Computational analysis of substituent effects on proton affinity and gas-phase basicity of TEMPO derivatives and their hydrogen bonding interactions with water molecules

The study investigates the molecular structure of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its derivatives in the gas phase using B3LYP and M06-2X functional methods. Intermolecular interactions are analyzed using natural bond orbital (NBO) and atoms in molecules (AIM) techniques. NO2-substituted TEMPO displays high reactivity, less stability, and softer properties. The study reveals that the stability of TEMPO derivatives is mainly influenced by LP(e) → σ∗ electronic delocalization effects, with the highest stabilization observed on the oxygen atom of the nitroxide moiety. This work also considers electron density, atomic charges, and energetic and thermodynamic properties of the studied NO radicals, and their relative stability. The proton affinity and gas-phase basicity of the studied compounds were computed at T = 298 K for O-protonation and N-protonation, respectively. The studied DFT method calculations show that O-protonation is more stable than N-protonation, with an energy difference of 16.64-20.77 kcal/mol (22.80-25.68 kcal/mol) at the B3LYP (M06-2X) method. The AIM analysis reveals that the N-O…H interaction in H2O complexes has the most favorable hydrogen bond energy computed at bond critical points (3, - 1), and the planar configurations of TEMPO derivatives exhibit the highest EHB values. This indicates stronger hydrogen bonding interactions between the N-O group and water molecules.

A new strategy for making a sensitive sensor for aspirin drug: first-principles investigations by using pure and metal-doped BN nano-heterostructures

The present study used the DFT method to investigate aspirin's intermolecular interactions with boron nitride (BN) nanotubes modified with aluminum, gallium, and zinc. Our experiments obtained adsorption energy of -40.4 kJ/mol for aspirin on BN nanotubes. By doping each of the above metals on the surface of the BN nanotube, the aspirin adsorption energy increased dramatically. For BN nanotubes doped with Al, Ga, and Zn, this energy was -255, -251, and -250 kJ/mol. Thermodynamic analyses proved that all surface adsorptions are exothermic and spontaneous. Nanotubes' electronic structures and dipole moments have been examined following aspirin adsorption. In addition, AIM analysis has been performed for all systems in order to understand how the links were formed. According to the obtained results, BN nanotubes doped with metals, as mentioned previously, have a very high electron sensitivity to aspirin. These nanotubes can therefore be used to manufacture aspirin-sensitive electrochemical sensors.Communicated by Ramaswamy H. Sarma.

Atg8 family proteins, LIR/AIM motifs and other interaction modes

The Atg8 family of ubiquitin-like proteins play pivotal roles in autophagy and other processes involving vesicle fusion and transport where the lysosome/vacuole is the end station. Nuclear roles of Atg8 proteins are also emerging. Here, we review the structural and functional features of Atg8 family proteins and their protein-protein interaction modes in model organisms such as yeast, Arabidopsis, C. elegans and Drosophila to humans. Although varying in number of homologs, from one in yeast to seven in humans, and more than ten in some plants, there is a strong evolutionary conservation of structural features and interaction modes. The most prominent interaction mode is between the LC3 interacting region (LIR), also called Atg8 interacting motif (AIM), binding to the LIR docking site (LDS) in Atg8 homologs. There are variants of these motifs like "half-LIRs" and helical LIRs. We discuss details of the binding modes and how selectivity is achieved as well as the role of multivalent LIR-LDS interactions in selective autophagy. A number of LIR-LDS interactions are known to be regulated by phosphorylation. New methods to predict LIR motifs in proteins have emerged that will aid in discovery and analyses. There are also other interaction surfaces than the LDS becoming known where we presently lack detailed structural information, like the N-terminal arm region and the UIM-docking site (UDS). More interaction modes are likely to be discovered in future studies.

Search for Osme Bonds with π Systems as Electron Donors

The Osme bond is defined as pairing a Group 8 metal atom as an electron acceptor in a noncovalent interaction with a nucleophile. DFT calculations with the ωB97XD functional consider MO4 (M = Ru, Os) as the Lewis acid, paired with a series of π electron donors C2H2, C2H4, C6H6, C4H5N, C4H4O, and C4H4S. The calculations establish interaction energies in the range between 9.5 and 26.4 kJ/mol. Os engages in stronger interactions than does Ru, and those involving more extensive π-systems within the aromatic rings form stronger bonds than do the smaller ethylene and acetylene. Extensive analysis questions the existence of a true Osme bond, as the bonding chiefly involves interactions with the three O atoms of MO4 that lie closest to the π-system, via π(C-C)→σ*(M-O) transfers. These interactions are supplemented by back donation from M-O bonds to the π*(CC) antibonding orbitals of the π-systems. Dispersion makes a large contribution to these interactions, higher than electrostatics and much greater than induction.

Artificial intelligence/neural network system that accurately diagnoses hepatocellular carcinoma in nonalcoholic steatohepatitis

BACKGROUND AND AIM

The aim of this study was to develop a novel noninvasive test using an artificial intelligence/neural network system (called HCC-Scope) to diagnose early-stage hepatocellular carcinoma (HCC) on the background of nonalcoholic steatohepatitis (NASH).

METHODS

In total, 175 patients with histologically proven nonalcoholic fatty liver disease and 55 patients with NASH-HCC were enrolled for training and validation studies. Of the 55 patients with NASH-HCC, 27 (49.1%) had very early-stage HCC, and six (10.9%) had early-stage HCC based on the Barcelona Clinic Liver Cancer staging system. Diagnosis with HCC-Scope was performed based on 12 items: age, sex, height, weight, AST level, ALT level, gamma-glutamyl transferase level, cholesterol level, triglyceride level, platelet count, diabetes status, and IgM-free apoptosis inhibitor of macrophage level. The FMVWG2U47 hardware (Fujitsu Co. Ltd, Tokyo, Japan) and the originally developed software were used.

RESULTS

HCC-Scope had sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 100% for the differential diagnosis between non-HCC and HCC in a training study with gray zone analysis. It was also excellent in the validation study (95.0% sensitivity, 100% specificity, 100% PPV, and 97.1% NPV with gray zone analysis and 95.2% sensitivity, 100% specificity, 100% PPV, and 97.1% NPV without gray zone analysis). HCC-Scope had a significantly higher sensitivity (85.3%) and specificity (85.1%) than alpha-fetoprotein (AFP) level, AFP-L3 level, des-gamma-carboxy prothrombin (DCP) level, and the gender-age-AFP-L3-AFP-DCP (GALAD) score.

CONCLUSIONS

HCC-Scope can accurately differentially diagnose between non-HCC NASH and NASH-HCC, including very early-stage NASH-HCC.

Relation between Halogen Bond Strength and IR and NMR Spectroscopic Markers

The relationship between the strength of a halogen bond (XB) and various IR and NMR spectroscopic quantities is assessed through DFT calculations. Three different Lewis acids place a Br or I atom on a phenyl ring; each is paired with a collection of N and O bases of varying electron donor power. The weakest of the XBs display a C-X bond contraction coupled with a blue shift in the associated frequency, whereas the reverse trends occur for the stronger bonds. The best correlations with the XB interaction energy are observed with the NMR shielding of the C atom directly bonded to X and the coupling constants involving the C-X bond and the C-H/F bond that lies ortho to the X substituent, but these correlations are not accurate enough for the quantitative assessment of energy. These correlations tend to improve as the Lewis acid becomes more potent, which makes for a wider range of XB strengths.

The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses

Epitopes recognized by T cells are a collection of short peptide fragments derived from specific antigens or proteins. Immunological research to study T cell responses is hindered by the extreme degree of heterogeneity of epitope targets, which are usually derived from multiple antigens; within a given antigen, hundreds of different T cell epitopes can be recognized, differing from one individual to the next because T cell epitope recognition is restricted by the epitopes' ability to bind to MHC molecules, which are extremely polymorphic in different individuals. Testing large pools encompassing hundreds of peptides is technically challenging because of logistical considerations regarding solvent-induced toxicity. To address this issue, we developed the MegaPool (MP) approach based on sequential lyophilization of large numbers of peptides that can be used in a variety of assays to measure T cell responses, including ELISPOT, intracellular cytokine staining, and activation-induced marker assays, and that has been validated in the study of infectious diseases, allergies, and autoimmunity. Here, we describe the procedures for generating and testing MPs, starting with peptide synthesis and lyophilization, as well as a step-by-step guide and recommendations for their handling and experimental usage. Overall, the MP approach is a powerful strategy for studying T cell responses and understanding the immune system's role in health and disease. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generation of peptide pools ("MegaPools") Basic Protocol 2: MegaPool testing and quantitation of antigen-specific T cell responses.

Molecular Factors in PAD2 (PADI2) and PAD4 (PADI4) Are Associated with Interstitial Lung Disease Susceptibility in Rheumatoid Arthritis Patients

Around 50% of rheumatoid arthritis (RA) patients show some extra-articular manifestation, with the lung a usually affected organ; in addition, the presence of anti-citrullinated protein antibodies (ACPA) is a common feature, which is caused by protein citrullination modifications, catalyzed by the peptidyl arginine deiminases (PAD) enzymes. We aimed to identify single nucleotide variants (SNV) in PADI2 and PADI4 genes (PAD2 and PAD4 proteins, respectively) associated with susceptibility to interstitial lung disease (ILD) in RA patients and the PAD2 and PAD4 levels. Material and methods: 867 subjects were included: 118 RA-ILD patients, 133 RA patients, and 616 clinically healthy subjects (CHS). Allelic discrimination was performed in eight SNVs using qPCR, four in PADI2 and four in PADI4. The ELISA technique determined PAD2 and PAD4 levels in serum and bronchoalveolar lavage (BAL) samples, and the population structure was evaluated using 14 informative ancestry markers. Results: The rs1005753-GG (OR = 4.9) in PADI2 and rs11203366-AA (OR = 3.08), rs11203367-GG (OR = 2.4) in PADI4 are associated with genetic susceptibility to RA-ILD as well as the ACTC haplotype (OR = 2.64). In addition, the PAD4 protein is increased in RA-ILD individuals harboring the minor allele homozygous genotype in PADI4 SNVs. Moreover, rs1748033 in PADI4, rs2057094, and rs2076615 in PADI2 are associated with RA susceptibility. In conclusion, in RA patients, single nucleotide variants in PADI4 and PADI2 are associated with ILD susceptibility. The rs1748033 in PADI4 and two different SNVs in PADI2 are associated with RA development but not ILD. PAD4 serum levels are increased in RA-ILD patients.

Charge-Shift Bonding Propensity in Halogen-Bonded BXY (B Is a Small Lewis Base H2O or NH3; X and Y Are Halogen Atoms) Complexes: An NBO/NRT/AIM Investigation

Charge-shift (CS) bonding is a new bonding paradigm in the field of chemical bonds. Our recent study has revealed that certain Cu/Ag/Au-bonds display both CS bonding and ω-bonding characters. In this investigation, we extend our study to halogen bonding. Our focus is on scrutinizing the CS bonding in halogen-bonded BXY (B is a small Lewis base H2O or NH3; X and Y are halogen atoms) complexes by using natural bond orbital (NBO) analysis, natural resonance theory (NRT), and atoms in molecules (AIM) methods. The primary objective is to establish a connection between halogen bonding (B-X) in BXY and CS bonding in free XY (di-halogens). The calculations indicate that the studied BXY can be classified into two types. One type with a weak halogen bond shows closed-shell interaction. The other type with a stronger B-X interaction exhibits both CS bonding and ω-bonding characters (as seen in NH3ClF, NH3BrF, and NH3IF). Another interesting finding is a novel propensity that the CS bonding in free XY tends to carry over the halogen bonding in BXY, and the same propensity is found in Cu/Ag/Au ω-bonded species. The present study may offer an approach to probe CS bonding in many more 3c/4e ω-bonded molecules.

C∙∙∙O and Si∙∙∙O Tetrel Bonds: Substituent Effects and Transfer of the SiF3 Group

The tetrel bond (TB) between 1,2-benzisothiazol-3-one-2-TF3-1,1-dioxide (T = C, Si) and the O atom of pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO2, CN, F, CH3, OH, OCH3, NH2, and Li) is examined by quantum chemical means. The Si∙∙∙O TB is quite strong, with interaction energies approaching a maximum of nearly 70 kcal/mol, while the C∙∙∙O TB is an order of magnitude weaker, with interaction energies between 2.0 and 2.6 kcal/mol. An electron-withdrawing substituent on the Lewis base weakens this TB, while an electron-donating group has the opposite effect. The SiF3 group transfers roughly halfway between the N of the acid and the O of the base without the aid of cooperative effects from a third entity.

T-cell activation-induced marker assays in health and disease

Activation-induced marker (AIM) assays have proven to be an accessible and rapid means of antigen-specific T-cell detection. The method typically involves short-term incubation of whole blood or peripheral blood mononuclear cells with antigens of interest, where autologous antigen-presenting cells process and present peptides in complex with major histocompatibility complex (MHC) molecules. Recognition of peptide-MHC complexes by T-cell receptors then induces upregulation of activation markers on the T cells that can be detected by flow cytometry. In this review, we highlight the most widely used activation markers for assays in the literature while identifying nuances and potential downfalls associated with the technique. We provide a summary of how AIM assays have been used in both discovery science and clinical studies, including studies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunity. This review primarily focuses on AIM assays using human blood or peripheral blood mononuclear cell samples, with some considerations noted for tissue-derived T cells and nonhuman samples. AIM assays are a powerful tool that enables detailed analysis of antigen-specific T-cell frequency, phenotype and function without needing to know the precise antigenic peptides and their MHC restriction elements, enabling a wider analysis of immunity generated following infection and/or vaccination.

The comprehensive role of apoptosis inhibitor of macrophage (AIM) in pathological conditions

CD5L/AIM (apoptosis inhibitor of macrophage), as an important component in maintaining tissue homeostasis and inflammation, is mainly produced and secreted by macrophages but partially dissociated and released from blood AIM-IgM. AIM plays a regulatory role in intracellular physiological mechanisms, including lipid metabolism and apoptosis. AIM not only increases in autoimmune diseases, directly targets liver cells in liver cancer and promotes cell clearance in acute kidney injury, but also causes arteriosclerosis and cardiovascular events, and aggravates inflammatory reactions in lung diseases and sepsis. Obviously, AIM plays a pleiotropic role in the body. However, to date, studies have failed to decipher the mechanisms behind its different roles (beneficial or harmful) in inflammatory regulation. The inflammatory response is a "double-edged sword," and maintaining balance is critical for effective host defense while minimizing the adverse side effects of acute inflammation. Enhancing the understanding of AIM function could provide the theoretical basis for new therapies in these pathological settings. In this review, we discuss recent studies on the roles of AIM in lipid metabolism, autoimmune diseases and organic tissues, such as liver cancer, myocardial infarction, and kidney disease.

Triel Bonds with Au Atoms as Electron Donors

The novel triel bonds of BX₃ (X=H, F, Cl, Br, and I) and C₅ H₅ B as electron acceptors and AuR₂ (R=Cl and CH₃ ) as an electron donor were explored. The triel bond is a primary driving force for most complexes, while the contribution from a halogen-chlorine interaction in BX₃ -AuCl₂ (X=Cl, Br, and I) and an iodine-Au interaction in BI₃ -Au(CH₃ )₃ is also very important. Interestingly, the positively charged Au atom of AuCl₂ can attractively bind with the holes of BX₃ and C₅ H₅ B. The interaction energy lies in the range of 1 and 80 kcal/mol, in the order X=F<H<Cl<Br<I. In most cases, the triel bond of C₅ H₅ B is stronger than the triel bond of BX₃ . In the formation of B-Au triel bond, electrostatic energy is not dominant, while polarization energy including orbital interaction has the largest contribution for the strongly bonded complexes and dispersion energy for the weak triel bond.

Exploring the Relationship between Reactivity and Electronic Structure in Isorhodanine Derivatives Using Computer Simulations

The electronic structure and reactivity of 22 isorhodanine (IsRd) derivatives in the Diels-Alder reaction with dimethyl maleate (DMm) were investigated under two different environments (gas phase and continuous solvent CH3COOH), using free Gibbs activation energy, free Gibbs reaction energy, and frontier molecular orbitals to analyze their reactivity. The results revealed both inverse electronic demand (IED) and normal electronic demand (NED) characteristics in the Diels-Alder reaction and also provided insights into the aromaticity of the IsRd ring by employing HOMA values. Additionally, the electronic structure of the IsRd core was analyzed through topological examination of the electron density and electron localization function (ELF). Specifically, the study demonstrated that ELF was able to successfully capture chemical reactivity, highlighting the potential of this method to provide valuable insights into the electronic structure and reactivity of molecules.

Trapping of Small Molecules within Single or Double Cyclo[18]carbon Rings

The encapsulation of a set of small molecules, H₂, CO, CO₂, SO₂, and SO₃, by a circular C₁₈ ring is investigated by quantum calculations. These ligands lie near the center of the ring but, with the exception of H₂, are disposed roughly perpendicular to the ring plane. Their binding energies with the C₁₈ vary from 1.5 kcal/mol for H₂ up to 5.7 kcal/mol for SO₂, and the bonding is dominated by dispersive interactions spread over the entire ring. The binding of these ligands on the outside of the ring is weaker but allows the opportunity for each to bond covalently with the ring. A pair of C₁₈ units lie parallel to one another. This pair can bind each of these ligands in the area between them with only small perturbations of the double ring geometry. The binding energies of these ligands to this double ring configuration are amplified by some 50% compared to the single ring systems. The presented data concerning the trapping of small molecules may have larger implications regarding hydrogen storage or air pollution reduction.

Unsupervised discovery of ancestry-informative markers and genetic admixture proportions in biobank-scale datasets

Admixture estimation plays a crucial role in ancestry inference and genome-wide association studies (GWASs). Computer programs such as ADMIXTURE and STRUCTURE are commonly employed to estimate the admixture proportions of sample individuals. However, these programs can be overwhelmed by the computational burdens imposed by the 10⁵ to 10⁶ samples and millions of markers commonly found in modern biobanks. An attractive strategy is to run these programs on a set of ancestry-informative SNP markers (AIMs) that exhibit substantially different frequencies across populations. Unfortunately, existing methods for identifying AIMs require knowing ancestry labels for a subset of the sample. This supervised learning approach creates a chicken and the egg scenario. In this paper, we present an unsupervised, scalable framework that seamlessly carries out AIM selection and likelihood-based estimation of admixture proportions. Our simulated and real data examples show that this approach is scalable to modern biobank datasets. OpenADMIXTURE, our Julia implementation of the method, is open source and available for free.

Development of Host Immune Response to Bacteriophage in a Lung Transplant Recipient on Adjunctive Phage Therapy for a Multidrug-Resistant Pneumonia

Bacteriophage therapy is the use of viruses to kill bacteria for the treatment of antibiotic-resistant infections. Little is known about the human immune response following phage therapy. We report the development of phage-specific CD4 T cells alongside rising phage-specific immunoglobulin G and neutralizing antibodies in response to adjunctive bacteriophage therapy used to treat a multidrug-resistant Pseudomonas aeruginosa pneumonia in a lung transplant recipient. Clinically, treatment was considered a success despite the development phage-specific immune responses.

Bonding situations in tricoordinated beryllium phenyl complexes

The bonding situation in the tricoordinated beryllium phenyl complexes [BePh₃ ]^- , [(pyridine)BePh₂ ] and [(trimethylsilyl-N-heterocyclic imine)BePh₂ ] is investigated experimentally and computationally. Comparison of the NMR spectroscopic properties of these complexes and of their structural parameters, which were determined by single crystal X-ray diffraction experiments, indicates the presence of π-interactions. Topology analysis of the electron density reveals elliptical electron density distributions at the bond critical points and the double bond character of the beryllium-element bonds is verified by energy decomposition analysis with the combination of natural orbital for chemical valence. The present beryllium-element bonds are highly polarized and the ligands around the central atom have a strong influence on the degree of π-delocalization. These results are compared to related triarylboranes.

AIM™ platform: A new immunotherapy approach for viral diseases

In addition to complications of acute diseases, chronic viral infections are linked to both malignancies and autoimmune disorders. Lack of adequate treatment options for Epstein-Barr virus (EBV), Human T-lymphotropic virus type 1 (HTLV-1), and human papillomavirus (HPV) remains. The NexImmune Artificial Immune Modulation (AIM) nanoparticle platform can be used to direct T cell responses by mimicking the dendritic cell function. In one application, AIM nanoparticles are used ex vivo to enrich and expand (E+E) rare populations of multi-antigen-specific CD8⁺ T cells for use of these cells as an AIM adoptive cell therapy. This study has demonstrated using E+E CD8⁺ T cells, the functional relevance of targeting EBV, HTLV-1, and HPV. Expanded T cells consist primarily of effector memory, central memory, and self-renewing stem-like memory T cells directed at selected viral antigen peptides presented by the AIM nanoparticle. T cells expanded against either EBV- or HPV-antigens were highly polyfunctional and displayed substantial in vitro cytotoxic activity against cell lines expressing the respective antigens. Our initial work was in the context of exploring T cells expanded from healthy donors and restricted to human leukocyte antigen (HLA)-A*02:01 serotype. AIM Adoptive Cell Therapies (ACT) are also being developed for other HLA class I serotypes. AIM adoptive cell therapies of autologous or allogeneic T cells specific to antigens associated with acute myeloid leukemia and multiple myeloma are currently in the clinic. The utility and flexibility of the AIM nanoparticle platform will be expanded as we advance the second application, an AIM injectable off-the-shelf nanoparticle, which targets multiple antigen-specific T cell populations to either activate, tolerize, or destroy these targeted CD8⁺ T cells directly in vivo, leaving non-target cells alone. The AIM injectable platform offers the potential to develop new multi-antigen specific therapies for treating infectious diseases, cancer, and autoimmune diseases.

Abnormalities of the Halogen Bonds in the Complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I)

In this work, the hydrogen bonds and halogen bonds in the complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I) have been studied by quantum chemical calculations. We found three interesting abnormalities regarding the interactions. Firstly, the strength of halogen bonds increases in the order of IF < BrF < ClF < F2. Secondly, the halogen bonds formed by F2 are very strong, with an interaction energy in the range between −199.8 and −233.1 kJ/mol. Thirdly, all the halogen bonds are stronger than the hydrogen bonds in the systems we examined. All these results are against the general understanding of halogen bonds. These apparent abnormal properties are reconciled with the high polarizability of the Te atom and the strong inducing effect of F on the Te atom of Y2CTe. These findings provide a new perspective on halogen bonds. Additionally, we also proposed bonding distance-based methods to compare the strength of halogen/hydrogen bonds formed between different donor atoms and the same acceptor atom.

A Comprehensive Study of N-Butyl-1H-Benzimidazole

Imidazole derivatives have found wide application in organic and medicinal chemistry. In particular, benzimidazoles have proven biological activity as antiviral, antimicrobial, and antitumor agents. In this work, we experimentally and theoretically investigated N-Butyl-1H-benzimidazole. It has been shown that the presence of a butyl substituent in the N position does not significantly affect the conjugation and structural organization of benzimidazole. The optimized molecular parameters were performed by the DFT/B3LYP method with 6-311++G(d,p) basis set. This level of theory shows excellent concurrence with the experimental data. The non-covalent interactions that existed within our compound N-Butyl-1H-benzimidazole were also analyzed by the AIM, RDG, ELF, and LOL topological methods. The color shades of the ELF and LOL maps confirm the presence of bonding and non-bonding electrons in N-Butyl-1H-benzimidazole. From DFT calculations, various methods such as molecular electrostatic potential (MEP), Fukui functions, Mulliken atomic charges, and frontier molecular orbital (HOMO-LUMO) were characterized. Furthermore, UV-Vis absorption and natural bond orbital (NBO) analysis were calculated. It is shown that the experimental and theoretical spectra of N-Butyl-1H-benzimidazole have a peak at 248 nm; in addition, the experimental spectrum has a peak near 295 nm. The NBO method shows that the delocalization of the aσ-electron from σ (C1-C2) is distributed into antibonding σ* (C1-C6), σ* (C1-N26), and σ* (C6-H11), which leads to stabilization energies of 4.63, 0.86, and 2.42 KJ/mol, respectively. Spectroscopic investigations of N-Butyl-1H-benzimidazole were carried out experimentally and theoretically to find FTIR vibrational spectra.

'Virtual' Action Research: Two examples

Action research is the predominant approach for organisational inquiry, but it comes in many guises and in some cases ends up as all action and no research. A common feature of all action research is the necessity to meet stakeholders in person in order to gain an understanding 'from within', this is particularly the case where 'soft' action research is the basis of the inquiry. In this paper first, we reflect, briefly, upon the history of action research and second, upon the lessons leant from the outcomes from two projects. The first project was conducted 'virtually', between a college in the USA and one in the UK and the second undertaken during the disruption caused by the restrictions arising from the Covid-19 pandemic. The experiences gained from these two 'virtual' action research projects and the lessons learnt are of interest to both the 'traditional' and 'soft' action research community.

Involvement of Arsenic Atom of AsF3 in Five Pnicogen Bonds: Differences between X-ray Structure and Theoretical Models

Bonding within the AsF₃ crystal is analyzed via quantum chemical methods so as to identify and quantify the pnicogen bonds that are present. The structure of a finite crystal segment containing nine molecules is compared with that of a fully optimized cluster of the same size. The geometries are qualitatively different, with a much larger binding energy within the optimized nonamer. Although the total interaction energy of a central unit with the remaining peripheral molecules is comparable for the two structures, the binding of the peripherals with one another is far larger in the optimized cluster. This distinction of much stronger total binding within the optimized cluster is not limited to the nonamer but repeats itself for smaller aggregates as well. The average binding energy of the cluster rises quickly with size, asymptotically approaching a value nearly triple that of the dimer.

DFT calculations, structural analysis, solvent effects, and non-covalent interaction study on the para-aminosalicylic acid complex as a tuberculosis drug: AIM, NBO, and NMR analyses

In this study, the effect of non-covalent interactions on the para-aminosalicylic acid complex is explored using density functional theory (DFT) in the gas phase and the solution. Our findings exhibit that the achieved binding energies considerably change on going from the gas phase to the solution. Based on the obtained results, the absolute value of the binding energy of the complex in the polar solvents is lower than the non-polar ones while in the gas phase it is higher than the solution. The atoms in molecules (AIM) and the natural bond orbital (NBO) analyses are applied to estimate the topological properties and the charge transfer during complexation, respectively. The results indicate that the presence of the cation-π interaction increases the strength of the intramolecular hydrogen bond in the studied complex. Finally, the various electronic descriptors such as energy gap, hardness, softness, and electronic chemical potential are investigated to gain further insight into these interactions. According to the achieved results, the high energy gap of the complex in the water solvent indicates high chemical stability and low reactivity compared to the others. On the other hand, the most reactive as well as the softest complex belongs to the gas phase.

Interaction of 5-fluorouracil anticancer drug with nucleobases: insight from DFT, TD-DFT, and AIM calculations

In this study, the interaction of 5-fluorouracil (5FU) drug with adenine (A), guanine(G), cytosine(C), uracil (U), and thymine (T) nucleobases of DNA and RNA are surveyed at the ωB97XD/LANL2DZ, M06-2X/6-31G (d, p), MPW1PWQ1/6-31G(d, p), PBEPBE/6-31(d, p) and ωB97XD/6-31G(d, p) levels of density functional theory (DFT). The considered complexes of 5FU drug with nucleobases are optimized at the above level of theories. Max Force and RMS of optimization criteria are 0.00035 (Ha), and 0.0003 respectively. From optimized structures, the adsorption energy, thermodynamic parameters in gas and solvent media, quantum theory atom in molecule (QTAIM), electron localized function (ELF), and reduced density gradient (RDG) are calculated at ωB97XD/LANL2DZ and M06-2X/6-31G (d, p) level of DFT theory. The QTAIM, ELF, and RDG results confirm that the nature of bonding between 5FU drug with A, C, G, U, and T nucleobases is electrostatic or hydrogen bond type. The adsorption and thermodynamic energy results demonstrate that the interaction of the 5FU drug with C and G nucleobases is stronger than other nucleobases. The results of this study can be suggested the mechanism of interaction of the 5FU drug with nucleobases of DNA and RNA.Communicated by Ramaswamy H. Sarma.

Electronic sensors for alkali and alkaline earth cations based on Fullerene-C60 and silicon doped on C60 nanocages: a computational study

In this research, we have reported the electrical sensitivity of pristine C60 and silicon doped on C60 (SiC59) nanocages as sensors that can be used for detecting the presence of alkali (Li⁺, Na⁺, K⁺) and alkaline earth (Be²⁺, Mg²⁺, Ca²⁺) cations. The computations are carried out at the B3LYP level of theory with a 6-31G(d) basis set. The atoms in molecules (AIM) and natural bond orbital (NBO) analyses are performed to evaluate the intermolecular interactions between cations and nanocages. The physical properties of the selected complexes are also analyzed by the frontier molecular orbital, energy gap, electronegativity, chemical hardness, softness, and other quantities such as work function, number of transferred electron, and dipole moment. The results show that the adsorption process is exothermic and with increasing the charge of cations, the adsorption energies enhance. Our findings also reveal a decrease in the energy gap along with an increase in the electrical conductivity of the respective complexes. Finally, the density of state calculations is presented to confirm the obtained results.

Revealing Intra- and Intermolecular Interactions Determining Physico-Chemical Features of Selected Quinolone Carboxylic Acid Derivatives

The intra- and intermolecular interactions of selected quinolone carboxylic acid derivatives were studied in monomers, dimers and crystals. The investigated compounds are well-recognized as medicines or as bases for further studies in drug design. We employed density functional theory (DFT) in its classical formulation to develop gas-phase and solvent reaction field (PCM) models describing geometric, energetic and electronic structure parameters for monomers and dimers. The electronic structure was investigated based on the atoms in molecules (AIM) and natural bond orbital (NBO) theories. Special attention was devoted to the intramolecular hydrogen bonds (HB) present in the investigated compounds. The characterization of energy components was performed using symmetry-adapted perturbation theory (SAPT). Finally, the time-evolution methods of Car-Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) were employed to describe the hydrogen bond dynamics as well as the spectroscopic signatures. The vibrational features of the O-H stretching were studied using Fourier transformation of the autocorrelation function of atomic velocity. The inclusion of quantum nuclear effects provided an accurate depiction of the bridged proton delocalization. The CPMD and PIMD simulations were carried out in the gas and crystalline phases. It was found that the polar environment enhances the strength of the intramolecular hydrogen bonds. The SAPT analysis revealed that the dispersive forces are decisive factors in the intermolecular interactions. In the electronic ground state, the proton-transfer phenomena are not favourable. The CPMD results showed generally that the bridged proton is localized at the donor side, with possible proton-sharing events in the solid-phase simulation of stronger hydrogen bridges. However, the PIMD enabled the quantitative estimation of the quantum effects inclusion-the proton position was moved towards the bridge midpoint, but no qualitative changes were detected. It was found that the interatomic distance between the donor and acceptor atoms was shortened and that the bridged proton was strongly delocalized.

The Role of Hydrogen Bonds in Interactions between [PdCl4]2- Dianions in Crystal

[PdCl₄]^2- dianions are oriented within a crystal in such a way that a Cl of one unit approaches the Pd of another from directly above. Quantum calculations find this interaction to be highly repulsive with a large positive interaction energy. The placement of neutral ligands in their vicinity reduces the repulsion, but the interaction remains highly endothermic. When the ligands acquire a unit positive charge, the electrostatic component and the full interaction energy become quite negative, signalling an exothermic association. Raising the charge on these counterions to +2 has little further stabilizing effect, and in fact reduces the electrostatic attraction. The ability of the counterions to promote the interaction is attributed in part to the H-bonds which they form with both dianions, acting as a sort of glue.

Intermolecular Interactions and Spectroscopic Signatures of the Hydrogen-Bonded System-n-Octanol in Experimental and Theoretical Studies

n-Octanol is the object of experimental and theoretical study of spectroscopic signatures and intermolecular interactions. The FTIR measurements were carried out at 293 K for n-octanol and its deuterated form. Special attention was paid to the vibrational features associated with the O-H stretching and the isotope effect. Density Functional Theory (DFT) in its classical formulations was applied to develop static models describing intermolecular hydrogen bond (HB) and isotope effect in the gas phase and using solvent reaction field reproduced by Polarizable Continuum Model (PCM). The Atoms in Molecules (AIM) theory enabled electronic structure and molecular topology study. The Symmetry-Adapted Perturbation Theory (SAPT) was used for energy decomposition in the dimers of n-octanol. Finally, time-evolution methods, namely classical molecular dynamics (MD) and Car-Parrinello Molecular Dynamics (CPMD) were employed to shed light onto dynamical nature of liquid n-octanol with emphasis put on metric and vibrational features. As a reference, CPMD gas phase results were applied. Nuclear quantum effects were included using Path Integral Molecular Dynamics (PIMD) and a posteriori method by solving vibrational Schrödinger equation. The latter applied procedure allowed to study the deuterium isotope effect.

An ALS-associated variant of the autophagy receptor SQSTM1/p62 reprograms binding selectivity toward the autophagy-related hATG8 proteins

Recognition of human autophagy-related 8 (hATG8) proteins by autophagy receptors represents a critical step within this cellular quality control system. Autophagy impairment is known to be a pathogenic mechanism in the motor neuron disorder amyotrophic lateral sclerosis (ALS). Overlapping but specific roles of hATG8 proteins belonging to the LC3 and GABARAP subfamilies are incompletely understood, and binding selectivity is typically overlooked. We previously showed that an ALS-associated variant of the SQSTM1/p62 (p62) autophagy receptor bearing an L341V mutation within its ATG8-interacting motif (AIM) impairs recognition of LC3B in vitro, yielding an autophagy-deficient phenotype. Improvements in understanding of hATG8 recognition by AIMs now distinguish LC3-interaction and GABARAP-interaction motifs and predict the effects of L341V substitution may extend beyond loss of function to biasing AIM binding preference. Through biophysical analyses, we confirm impaired binding of the L341V-AIM mutant to LC3A, LC3B, GABARAP, and GABARAPL1. In contrast, p62 AIM interactions with LC3C and GABARAPL2 are unaffected by this mutation. Isothermal titration calorimetry and NMR investigations provided insights into the entropy-driven GABARAPL2/p62 interaction and how the L341V mutation may be tolerated. Competition binding demonstrated reduced association of the L341V-AIM with one hATG8 manifests as a relative increase in association with alternate hATG8s, indicating effective reprogramming of hATG8 selectivity. These data highlight how a single AIM peptide might compete for binding with different hATG8s and suggest that the L341V-AIM mutation may be neomorphic, representative of a disease mechanism that likely extends into other human disorders.

Structural and molecular properties of complexes of biomolecules and metal-organic frameworks: dispersion-corrected DFT treatment

Investigation of complexes of nanostructured materials and biomolecules has attracted much attention by various researchers as it can contribute to coherent growth and extended application of nanostructures in different technologies. In this research, following a comprehensive approach, we examined the interaction between different amino acids and metal-organic frameworks (MOFs) at atomic scale using computational chemistry. For this purpose, we employed the density functional theory (DFT-D2) calculations to afford a molecular description of the interaction properties of the amino acids and MOF-5 by examining the interaction energy and the electronic structure of the amino acid/MOF complexes. We found strong interactions between the amino acids and MOF through their polar groups as well as aromatic rings in the gas phase. However, our findings were significantly different in solvent media, where water molecules prevent the amino acids from approaching the active sites of MOF, causing weak attractions between them. The evaluation of nature of interaction between the amino acids and MOF by the atoms-in-molecules (AIM) theory shows that the electrostatic attractions are the main force contributing to bond formation between the interacting entities. Furthermore, our DFT-PBE model of theory was validated against the comprehensive MP2 quantum level of theory.

DFT study on the structural and chemical properties of Janus kinase inhibitor drug Baricitinib

Baricitinib is a small molecule used to treat moderate to severe rheumatoid arthritis (RA) in adults. It is an inhibitor of Janus kinase 1 and 2 (JAK1 and JAK2). It has also been repurposed as a potential treatment for Covid 19. The current study has been carried out to understand the structural and chemical properties of this molecule. The molecule is optimized by using density functional theory (DFT) method. The DFT calculations are performed using Gaussian 09 W software package. The bond lengths and bond angles between atoms in the molecules are investigated. The intramolecular interaction within the molecule is identified using the natural bond orbital (NBO) study. The atom in molecule (AIM) study is performed using Multiwfn software. All the calculations are performed at B3LYP /6311G++ (d, p) level of theory. The molecular parameters, such as first-order hyperpolarizability, HOMO-LUMO energy gap, global electrophilicity index, dipole moment, chemical potential, hardness, ionization energy and electron affinity are determined from the calculation. The molecular docking analysis of Baricitinib is also carried out against different target proteins such as 6VSB, 6W9C and 6LU7.

Enhancement of the Tetrel Bond by the Effects of Substituents, Cooperativity, and Electric Field: Transition from Noncovalent to Covalent Bond

The T⋅⋅⋅N tetrel bond (TB) formed between TX₃ OH (T=C, Si, Ge; X=H, F) and the Lewis base N≡CM (M=H, Li, Na) is studied by ab initio calculations at the MP2/aug-cc-pVTZ level. Complexes involving TH₃ OH contain a conventional TB with interaction energy less than 10 kcal/mol. This bond is substantially strengthened, approaching 35 kcal/mol and covalent character, when fluorosubstituted TF₃ OH is combined with NCLi or NCNa. Along with this enhanced binding comes a near equalization of the TB T⋅⋅⋅N and the internal T-O bond lengths, and the associated structure acquires a trigonal bipyramidal shape, despite a high internal deformation energy. This structural transformation becomes more complete, and the TB is further strengthened upon adding an electron acceptor BeCl₂ to the Lewis acid and a base to the NCM unit. This same TB strengthening can be accomplished also by imposition of an external electric field.

Substitution effects via aromaticity, polarizability, APT, AIM, IR analysis, and hydrogen adsorption in C20-nTin nanostructures: a DFT survey

In this paper, the substitution effects of titanium heteroatom(s) on aromaticity, the average isotropic polarizability (< α >), the atomic polar tensor (APT) charge, the electrostatic potential (ESP) map, and the atoms in molecule (AIM) analysis along with infrared (IR) spectroscopy of C₂₀ fullerene and its C_20-nTi_n derivatives (n = 1-5) are probed via density functional theory (DFT). The nucleus-independent chemical shifts (NICS) specify that substitution effect causes more aromaticity character of the optimized heterofullerenes than benzene molecule and higher APT charge distribution upon surfaces of them than pure cage. The highest negative and positive APT charge distribution on carbons of C₁₅Ti₅ and titanium substitutions of C₁₆Ti_4-2 implies that these sites can be attacked more readily by electrophilic and nucleophilic regents, respectively. We are very pleased to state that isolating the Ti-Ti single bonds by intermediacy of one or two C atoms is an applicable strategy for attaining the highest APT charge distribution on Ti atoms of C₁₆Ti_4-2 as suitable hydrogen storage. AIM analysis of the studied C_20-nAl_n derivatives signifies the highest electron density (ρ (r)) of 0.294 a.u. and the highest positive Laplacian of electron density (∇²ρ (r)) of 0.190 a.u., at bond critical points (BCPs) of C-Ti bond in the most stable C₁₉Ti₁ species. This heterofullerene shows the lowest < α > between the studied structures. IR spectroscopy shows that exclusive of C₁₆Ti_4-1 (as transition state), the other optimized hollow cages (as global minima) have no imaginary frequency.

Ability of Lewis Acids with Shallow σ-Holes to Engage in Chalcogen Bonds in Different Environments

Molecules of the type XYT = Ch (T = C, Si, Ge; Ch = S, Se; X,Y = H, CH₃, Cl, Br, I) contain a σ-hole along the T = Ch bond extension. This hole can engage with the N lone pair of NCH and NCCH₃ so as to form a chalcogen bond. In the case of T = C, these bonds are rather weak, less than 3 kcal/mol, and are slightly weakened in acetone or water. They owe their stability to attractive electrostatic energy, supplemented by dispersion, and a much smaller polarization term. Immersion in solvent reverses the electrostatic interaction to repulsive, while amplifying the polarization energy. The σ-holes are smaller for T = Si and Ge, even negative in many cases. These Lewis acids can nonetheless engage in a weak chalcogen bond. This bond owes its stability to dispersion in the gas phase, but it is polarization that dominates in solution.

Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate. A DFT and molecular docking study

In this research, the impact of non-covalent interactions on the FT-IR spectrum and structural, electronic, topological and vibrational properties of hybrid 4-methylbenzylammonium nitrate (4MBN) have been studied combining B3LYP/CC-PVTZ calculations with molecular docking. 4MBN was synthesized and characterized by using the FT-IR spectrum while the optimized structures in gas phase and in ethanol and aqueous solutions have evidenced monodentate coordination between the nitrate and methylbenzylammonium groups, in agreement with that experimental determined for this species by X-ray diffraction. Here, non-covalent interactions were deeply analyzed in terms of topological parameters (AIM), electron localization function (ELF), localized orbital locator (LOL), Hirshfeld surface and reduced density gradient (RDG) method. Weak interactions such as H-bonds, VDW and steric effect in 4MBN were visualized and quantified by the independent gradient density (IGM) based on the promolecular density. The hyper-conjugative and the delocalization of charge in 4MBN have been elucidated by natural bonding orbital (NBO) while its chemical reactivity was studied and discussed by using molecular electrostatic potential surface (MESP), frontier molecular orbital (FMOs), density of state (DOS) and partial density of state (PDOS). The complete vibrational assignments of 69 vibration modes expected for 4MBN are reported together with the scaled force constants while the electronic transitions were evaluated by TD-DFT calculations in ethanol solution. Thermal analysis (DTA and DSC) was also determined. Molecular docking calculations have suggested that 4MBN presents biological activity and could act as a good inhibitor against schizophrenia disease.

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller-Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers' stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm-1-1700 cm-1 and 2300 cm-1-3400 cm-1 in the gas phase and 600 cm-1-1800 cm-1 and 2200 cm-1-3400 cm-1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm-1-1700 cm-1 and 2300 cm-1-3300 cm-1 for the gas phase and one broad absorption region in the solid state between 700 cm-1 and 3100 cm-1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.

Concomitant High Apoptosis Inhibitor of Macrophage (AIM) and Low Prostate-Specific Antigen (PSA) Indicates Activated T Cell-Mediated Anticancer Immunity, Enhance Sensitivity to Pembrolizumab, and Elicit Good Prognosis in Prostate Cancer

BACKGROUND

Despite its widespread use, the use of prostate-specific antigen (PSA) alone as a screening biomarker for prostate cancer (PCa) leads often to unwarranted prostate biopsy, over-diagnosis, and consequently, over-treatment, because of its limited specificity. There are reports that the apoptosis inhibitor of macrophage (AIM), secreted mainly by macrophages and epithelial cells, is upregulated during inflammation and facilitates immune recognition of cancerous cells by blocking human regulator of complement activation.

OBJECTIVE

These controversies around the PSA utility necessitate a reexamination of its use as a screening tool. More so, despite the suggested implication of AIM in anticancer immunosurveillance, there is a dearth of information on its role in therapy response, disease progression, and clinical outcomes of patients with PCa. These inform the present study to probe the nature and role of AIM/PSA signaling in anticancer immunity and prognosis in PCa.

METHODS

A combination of bioinformatics-aided statistical analyses, gene function annotation, and immune infiltrate analyses, coupled with tissue staining, and function assays, namely migration, invasion, and clonogenicity assays, we employed.

RESULTS

We demonstrated that AIM and PSA expression levels are inversely correlated in PCa clinical samples and cell lines, with AIM^lowPSA^high defining PCa, compared to AIM^highPSA^low in normal samples. Concomitant aberrant PSA and significantly suppressed AIM expression levels positively correlated with high-grade disease and characterized by advanced stage prostate cancer, regardless of mutation status. We found that a high PSA/AIM ratio is associated with disease recurrence in patients with prostate cancer but is equivocal for overall survival. In addition, PSA-associated AIM suppression is implicated in the enhanced 'metastability' of PCa and a high AIM/PSA ratio is associated with strong castration-induced regression. CRISPR-mediated AIM knockout was associated with higher PSA expression while ectopic expression of AIM significantly attenuated the migration and invasive capability of PC3 and DU145 cells. Interestingly, compared to normal samples, we observed that AIM, biomarkers of T-cell activation and M1 phenotype markers are co-suppressed in PCa samples.

CONCLUSION

Herein, we demonstrate that AIM/CD5L binds to PSA and that a high PSA/AIM ratio defines advanced stage PCa (regardless of mutation status), is implicated in enhanced metastability, and associated with disease recurrence, while a high AIM/PSA ratio is associated with strong castration-induced regression. More so, the ectopic expression of AIM significantly enhances the anticancer effect of Pembrolizumab and elicits an increased CD8+ T-cell count in AIM^hiPSA^loPDL1+ PCa cases that are respondent to Pembrolizumab treatment.

Rapid induction of antigen-specific CD4+ T cells is associated with coordinated humoral and cellular immunity to SARS-CoV-2 mRNA vaccination

SARS-CoV-2 mRNA vaccines have shown remarkable clinical efficacy, but questions remain about the nature and kinetics of T cell priming. We performed longitudinal antigen-specific T cell analyses on healthy SARS-CoV-2-naive and recovered individuals prior to and following mRNA prime and boost vaccination. Vaccination induced rapid antigen-specific CD4+ T cell responses in naive subjects after the first dose, whereas CD8+ T cell responses developed gradually and were variable in magnitude. Vaccine-induced Th1 and Tfh cell responses following the first dose correlated with post-boost CD8+ T cells and neutralizing antibodies, respectively. Integrated analysis revealed coordinated immune responses with distinct trajectories in SARS-CoV-2-naive and recovered individuals. Last, whereas booster vaccination improved T cell responses in SARS-CoV-2-naive subjects, the second dose had little effect in SARS-CoV-2-recovered individuals. These findings highlight the role of rapidly primed CD4+ T cells in coordinating responses to the second vaccine dose in SARS-CoV-2-naive individuals.

Identification of a Grotthuss proton hopping mechanism at protonated polyhedral oligomeric silsesquioxane (POSS) - water interface

The attachment and dissociation of a proton from a water molecule and the proton transfers at solid-liquid interfaces play vital roles in numerous biological, chemical processes and for the development of sustainable functional materials for energy harvesting and conversion applications. Using first-principles computational methodologies, we investigated the protonated forms of polyhedral oligomeric silsesquioxane (POSS-H⁺) interacting with water clusters (W_n, where n = 1-6) as a model to quantify the proton conducting and localization ability at solid-liquid interfaces. Successive addition of explicit water molecules to POSS-H⁺ shows that the assistance of at least three water molecules is required to dissociate the proton from POSS with the formation of an Eigen cation (H₉O₄⁺), whereas the presence of a fourth water molecule highly favors the formation of a Zundel ion (H₅O₂⁺). Reaction pathway and energy barrier analysis reveal that the formation of the Eigen cation requires significantly higher energy than the Zundel features. This confirms that the Zundel ion is destabilized and promptly converts in to Eigen ion at this interface. Moreover, we identified a Grotthuss-type mechanism for the proton transfer through a water chain close to the interface, where symmetrical and unsymmetrical arrangements of water molecules around H⁺ of protonated POSS-H⁺ are involved in the conduction of proton through water wires where successive Eigen-to-Zundel and Zundel-to-Eigen transformations are observed in quick succession.

Non-Covalent Forces in Naphthazarin-Cooperativity or Competition in the Light of Theoretical Approaches

Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

The Role of Renal Macrophage, AIM, and TGF-β1 Expression in Renal Fibrosis Progression in IgAN Patients

Objective

To analyze the expression of macrophages, AIM, TGF-β1 in the kidney of IgAN patients, and to explore the role of macrophages, AIM, TGF-β1 in the progression of renal fibrosis in IgAN patients.

Methods

The paraffin specimens of renal tissue from 40 IgAN patients were selected as the observation group. At the same time, paraffin specimens of normal renal tissue from 11 patients treated by nephrectomy were selected as the normal control group. We observed the distribution of macrophages, the expression of AIM and TGF-β1 by immunohistochemical staining and/or immunofluorescence.

Result

The number of M0, M1, M2 macrophages could be found increased in IgAN patients. M0 macrophages are mainly polarized towards M2 macrophages. The expression of AIM and TGF-β1 were significantly higher in IgAN patients than in NC. M2 macrophage, AIM and TGF-β1 were positively correlated with serum creatinine and 24-hour proteinuria, but negatively correlated with eGFR. M2 macrophages, AIM, TGF-β1 were positively correlated with fibrotic area.

Conclusion

M2 macrophages, AIM and TGF-β1 play important roles in the process of IgAN fibrosis, and the three influence each other.

Competition of Intra- and Intermolecular Forces in Anthraquinone and Its Selected Derivatives

Intra- and intermolecular forces competition was investigated in the 9,10-anthraquinone (1) and its derivatives both in vacuo and in the crystalline phase. The 1,8-dihydroxy-9,10-anthraquinone (2) and 1,8-dinitro-4,5-dihydroxy-anthraquinone (3) contain Resonance-Assisted Hydrogen Bonds (RAHBs). The intramolecular hydrogen bonds properties were studied in the electronic ground and excited states employing Møller-Plesset second-order perturbation theory (MP2), Density Functional Theory (DFT) method in its classical formulation as well as its time-dependent extension (TD-DFT). The proton potential functions were obtained via scanning the OH distance and the dihedral angle related to the OH group rotation. The topological analysis was carried out on the basis of theories of Atoms in Molecules (AIM-molecular topology, properties of critical points, AIM charges) and Electron Localization Function (ELF-2D maps showing bonding patterns, calculation of electron populations in the hydrogen bonds). The Symmetry-Adapted Perturbation Theory (SAPT) was applied for the energy decomposition in the dimers. Finally, Car-Parrinello molecular dynamics (CPMD) simulations were performed to shed light onto bridge protons dynamics upon environmental influence. The vibrational features of the OH stretching were revealed using Fourier transformation of the autocorrelation function of atomic velocity. It was found that the presence of OH and NO2 substituents influenced the geometric and electronic structure of the anthraquinone moiety. The AIM and ELF analyses showed that the quantitative differences between hydrogen bonds properties could be neglected. The bridged protons are localized on the donor side in the electronic ground state, but the Excited-State Intramolecular Proton Transfer (ESIPT) was noticed as a result of the TD-DFT calculations. The hierarchy of interactions determined by SAPT method indicated that weak hydrogen bonds play modifying role in the organization of these crystal structures, but primary ordering factor is dispersion. The CPMD crystalline phase results indicated bridged proton-sharing in the compound 2.

Competition between Inter and Intramolecular Tetrel Bonds: Theoretical Studies Complemented by CSD Survey

Crystal structures document the ability of a TF₃ group (T=Si, Ge, Sn, Pb) situated on a naphthalene system to engage in an intramolecular tetrel bond (TB) with an amino group on the adjoining ring. Ab initio calculations evaluate the strength of this bond and evaluate whether it can influence the ability of the T atom to engage in a second, intermolecular TB with another nucleophile. A very strong CN^- anionic base can approach the T either along the extension of a T-C or T-F bond and form a strong TB with an interaction energy approaching 100 kcal/mol, although this bond is weakened a bit by the presence of the internal T⋅⋅⋅N bond. The much less potent NCH base engages in a correspondingly longer and weaker TB, less than 10 kcal/mol. Such an intermolecular TB is weakened by the presence of the internal TB, to the point that it only occurs for the two heavier tetrel atoms Sn and Pb.

Multifaceted Roles of CD5L in Infectious and Sterile Inflammation

CD5L, a protein expressed and secreted mainly by macrophages, is emerging as a critical immune effector. In addition to its well-defined function as an anti-apoptotic protein, research over the last decade has uncovered additional roles that range from pattern recognition to autophagy, cell polarization, and the regulation of lipid metabolism. By modulating all these processes, CD5L plays a key role in highly prevalent diseases that develop by either acute or chronic inflammation, including several infectious, metabolic, and autoimmune conditions. In this review, we summarize the current knowledge of CD5L and focus on the relevance of this protein during infection- and sterile-driven inflammatory pathogenesis, highlighting its divergent roles in the modulation of inflammation.

Anion-Anion Interactions in Aerogen-Bonded Complexes. Influence of Solvent Environment

Ab initio calculations are applied to the question as to whether a AeX₅^- anion (Ae = Kr, Xe) can engage in a stable complex with another anion: F^-, Cl^-, or CN^-. The latter approaches the central Ae atom from above the molecular plane, along its C₅ axis. While the electrostatic repulsion between the two anions prevents their association in the gas phase, immersion of the system in a polar medium allows dimerization to proceed. The aerogen bond is a weak one, with binding energies less than 2 kcal/mol, even in highly polar aqueous solvent. The complexes are metastable in the less polar solvents THF and DMF, with dissociation opposed by a small energy barrier.

Comparison of Bifurcated Halogen with Hydrogen Bonds

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way around where two acids engage with the lone pair of a single base. In comparison to FBr and FI, the H-bonding FH acid is better able to participate in a bifurcated sharing with two bases. This behavior is traced to the properties of the monomers, in particular the specific shape of the molecular electrostatic potential, the anisotropy of the orbitals of the acid and base that interact directly with one another, and the angular extent of the total electron density of the two molecules.

Spindle cell carcinoma of the breast managed with neoadjuvant AIM: A case report

Spindle cell carcinoma (SpC), also known as metaplastic carcinoma—spindle cell type, is a subtype of metaplastic carcinoma. Metaplastic carcinomas of the breast are rare but are thought to be more aggressive than invasive ductal carcinomas. Due to their rarity, there are few randomized trials that can inform any standardized approaches to treatment. Treatment is instead extrapolated from other types of breast cancer or metaplastic carcinomas of different locations. Here we present the first known case report of a patient with spindle cell carcinoma of the breast successfully treated with a standard sarcoma neoadjuvant regimen of doxorubicin, ifosfamide, and mesna (AIM) that resulted in >99% necrosis of the tumor and negative margins at the time of resection.

Reliable Comparison of Pnicogen, Chalcogen, and Halogen Bonds in Complexes of 6-OXF2-Fulvene (X = As, Sb, Se, Te, Be, I) With Three Electron Donors

The pnicogen, chalcogen, and halogen bonds between 6-OXF₂-fulvene (X = As, Sb, Se, Te, Br, and I) and three nitrogen-containing bases (FCN, HCN, and NH₃) are compared. For each nitrogen base, the halogen bond is strongest, followed by the pnicogen bond, and the chalcogen bond is weakest. For each type of bond, the binding increases in the FCN < HCN < NH₃ pattern. Both FCN and HCN engage in a bond with comparable strengths and the interaction energies of most bonds are < -6 kcal/mol. However, the strongest base NH₃ forms a much more stable complex, particularly for the halogen bond with the interaction energy going up to -18 kcal/mol. For the same type of interaction, its strength increases as the mass of the central X atom increases. These bonds are different in strength, but all of them are dominated by the electrostatic interaction, with the polarization contribution important for the stronger interaction. The presence of these bonds changes the geometries of 6-OXF₂-fulvene, particularly for the halogen bond formed by NH₃, where the F-X-F arrangement is almost vertical to the fulvene ring.

The effect of cation-π interactions on the stability and electronic properties of anticancer drug Altretamine: a theoretical study

The present work utilizes density functional theory (DFT) calculations to study the influence of cation-π interactions on the electronic properties of the complexes formed by Altretamine [2,4,6-tris(dimethylamino)-1,3,5-triazine], an anticancer drug, with mono- and divalent (Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺ and Ca²⁺) metal cations. The structures were optimized with the M06-2X method and the 6-311++G(d,p) basis set in the gas phase and in solution. The theory of `Atoms in Molecules' (AIM) was applied to study the nature of the interactions by calculating the electron density ρ(r) and its Laplacian at the bond critical points. The charge-transfer process during complexation was evaluated using natural bond orbital (NBO) analysis. The results of DFT calculations demonstrate that the strongest/weakest interactions belong to Be²⁺/K⁺ complexes. There are good correlations between the achieved densities and the amounts of charge transfer with the interaction energies. Finally, the stability and reactivity of the cation-π interactions can be determined by quantum chemical computation based on the molecular orbital (MO) theory.