLUSION

We found a high burden of bone disease and hypogonadism in HIV-infected men, and we showed that the impact of gonadal function on bone health is more evident on VFs than on BMD.

Ring Vibrations to Sense Anionic Ibuprofen in Aqueous Solution as Revealed by Resonance Raman

We unravel the potentialities of resonance Raman spectroscopy to detect ibuprofen in diluted aqueous solutions. In particular, we exploit a fully polarizable quantum mechanics/molecular mechanics (QM/MM) methodology based on fluctuating charges coupled to molecular dynamics (MD) in order to take into account the dynamical aspects of the solvation phenomenon. Our findings, which are discussed in light of a natural bond orbital (NBO) analysis, reveal that a selective enhancement of the Raman signal due to the normal mode associated with the C-C stretching in the ring, νC=C, can be achieved by properly tuning the incident wavelength, thus facilitating the recognition of ibuprofen in water samples.

Quantum Mechanics/Fluctuating Charge Protocol to Compute Solvatochromic Shifts

Despite the potentialities of the quantum mechanics (QM)/fluctuating charge (FQ) approach to model the spectral properties of solvated systems, its extensive use has been hampered by the lack of reliable parametrizations of solvents other than water. In this paper, we substantially extend the applicability of QM/FQ to solvating environments of different polarities and hydrogen-bonding capabilities. The reliability and robustness of the approach are demonstrated by challenging the model to simulate solvatochromic shifts of four organic chromophores, which display large shifts when dissolved in apolar, aprotic or polar, protic solvents.

Going Beyond the Limits of Classical Atomistic Modeling of Plasmonic Nanostructures

Theoretical modeling of plasmonic phenomena is of fundamental importance for rationalizing experimental measurements. Despite the great success of classical continuum modeling, recent technological advances allowing for the fabrication of structures defined at the atomic level require to be modeled through atomistic approaches. From a computational point of view, the latter approaches are generally associated with high computational costs, which have substantially hampered their extensive use. In this work, we report on a computationally fast formulation of a classical, fully atomistic approach, able to accurately describe both metal nanoparticles and graphene-like nanostructures composed of roughly 1 million atoms and characterized by structural defects.

Atom Probe Tomography Analysis of Mica

Laser-assisted atom probe tomography (APT) is a relatively new, powerful technique for sub-nanometric mineral and biomineral analysis. However, the laser-assisted APT analysis of highly anisotropic and chemically diverse minerals, such as phyllosilicates, may prove especially challenging due to the complex interaction between the crystal structure and the laser pulse upon applying a high electric field. Micas are a representative group of nonswelling clay minerals of relevance to a number of scientific and technological fields. In this study, a Mg-rich biotite was analyzed by APT to generate preliminary data on nonisotropic minerals and to investigate the effect of the crystallographic orientation on mica chemical composition and structure estimation. The difference in results obtained for specimens extracted from the (001) and (hk0) mica surfaces indicate the importance of both experimental parameters and the crystallography. Anisotropy of mica has a strong influence on the physicochemical properties of the mineral during field evaporation and the interpretation of APT data. The promising results obtained in the present study open the way to future innovative APT applications on mica and clay minerals and contribute to the general discussion on the challenges for the analysis of geomaterials by atom probe tomography.

Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes

The insertion process of Naproxen into model dimyristoylphosphatidylcholine (DMPC) membranes is studied by resorting to state-of-the-art classical and quantum mechanical atomistic computational approaches. Molecular dynamics simulations indicate that anionic Naproxen finds an equilibrium position right at the polar/nonpolar interphase when the process takes place in aqueous environments. With respect to the reference aqueous phase, the insertion process faces a small energy barrier of ≈5 kJ mol^-1 and yields a net stabilization of also ≈5 kJ mol^-1. Entropy changes along the insertion path, mainly due to a growing number of realizable microstates because of structural reorganization, are the main factors driving the insertion. An attractive fluxional wall of noncovalent interactions is characterized by all-quantum descriptors of chemical bonding (natural bond orbitals, quantum theory of atoms in molecules, noncovalent interaction, density differences, and natural charges). This attractive wall originates in the accumulation of tiny transfers of electron densities to the interstitial region between the fragments from a multitude of individual intermolecular contacts stabilizing the tertiary drug/water/membrane system.

A molecular twist on hydrophobicity

A thorough exploration of the molecular basis for hydrophobicity with a comprehensive set of theoretical tools and an extensive set of organic solvent S/water binary systems is discussed in this work. Without a single exception, regardless of the nature or structure of S, all quantum descriptors of bonding yield stabilizing S⋯water interactions, therefore, there is no evidence of repulsion and thus no reason for etymological hydrophobicity at the molecular level. Our results provide molecular insight behind the exclusion of S molecules by water, customarily invoked to explain phase separation and the formation of interfaces, in favor of a complex interplay between entropic, enthalpic, and dynamic factors. S⋯water interfaces are not just thin films separating the two phases; instead, they are non-isotropic regions with density gradients for each component whose macroscopic stability is provided by a large number of very weak dihydrogen contacts. We offer a definition of interface as the region in which the density of the components in the A/B binary system is not constant. At a fundamental level, our results contribute to better current understanding of hydrophobicity.

Notwithstanding the very weak nature of individual contacts, it is the cumulative effect of a large number of interactions (green NCI surfaces) which provides macroscopic stability to the interfaces.

On the Transition from a Biomimetic Molecular Switch to a Rotary Molecular Motor

The experimental investigation of the unidirectional motion characterizing the photoisomerization of single-molecule rotary motors requires accessible lab prototypes featuring an electronic circular dichroism (ECD) signal that is sensitive to the geometrical and electronic changes occurring during an ultrafast reactive process. Here we report a combined experimental/computational study of a candidate obtained via the asymmetrization of a light-driven biomimetic molecular switch. We show that the achieved motor has an ECD band that is remarkably sensitive to the isomerization motion, and it is therefore suitable for time-resolved ECD studies. However, we also find that, unexpectedly, the synthesized motor isomerizes on a time scale longer than the subpicosecond time measured for the achiral parent, a result that points to alternative candidates conserving a high reaction speed.

A polarizable three-layer frozen density embedding/molecular mechanics approach

We present a novel multilayer polarizable embedding approach in which the system is divided into three portions, two of which are treated using density functional theory and their interaction is based on frozen density embedding (FDE) theory, and both also mutually interact with a polarizable classical layer described using an atomistic model based on fluctuating charges (FQ). The efficacy of the model is demonstrated by extending the formalism to linear response properties and applying it to the simulation of the excitation energies of organic molecules in aqueous solution, where the solute and the first solvation shell are treated using FDE, while the rest of the solvent is modeled using FQ charges.

Multilevel Density Functional Theory

Following recent developments in multilevel embedding methods, we introduce a novel density matrix-based multilevel approach within the framework of density functional theory (DFT). In this multilevel DFT, the system is partitioned in an active and an inactive fragment, and all interactions are retained between the two parts. The decomposition of the total system is performed upon the density matrix. The orthogonality between the two parts is maintained by solving the Kohn–Sham equations in the MO basis for the active part only, while keeping the inactive density matrix frozen. This results in the reduction of computational cost. We outline the theory and implementation and discuss the differences and similarities with state-of-the-art DFT embedding methods. We present applications to aqueous solutions of methyloxirane and glycidol.

Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study

We present a detailed computational study of the UV/Vis spectra of four relevant flavonoids in aqueous solution, namely luteolin, kaempferol, quercetin, and myricetin. The absorption spectra are simulated by exploiting a fully polarizable quantum mechanical (QM)/molecular mechanics (MM) model, based on the fluctuating charge (FQ) force field. Such a model is coupled with configurational sampling obtained by performing classical molecular dynamics (MD) simulations. The calculated QM/FQ spectra are compared with the experiments. We show that an accurate reproduction of the UV/Vis spectra of the selected flavonoids can be obtained by appropriately taking into account the role of configurational sampling, polarization, and hydrogen bonding interactions.

Binding of SARS-CoV-2 to Cell Receptors: A Tale of Molecular Evolution

The magnified infectious power of the SARS‐CoV‐2 virus compared to its precursor SARS‐CoV is intimately linked to an enhanced ability in the mutated virus to find available hydrogen‐bond sites in the host cells. This characteristic is acquired during virus evolution because of the selective pressure exerted at the molecular level. We pinpoint the specific residue (in the virus) to residue (in the cell) contacts during the initial recognition and binding and show that the virus⋅⋅⋅cell interaction is mainly due to an extensive network of hydrogen bonds and to a large surface of noncovalent interactions. In addition to the formal quantum characterization of bonding interactions, computation of absorption spectra for the specific virus⋅⋅⋅cell interacting residues yields significant shifts of Δλ_max=47 and 66 nm in the wavelength for maximum absorption in the complex with respect to the isolated host and virus, respectively.

Calculation of Linear and Non-linear Electric Response Properties of Systems in Aqueous Solution: A Polarizable Quantum/Classical Approach with Quantum Repulsion Effects

We present a computational study of polarizabilities and hyperpolarizabilities of organic molecules in aqueous solutions, focusing on solute-water interactions and the way they affect a molecule's linear and non-linear electric response properties. We employ a polarizable quantum mechanics/molecular mechanics (QM/MM) computational model that treats the solute at the QM level while the solvent is treated classically using a force field that includes polarizable charges and dipoles, which dynamically respond to the solute's quantum-mechanical electron density. Quantum confinement effects are also treated by means of a recently implemented method that endows solvent molecules with a parametric electron density, which exerts Pauli repulsion forces upon the solute. By applying the method to a set of aromatic molecules in solution we show that, for both polarizabilities and first hyperpolarizabilities, observed solution values are the result of a delicate balance between electrostatics, hydrogen-bonding, and non-electrostatic solute solvent interactions.

Compared with classic Hashimoto's thyroiditis, chronic autoimmune serum-negative thyroiditis requires a lower substitution dose of L-thyroxine to correct hypothyroidism

PURPOSE

Serum-negative-chronic-autoimmune-thyroiditis (SN-CAT) is considered a milder variant of classic Hashimoto's thyroiditis (CHT). However, its prevalence remains unknown and it is still unclear whether SN-CAT behaves differently in terms of L-thyroxine (LT4) substitution treatment of hypothyroidism. Aims of this study were to estimate the prevalence of SN-CAT in a large series of hypothyroid patients and to compare LT4 requirements in hypothyroid patients with SN-CAT and CHT.

METHODS

Five-hundred-eighty-one consecutive patients with primary-autoimmune-hypothyroidism were enrolled in a cross-sectional study. LT4 requirements and thyroid-volume changes were longitudinally evaluated in 49 hypothyroid patients with SN-CAT and in 98 sex and age-matched hypothyroid patients with CHT.

RESULTS

In our series the prevalence of SN-CAT was 20.8%. At diagnosis, patients in the CHT and SN-CAT groups had similar male/female ratio, age and BMI, while serum TSH and thyroid-volume were significantly greater in the CHT group. In the longitudinal study, during a follow-up of 8.9 ± 4.6 years, 8 out of 49 (16.3%) SN-CAT patients developed positive tests for of circulating TPO-Ab and/or Tg-Ab. Thyroid-volume significantly decreased in CHT patients, but not in those with SN-CAT. The maximum daily substitution dose of LT4 was smaller in SN-CAT patients as compared with the CHT ones. Multivariate analysis showed that age, BMI, basal TSH and thyroid antibody status independently and significantly predicted the maximum daily substitution dose of LT4.

CONCLUSIONS

SN-CAT accounts for a significant proportion of patients with autoimmune hypothyroidism. Compared with hypothyroid patients diagnosed with CHT, the SN-CAT ones require smaller doses of LT4 to correct their hypothyroidism.

Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems

Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.

Graphene Plasmonics: Fully Atomistic Approach for Realistic Structures

We demonstrate that the plasmonic properties of realistic graphene and graphene-based materials can effectively and accurately be modeled by a novel, fully atomistic, yet classical, approach, named ωFQ. Such a model is able to reproduce all plasmonic features of these materials and their dependence on shape, dimension, and fundamental physical parameters (Fermi energy, relaxation time, and two-dimensional electron density). Remarkably, ωFQ is able to accurately reproduce experimental data for realistic structures of hundreds of nanometers (∼370k atoms), which cannot be afforded by any ab initio method. Also, the atomistic nature of ωFQ permits the investigation of complex shapes, which can hardly be dealt with by exploiting widespread continuum approaches.

Molecular spectroscopy of aqueous solutions: a theoretical perspective

Computational spectroscopy is an invaluable tool to both accurately reproduce the spectra of molecular systems and provide a rationalization for the underlying physics. However, the inherent difficulty to accurately model systems in aqueous solutions, owing to water's high polarity and ability to form hydrogen bonds, has severely hampered the development of the field. In this tutorial review we present a technique developed and tested in recent years based on a fully atomistic and polarizable classical modeling of water coupled with a quantum mechanical description of the solute. Thanks to its unparalleled accuracy and versatility, this method can change the perspective of computational and experimental chemists alike.

Effect of crystallographic orientation on atom probe tomography geochemical data?

The recent application of atom probe tomography (APT) to minerals is becoming a powerful tool to unravel geological information from the nanoscale perspective. Yet, there are still unknown fundamental aspects of this microscopy technique for geological applications and the potential crystallographic orientation effect is a significant one. Here, the influence of the crystallographic orientation on the quality of atom probe tomography geochemical data is investigated for two minerals with the same crystal system and different morphology: spinel (isometric, hexoctahedral, octahedron morphology) and galena (isometric, hexoctahedral, cube morphology). Two separate crystals of barite (orthorhombic, dipyramidal, prism morphology) were also analyzed to test the reproducibility of APT data. Despite the general absence of expected stoichiometry, overall bulk and isotopic chemical composition are not affected by crystallographic orientation. 3D data reconstructions of the specimens showed similar spatial distribution of the ion species for each mineral and 2D density maps showed identical (barite, galena) or specular (spinel) patterns for each pair of planes analyzed. Our findings indicate a negligible effect of the crystallographic orientation in APT geochemical data for standard highly symmetric minerals but also suggest the possible influence of the crystallographic structure and composition on the mineral stoichiometry and elements spatial distribution density.