TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules.

3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.

Use of Antimicrobial Silver Coatings on Fixed Orthodontic Appliances, Including Archwires, Brackets, and Microimplants: A Systematic Review.

Orthodontic treatments, while essential for achieving optimal oral health, present challenges in infection control due to the propensity for bacterial adhesion and biofilm formation on orthodontic appliances. Silver-coated orthodontic materials have emerged as a promising solution, leveraging the potent antimicrobial properties of silver nanoparticles (AgNPs). Antibacterial coatings are used in orthodontics to prevent the formation of bacterial biofilms. This systematic review evaluated the literature on antimicrobial silver coatings on fixed orthodontic appliances, including archwires, brackets, and microimplants. Two evaluators, working independently, rigorously conducted a comprehensive search of various databases, including PubMed, PubMed Central, Embase, Scopus and Web of Science. This systematic review comprehensively examined in vitro studies investigating the antimicrobial efficacy of silver-coated orthodontic archwires, brackets, and microimplants. The review registered in PROSPERO CRD42024509189 synthesized findings from 18 diverse studies, revealing consistent and significant reductions in bacterial adhesion, biofilm formation, and colony counts with the incorporation of AgNPs. Key studies demonstrated the effectiveness of silver-coated archwires and brackets against common oral bacteria, such as Streptococcus mutans and Staphylococcus aureus. Microimplants coated with AgNPs also exhibited notable antimicrobial activity against a range of microorganisms. The systematic review revealed potential mechanisms underlying these antimicrobial effects, highlighted implications for infection prevention in orthodontic practice, and suggested future research avenues. Despite some study heterogeneity and limitations, the collective evidence supports the potential of silver-coated orthodontic materials in mitigating bacterial complications, emphasizing their relevance in advancing infection control measures in orthodontics.

Role of the salt glands of Armeria maritima (halophyte) in removal of lead from tissues.

Armeria maritima is a halophyte exhibiting a strong tolerance to heavy metals. It grows on zinc-lead waste heaps. This study aimed to determine the role of salt glands in the removal of lead (Pb) from plants and to trace the path of lead from the shoots to the salt glands on the surface of leaves. Mechanisms allowing high tolerance to lead in A. maritima were also evaluated. These examinations were conducted on a lead-tolerant population and a lead-sensitive plant population. The plants were treated with Pb(NO3)2 and the path of lead was traced from the roots to the leaves. The lead-tolerant population transported twice as much lead as the sensitive population. The action of the salt glands resulted in 40% of the leaf lead content in the lead-tolerant population being expelled onto the surface of the leaves. These features indicate the high phytoremediation capabilities of these halophyte plants. The excretion of multi-ionic solutes by the salt glands results in the appearance of tiny crystals on the surface of the leaves. In this publication, for the first time, an attempt was made to determine what chemical compounds build up these crystals and to determine their crystal structure. Solving this problem was possible through the usage of single-crystal X-ray structural analysis.

Exploiting thiol-functionalized benzosiloxaboroles for achieving diverse substitution patterns - synthesis, characterization and biological evaluation of promising antibacterial agents.

Benzosiloxaboroles are an emerging class of medicinal agents possessing promising antimicrobial activity. Herein, the expedient synthesis of two novel thiol-functionalized benzosiloxaboroles 1e and 2e is reported. The presence of the SH group allowed for diverse structural modifications involving the thiol-Michael addition, oxidation, as well as nucleophilic substitution giving rise to a series of 27 new benzosiloxaboroles containing various polar functional groups, e.g., carbonyl, ester, amide, imide, nitrile, sulfonyl and sulfonamide, and pendant heterocyclic rings. The activity of the obtained compounds against selected bacterial and yeast strains, including multidrug-resistant clinical strains, was investigated. Compounds 6, 12, 20 and 22-24 show high activity against Staphylococcus aureus, including both methicillin-sensitive (MSSA) and methicillin-resistant (MRSA) strains, with MIC values in the range of 1.56-12.5 µg mL-1, while their cytotoxicity is relatively low. The in vitro assay performed with 2-(phenylsulfonyl)ethylthio derivative 20 revealed that, in contrast to the majority of known antibacterial oxaboroles, the plausible mechanism of antibacterial action, involving inhibition of the leucyl-tRNA synthetase enzyme, is not responsible for the antibacterial activity. Structural bioinformatic analysis involving molecular dynamics simulations provided a possible explanation for this finding.

Electromyographic Assessment of Muscle Activity in Children Undergoing Orthodontic Treatment-A Systematic Review.

Background: Surface electromyography (sEMG) can provide an objective and quantitative image of the functional state of neuromuscular balance in the stomatognathic system. The objective of this systematic review is to examine current scientific evidence regarding the effects of orthodontic treatment on muscle electromyographic (EMG) activity in children. Methods: The search strategy included the PubMed, PubMed Central, Web of Science, Scopus, and Embase databases. The inclusion criteria were studies assessing EMG muscle activity in children undergoing orthodontic treatment compared with untreated children. The Cochrane risk-of-bias tool (RoB2) and the Newcastle-Ottawa Scale (NOS) were used to evaluate the quality of the studies. The quality of evidence assessment was performed using GRADE analysis. The PRISMA diagram visually represented the search strategy, as well as screening and inclusion process. Results: The search strategy identified 540 potential articles. Fourteen papers met the inclusion criteria. Six studies were judged at a low risk of bias. The certainty of evidence was rated as moderate to low, according to the GRADE criteria. Studies showed alterations in EMG muscle activity in children undergoing orthodontic treatment. Conclusions: Orthodontic treatment appears to affect muscle activity in children undergoing orthodontic treatment. However, the quality of evidence is low and, therefore, it is not possible to definitively state this effect. Further long-term studies are needed to confirm the findings of this review. Study protocol number in PROSPERO database: CRD42023491005.

Electronic and Magnetic Interactions in 6-Oxoverdazyl Diradicals: Connection through N(1) vs C(3) Revisited.

Four isomeric di-6-oxoverdazyl diradicals connected at their N(1) or C(3) positions with either 1,3- or 1,4-phenylene linkers were obtained and characterized by spectroscopic, electrochemical, magnetic, and structural methods. These results were compared to those for the corresponding 6-oxoverdazyl monoradicals. UV-vis spectroscopy demonstrated that only the N(1)-connected para-through-benzene diradical has a distinct spectrum with significant bathochromic and hypsochromic shifts relative to the remaining species. Electrochemical analysis revealed two one-electron reduction processes in all diradiacals, while only the N(1)-connected para-through-benzene diradical exhibits two one-electron oxidation processes separated by 0.10 V. Variable temperature EPR measurements in polystyrene solid solutions gave negative mean exchange interaction energies J for all diradicals, suggesting the dominance of conformers with significant intramolecular antiferromagnetic interactions for the meta-through-benzene isomers. DFT calculations predict a small preference for the triplet state with the ΔES-T of about 0.25 kcal mol-1 for both meta-through-benzene connected diradicals.

Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors.

Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen-Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen-Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen-Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Šresolution) took only 68 s using 12 CPU cores.

Influence of N-protonation on electronic properties of acridine derivatives by quantum crystallography.

Applications of 9-aminoacridine (9aa) and its derivatives span fields such as chemistry, biology, and medicine, including anticancer and antimicrobial activities. Protonation of such molecules can alter their bioavailability as weakly basic drugs like aminoacridines exhibit reduced solubility at high pH levels potentially limiting their effectiveness in patients with elevated gastric pH. In this study, we analyse the influence of protonation on the electronic characteristics of the molecular organic crystals of 9-aminoacridine. The application of quantum crystallography, including aspherical atom refinement, has enriched the depiction of electron density in the studied systems and non-covalent interactions, providing more details than previous studies. Our experimental results, combined with a topological analysis of the electron density and its Laplacian, provided detailed descriptions of how protonation changes the electron density distribution around the amine group and water molecule, concurrently decreasing the electron density at bond critical points of N/O-H bonds. Protonation also alters the molecular architecture of the systems under investigation. This is reflected in different proportions of the N⋯H and O⋯H intermolecular contacts for the neutral and protonated forms. Periodic DFT calculations of the cohesive energies of the crystal lattice, as well as computed interaction energies between molecules in the crystal, confirm that protonation stabilises the crystal structure due to a positive synergy between strong halogen and hydrogen bonds. Our findings highlight the potential of quantum crystallography in predicting crystal structure properties and point to its possible applications in developing new formulations for poorly soluble drugs.

Laryngeal cartilage calcifications on lateral cephalometric radiographs.

The aim of this study was to determine the influence of age and gender on the incidence of calcification in laryngeal cartilage diagnosed on lateral cephalometric radiographs routinely taken for orthodontic diagnosis. The lateral cephalometric radiographs of 957 patients who met the study criteria were analyzed from among the 1000 lateral radiographs originally collected. The images were evaluated independently by two investigators. Given the dichotomous dependent variable (calcification or no calcification), a mixed logistic regression model was used to test how age and gender affected calcification. The effect of age and gender reliably determined the likelihood of laryngeal cartilage calcification. The greatest differences in the degree of calcification by gender were found at ages 20-25 years. The degree of calcification increased with age, reaching 100% in women at age 30 and in men at age 50. In women, the degree of calcification was higher than in men from the age of 13 years and levelled off at the age of 50 years. The interrater agreement was strong k = 0.97, z = 30.0, p < .001. Calcification can be detected by orthodontists trained in lateral cephalogram analysis and can be used as a screening or diagnostic tool to detect calcified areas in the larynx.

Enhancing hydrogen positions in X-ray structures of transition metal hydride complexes with dynamic quantum crystallography.

Hirshfeld atom refinement (HAR) is a method which enables the user to obtain more accurate positions of hydrogen atoms bonded to light chemical elements using X-ray data. When data quality permits, this method can be extended to hydrogen-bonded transition metals (TMs), as in hydride complexes. However, addressing hydrogen thermal motions with HAR, particularly in TM hydrides, presents a challenge. At the same time, proper description of thermal vibrations can be vital for determining hydrogen positions correctly. In this study, we employ tools such as SHADE3 and Normal Mode Refinement (NoMoRe) to estimate anisotropic displacement parameters (ADPs) for hydrogen atoms during HAR and IAM refinements performed for seven structures of TM (Fe, Ni, Cr, Nb, Rh and Os) and metalloid (Sb) hydride complexes for which both the neutron and the X-ray structures have been determined. A direct comparison between neutron and HAR/SHADE3/NoMoRe ADPs reveals that the similarity between neutron hydrogen ADPs and those estimated with NoMoRe or SHADE3 is significantly higher than when hydrogen ADPs are refined with HAR. Regarding TM-H bond lengths, traditional HAR exhibits a slight advantage over the other methods. However, combining NoMoRe/SHADE3 with HAR results in a minor decrease in agreement with neutron TM-H bond lengths. For the Cr complex, for which high-resolution X-ray data were collected, an investigation of resolution-related effects was possible.

Superior mesenteric artery clinical classification and morphometrical analysis.

BACKGROUND: The superior mesenteric artery is one of the most important arteries in the abdominal cavity, which is of great clinical importance, especially in surgical procedures and fatal ischemic complications. The aim of this study was to develop a clinical classification of the superior mesenteric artery. MATERIALS AND METHODS: Postmortem contrast-enhanced computed tomography of 104 (29.8% female, age 50.7±18.7) human bodies were analyzed. Based on anatomic predisposition to ischemic and iatrogenic complications, a three-tiered clinical classification of the superior mesenteric artery was developed. Type 0 was defined as standard risk for ischemic and iatrogenic complications. Type 1 was defined as increased thromboembolic risk with decreased risk of iatrogenic bleeding, and type 2 was defined as decreased ischemic risk with increased risk of iatrogenic bleeding. The supply area of the superior mesenteric artery was divided into 4 regions: pancreas, caecum, ascending colon, and transverse colon. RESULTS: Type 0 (standard risk) was found in 62.5% of cases. Type 1 was most frequently observed in the ascending colon region (15.4%). Type 2 was most frequently observed in the pancreatic region (17.3%). Regarding type, most abnormalities were found in the region of the ascending colon (18.3%), pancreas region (17.3%), and transverse colon (16.3%). CONCLUSIONS: The proposed clinical classification of SMA links anatomic variations in morphology with their clinical significance. A simple, three-level classification can be easily applied in daily practice and serve as a great support for preoperative evaluation and recognition of patients at risk of iatrogenic or thromboembolic complications.

Highly electron-deficient 3,6-diaza-9-borafluorene scaffolds for the construction of luminescent chelate complexes.

The synthesis and characterization of two fluorinated 3,6-diaza-9-hydroxy-9-borafluorene oxonium acids featuring improved hydrolytic stability and the strong electron-deficient character of the diazaborafluorene core is reported. These boracycles served as precursors of fluorescent spiro-type complexes with (O,N)-chelating ligands which revealed specific properties such as delayed emission, white light emission in the solid state and photocatalytic performance in singlet oxygen-mediated oxidation reactions.

Analysis of various radiological age-assessment methods in children, adolescents and young adults regarding the differences between the sexes and sides of the body - A comparative review.

A total of 76 articles published within the last twenty years, indexed in the PubMed and ResearchGate databases, were reviewed in order to compare medical imaging-based methods of age estimation of children, adolescents and young adults. The evaluated studies were analyzed for any statistically significant differences between the sexes and sides of the body, sample sizes, and population age. Irrespective of the evaluation method, there were some studies that showed a statistically significant differences in ossification stages between the male and female groups. Most of the studies whose authors conducted a statistical analysis demonstrated no significant differences between the left and right side of the body.

Oral Microbiota in Children with Cleft Lip and Palate: A Systematic Review.

BACKGROUND: Cleft in the lip and/or palate (CLP) is a congenital facial deformity that significantly impacts the oral cavity's structure and function. This malformation can affect the oral microbiota. The objective of this systematic review was to examine and consolidate the current scientific evidence on the oral microflora in children with CLP. METHODS: The search strategy included the PubMed, PubMed Central, Web of Science, Scopus, and Embase databases. The inclusion criteria were studies assessing oral microbiota in children with CLP. The Newcastle-Ottawa Scale (NOS) was used to evaluate the quality of the included studies. RESULTS: The search strategy identified 422 potential articles. Twelve papers met the inclusion criteria. High heterogeneity was observed in methodologies, sample sites, and patient characteristics. Eight studies assessed the levels of Streptococcus mutans and Lactobacillus in saliva, with some reporting significantly higher levels in the cleft group compared to controls, while others found no differences. One study reported a significantly higher colonization rate of Candida species in patients with cleft lip and/or palate. CONCLUSION: The results of the available studies are unclear. Further research is needed to gain a comprehensive understanding of the oral microbiota and potential implications for oral health management in this population. The review was not registered Registration Statement.

The evaluation of vasculature in post-mortem angio-computed tomography for anatomy research purposes: method description based on celiac trunk analysis.

BACKGROUND: Anatomical research based on deceased body specimens is a time-consuming process that requires a great deal of skill and time to perform correctly. Three-dimensional medical image analysis is an excellent tool for anatomic evaluation, but it often includes patients with comorbidities in the study group, which can skew the results. The purpose of this study was to develop and evaluate methods for anatomic research based on postmortem contrast-enhanced computed tomography angiography 3D reconstruction of the celiac trunk. MATERIALS AND METHODS: Postmortem contrast-enhanced computed tomography angiography of 105 (28.6% female, age 50.8±18.7) decedents without abdominal trauma or tumor was analyzed. The abdominal portion of the aorta and the celiac trunk with its branches were reconstructed and evaluated. The type of celiac trunk was evaluated. The results were analyzed. RESULTS: The celiac trunk, splenic artery, and common hepatic artery were visualized in all cases. The left gastric artery was visible in 97.1% of cases. The dorsal pancreatic artery was visualized in 61.0% of cases. The most common type of celiac trunk was 1 (88.6%), and the rarest types were 2, 3, and 6 (1.0%). We observed 4 morphologies of the truncus celiacus that did not fit the classification presented previously. CONCLUSIONS: This study has demonstrated that three-dimensional reconstruction of postmortem contrast-enhanced computed tomography is an excellent tool for performing accurate morphometric analyzes for anatomic research purposes. This method can serve as a source for anatomic studies in the healthy population.

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State.

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the P-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

Postmortem computed tomography assessment of skeletal and dental age in Polish children, adolescents, and young adults.

This paper presents a retrospective analysis of postmortem computed tomography (PMCT) scans of secondary ossification centers in the medial clavicular epiphysis, iliac crest apophysis, proximal humeral epiphysis, distal femoral epiphysis, proximal tibial epiphysis, and distal tibial epiphysis. At the same time, we analyzed PMCT scans of the maxillary and mandibular incisors, canines, premolars, and molars. We assessed 203 corpses, whose age ranged from 2 to 30 years, including 156 males and 47 females. The purpose of our study was to compare the processes of secondary ossification center fusion and permanent tooth maturation. Our research hypothesis was that certain stages of skeletal and dental maturation occur along consistent timelines that can be related to the chronological age. Secondary ossification center fusion was evaluated based on Kreitner and also McKern and Steward's classifications. The process of permanent tooth maturation was evaluated with Demirjian's method. Spearman's correlation coefficients (Rho) were positive in all analyses, which indicates that epiphyseal fusion progresses with age. The strongest relationship between the age and the stages of ossification was observed in the proximal tibial epiphysis (p < 0.001; Rho = 0.93) in females and in the medial clavicular epiphysis (p < 0.001; Rho = 0.77) in males. Studies show the importance of concomitant analysis of skeletal and dental maturation with a subsequent comparison of the results to achieve a greater precision in age estimation. A comparison of the results obtained in the study population of Polish children, adolescents, and young adults with the results of other studies in populations of similar ages showed a number of similarities in the time windows of dental and skeletal maturation. These similarities may help in age estimation.

Hirshfeld atom refinement of metal-organic frameworks for accurate positioning of hydrogen atoms and disorder analysis.

The application of Hirshfeld atom refinement (HAR) fragmentation is demonstrated for the refinement of metal-organic framework (MOF) crystal structures. The presented method enables anisotropic refinement of imidazolate hydrogen atoms, as well as complex analysis of solvent disorder within MOF pores. The data used were derived from standard resolution in-house single crystal X-ray diffraction measurements, demonstrating that high quality structural analysis of MOFs no longer requires access to neutron or synchrotron facilities.

d-Glucose- and d-mannose-based antimetabolites. Part 4: Facile synthesis of mono- and di-acetates of 2-deoxy-d-glucose prodrugs as potentially useful antimetabolites.

2-Deoxy-d-glucose (2-DG), a compound known to interfere with d-glucose and d-mannose metabolism, has been tested as a potential anticancer and antiviral agent. Preclinical and clinical studies focused on 2-DG have highlighted several limitations related to 2-DG drug-like properties, such as poor pharmacokinetic properties. To overcome this problem, we proposed design and synthesis of novel 2-DG prodrugs that subsequently could be tested using a variety of biochemical and molecular methods. We narrowed here our focus to esters of 2-DG as potential prodrugs based on the hypothesis that ubiquitous esterases will regenerate 2-DG, leading to increased circulation time of drug and adequate organ and tumor penetration. Testing this hypothesis in vitro and, especially, in vivo requires significant amounts of respective pure mono- and previously unknown di-acetylated water-soluble derivatives of 2-DG. Development of their efficient and practical method of synthesis was imperative. We describe novel facile and scalable syntheses of seven selectively acetylated water-soluble derivatives of 2-DG and present a detailed 1H and 13C NMR analysis of all final products. X-ray diffraction analysis has been performed for compound WP1122 that was selected for detailed preclinical and subsequent clinical evaluation as potential anticancer or antiviral agent.

Skeletal and dental age estimation via postmortem computed tomography in Polish subadults group.

This article is a retrospective analysis of postmortem computed tomography scans of ossification stages of the anterior and posterior intra-occipital sutures, the anterior arch of the atlas, and the neurocentral junction of the axis. We also analyzed the development of secondary ossification centers in the proximal humeral, femoral, and tibial epiphyses, and the distal femoral and tibial epiphyses. Additionally, the development of primary ossification centers in the wrist and metacarpals, and maxillary and mandibular deciduous tooth maturation. A total of 58 cadavers (35 males, 23 females), whose age ranged from 3rd month of pregnancy to 14 years, were analyzed. The results of this study show that analysis of synchondrosis closure, primary, and secondary ossification center development and deciduous tooth changes are a good tool for age estimation in subadults group (fetuses, newborns, infants, and children). The results of the study in a Polish population are consistent with those reported by other authors.