Efficient determination of Born-effective charges, LO-TO splitting, and Raman tensors of solids with a real-space atom-centered deep learning approach.

We introduce a deep neural network (DNN) framework called the Real-space Atomic Decomposition NETwork (RADNET), which is capable of making accurate predictions of polarization and of electronic dielectric permittivity tensors in solids. This framework builds on previous, atom-centered approaches while utilizing deep convolutional neural networks. We report excellent accuracies on direct predictions for two prototypical examples: GaAs and BN. We then use automatic differentiation to calculate the Born-effective charges, longitudinal optical-transverse optical (LO-TO) splitting frequencies, and Raman tensors of these materials. We compute the Raman spectra, and find agreement with ab initio results. Lastly, we explore ways to generalize polarization predictions while taking into account periodic boundary conditions and symmetries.

MB38(M=Be and Zn): A Quasi-Planar Structure Rather Than A Core-Shell Octahedral Borospherene Structure.

In a recent paper (ChemPhysChem, 2023, 24, e202200947), based on the results computed using DFT method, the perfect core-shell octahedral configuration Be@B38 and Zn@B38 was reported to be the global minima of the MB38(M=Be and Zn) clusters. However, this paper presents the lower energy structures of MB38(M=Be and Zn) clusters as a quasi-planar configuration, the Be atom is found to reside on the convex surface of the quasi-planar B38 isomer, while the Zn atom tends to be attached to the top three B atoms of the quasi-planar B38 isomer. Our results show that quasi-planar MB38(M=Be and Zn) at DFT method have lower energy than core-shell octahedral configuration M@B38(M=Be and Zn). Natural atomic charges, valence electron density, electron localization function (ELF) analyses identify the MB38(M=Be and Zn) to be charge transfer complexes (Be2+B382-and Be1+B381-) and suggest primarily the electrostatic interactions between doped atom and B38 fragment. The photoelectron spectra of the corresponding anionic structures were simulated, providing theoretical basis for future structural identification.

Dimers and 2D Networks of Adamantane-Related Ternary Organosilicon Coinage Metal Sulfide Clusters.

Adamantane-type organotin sulfide clusters were recently shown to react with coinage metal phosphine complexes under replacement of an organic substituent by a metal-phosphine unit. An extension of such studies involving the silicon-based congener [(PhSi)4S6] (A) revealed that the cluster core will be partly disassembled and a {PhSi} moiety is replaced by a coinage metal phosphine complex to form [(Et3PAg)3(PhSi)3S6] (B) and [Na2(thf)2.33][(Me3PCu)(PhSi)3S6] (C). Herein, we present an extension of this work upon variation of the reactants and reaction conditions. Besides the isolation of crystalline precursor complexes [CuCl(PMe2Ph)3] (1) and [AgCl(PMe2Ph)2]2 (2), the study addresses reactions of A with AgCl and a phosphine ligand in CH2Cl2, upon which A is completely disassembled to form [(Ph3P)3Ag(µ-S)SiCl2Ph] (3). In another case a CH2 group, most likely stemming from CH2Cl2, was attached to the ligand, thus generating [{PhCl(S)SiSCH2P(Ph2)CH2CH2}2] (4). Upon using CuCl and 1,4­bis(diphenylphosphino)butane (dppb) we isolated the phosphine-bridged analog of B, [{(dppbCu2)CuP(Ph2)(CH2CH2)(PhSi)3S6}2] (5). In order to receive the yet elusive silver homolog of C, we used PMe2Ph as a bulkier ligand. This way we generated a 2D coordination polymer of the desired composition, [Na2(thf)1.5][(Me2PhPAg)(PhSi)3S6] (6). UV-visible spectra of 6 indicated a bandgap of 3.89 eV, thus blue-shifted in regards to B and C.

Cross polarization stability in multidimensional NMR spectroscopy of biological solids.

Magic-angle spinning (MAS) solid-state nuclear magnetic resonance (SSNMR) spectroscopy is a powerful and versatile technique for probing structure and dynamics in large, insoluble biological systems at atomic resolution. With many recent advances in instrumentation and polarization methods, technology development in SSNMR remains an active area of research and presents opportunities to further improve data collection, processing, and analysis of samples with low sensitivity and complex tertiary and quaternary structures. SSNMR spectra are often collected as multidimensional data, requiring stable experimental conditions to minimize signal fluctuations (t1 noise). In this work, we examine the factors adversely affecting signal stability as well as strategies used to mitigate them, considering laboratory environmental requirements, configuration of amplifiers, and pulse sequence parameter selection. We show that Thermopad® temperature variable attenuators (TVAs) can partially compensate for the changes in amplifier output power as a function of temperature and thereby ameliorate one significant source of instability for some spectrometers and pulse sequences. We also consider the selection of tangent ramped cross polarization (CP) waveform shapes, to balance the requirements of sensitivity and instrumental stability. These findings collectively enable improved stability and overall performance for CP-based multidimensional spectra of microcrystalline, membrane, and fibrous proteins performed at multiple magnetic field strengths.

Exploring secular variation of the gravitational constant from high-resolution quasar spectra.

The exploration of potential variations in fundamental physical constants is crucial for testing of Grand Unification Theories (GUTs), which aim to unify the fundamental forces of nature. This study utilizes direct observational tests to explore these variations, offering a deep-look into the universe's distant past. By analyzing high-resolution quasar spectra of HE 0515-4414* and comparing them with laboratory-calibrated Ritz wavelengths, we establish an upper limit on the possible cosmological deviation of the gravitational constant: G ˙ / G = ( 0.918 ± 2.830 ) × 10 - 15 yr - 1 over cosmic timescales. Our findings provide a novel tool for probing the physical implications of GUTs, contributing to our understanding of fundamental physics.

Interpretation of Tandem Mass Spectrometry (MS-MS) Spectra for Peptide Analysis.

The aim of this chapter is to give a short introduction to peptide analysis by mass spectrometry (MS) and interpretation of fragment mass spectra. Through examples and guidelines, we will demonstrate how to understand and validate search results and how to perform de novo sequencing based on the often very complex fragmentation pattern obtained by tandem mass spectrometry (also referred to as MSMS). The focus will be on simple rules for interpretation of MSMS spectra of tryptic as well as non-tryptic peptides.

The Application of Microsampling Disks in Circular Dichroism Spectroscopy for Peptide and Nucleic Acid Drugs.

In recent years, there has been a growing focus on the development of medium-sized drugs based on peptides or nucleic acids owing to their potential therapeutic benefits. As some of these medium-sized drugs exert their therapeutic effects by adopting specific secondary structures, evaluating their conformational states is crucial to ensure the efficacy, quality, and safety of the drug products. It is important to assess the structural integrity of biomolecular therapeutics to guarantee their intended pharmacological activity and maintain the required standards for drug development and manufacturing. One widely utilized technique for quality evaluation is secondary structural analysis using circular dichroism (CD) spectroscopy. Given the higher production and quality control costs associated with medium-sized drugs compared with small-molecule drugs, developing analytical techniques that enable CD analysis with reduced sample volumes is highly desirable. Herein, we focused on a microsampling disk-type cell as a potential solution for reducing the required sample volume. We investigated whether CD spectral analysis using a microsampling disk could provide equivalent spectra compared with the standard cell (sample volume: approx. 300 µL). Our findings demonstrated that the microsampling disk (sample volume: 2-10 µL) could be successfully applied to CD spectral analysis of peptide and nucleic acid drugs, paving the way for more efficient and cost-effective quality evaluation processes.

Classification of osteoarthritic and healthy cartilage using deep learning with Raman spectra.

Raman spectroscopy is a rapid method for analysing the molecular composition of biological material. However, noise contamination in the spectral data necessitates careful pre-processing prior to analysis. Here we propose an end-to-end Convolutional Neural Network to automatically learn an optimal combination of pre-processing strategies, for the classification of Raman spectra of superficial and deep layers of cartilage harvested from 45 Osteoarthritis and 19 Osteoporosis (Healthy controls) patients. Using 6-fold cross-validation, the Multi-Convolutional Neural Network achieves comparable or improved classification accuracy against the best-performing Convolutional Neural Network applied to either the raw or pre-processed spectra. We utilised Integrated Gradients to identify the contributing features (Raman signatures) in the network decision process, showing they are biologically relevant. Using these features, we compared Artificial Neural Networks, Decision Trees and Support Vector Machines for the feature selection task. Results show that training on fewer than 3 and 300 features, respectively, for the disease classification and layer assignment task provide performance comparable to the best-performing CNN-based network applied to the full dataset. Our approach, incorporating multi-channel input and Integrated Gradients, can potentially facilitate the clinical translation of Raman spectroscopy-based diagnosis without the need for laborious manual pre-processing and feature selection.

Quantum Computational and Spectroscopic Investigation of 3-aminosalicylic Acid.

Quantum chemical calculations of 3-aminosalicylic acid (3ASA) (monomer and dimer forms) have been performed using DFT and TD-DFT theories with B3LYP/6-311 G(d,p) functional level in the ground and excited states. Using TD-DFT with IEF-PCM model, the electronic spectra of 3ASA in solvents were computed and correlated with the experimental data. The theoretically calculated absorption and emission maxima of 3ASA (monomer) are observed in the range of 343 - 347 nm (S0 → S1 transition) and 429 - 448 nm (S1 → S0 transition), respectively. The natural bond orbital (NBO) analysis shows that charge transfer interaction contributes significantly to stabilize the molecular system. In the case of dimer, hydrogen bonding plays a dominant role in stabilizing the molecular framework. Additionally, the obtained nonlinear optical (NLO) properties: polarizability (13.86 × 10-24 e.s.u for monomer and 29.46 × 10-24 e.s.u. for dimer), first-order hyperpolarizability (4.21 × 10-30 e.s.u for monomer and 0.18 × 10-30 e.s.u for dimer) and second-order hyperpolarizability (7.44 × 10-36 e.s.u. for monomer and 14.32 × 10-36 e.s.u. for dimer) were found to be larger than those of standard organic compounds suggesting that 3ASA has a significant NLO character for optoelectronic applications. The NLO properties of dimer may differ from monomer due to dimerization. Further, the radiative lifetime, light harvesting efficiency and band gap energy were calculated, and proposed that 3ASA may be useful in photovoltaics and wide bandgap power devices. HIGHLIGHTS: • DFT and TD-DFT theories were employed to calculate structural and molecular properties of 3ASA (monomer and dimer) in ground and excited states. • HOMO-LUMO study shows monomer and dimer of 3ASA are good reactive. • NBO analysis reflects that charge transfer interactions stabilized the 3ASA molecule. • Electronic absorption/emission spectra in solvents calculated by IEF-PCM/TD-DFT method correlate with experimental results. • Calculated NLO parameters suggested that 3ASA is a potential candidate for NLO material.

Spatially offset Raman scattering line-mapping as an adaptive tool ensuring accuracy for determination of component concentrations in tablets with different particle sizes.

Spatially offset Raman scattering (SORS) line-mapping was explored as a versatile tool to examine accuracy variations in compositional analyses of tablets with different particle sizes. SORS spectra collected near the laser irradiation were less representative of tablet composition due to the limited spectroscopic sampling volume, while the signal-to-noise (S/N) ratios of corresponding spectra were higher. On the other hand, SORS spectra at longer offset distances were better representative of tablet composition, while their S/N ratios were decreased considerably. Therefore, the use of only a certain portion of sliced (line-mapped) spectra balanced with the sample representation and S/N ratio could be advantageous to enhance accuracy. Moreover, a group of optimal slice spectra is expected to vary when the particle size of the tablet changes since the characteristics of internal photon propagation also would change. For the overall examination, SORS spectra of 30 Anaprox tablets (composed of 4 constituents including naproxen sodium) with 2 particle sizes (88.4 ± 11.8 µm and 118.9 ± 38.8 µm) were analyzed, and the concentrations of three components in these tablets were determined. A total of 6 cases (3 components and 2 particle sizes) were examined. When the average optimal slice spectra were employed in each case, the errors were lower compared to those using the average of all slice spectra. The demonstrated scheme was versatile to study the offset distance-dependent accuracy variations according to particle size and target component.

Successful Therapeutic Leukapheresis for Chronic Myeloid Leukemia Identified by Persistent Erection: A Case Report.

Cytoreduction in leukostasis can be achieved using leukapheresis. We report a case of chronic myeloid leukemia (CML) identified by a persistent erection, which was successfully treated using the Spectra Optia®ï¸Ž apheresis system. A 29-year-old male presented with an erection for 12 hours without identified triggers and no improvement despite penile corpus cavernosum puncture. His white blood cell count was 458,930/µL. A diagnosis of CML-induced persistent erection with secondary hyperleukocytosis was established. Following an emergency bilateral penile corpus cavernosum incision (distal shunting), he received hydroxyurea and febuxostat. Persistent erection resolved after leukapheresis for two consecutive days. Rapid leukocyte count reduction can effectively address leukostasis in CML without major complications.

Study on the Infrared and Raman spectra of Ti3AlB2, Zr3AlB2, Hf3AlB2, and Ta3AlB2 by first-principles calculations.

In this paper, the crystal geometry, electronic structure, lattice vibration, Infrared and Raman spectra of ternary layered borides M3AlB2 (M = Ti, Zr, Hf, Ta) are studied by using first principles calculation method based on the density functional theory. The electronic structure of M3AlB2 indicates that they are all electrical conductors, and the d orbitals of Ti, Zr, Hf, and Ta occupy most of the bottom of the conduction band and most of the top of the valence band. Al and B have lower contributions near their Fermi level. The lightweight and stronger chemical bonds of atom B are important factors that correspond to higher levels of peak positions in the Infrared and Raman spectra. However, the vibration frequencies, phonon density of states, and peak positions of Infrared and Raman spectra are significantly lower because of heavier masses and weaker chemical bonds for M and Al atoms. And, there are 6 Infrared active modes A2u and E1u, and 7 Raman active modes, namely A1g, E2g, and E1g corresponding to different vibration frequencies in M3AlB2. Furthermore, the Infrared and Raman spectra of M3AlB2 were obtained respectively, which intuitively provided a reliable Infrared and Raman vibration position and intensity theoretical basis for the experimental study.

Distinguishing Isomeric Cyclobutane Thymidine Dimers by Ion Mobility and Tandem Mass Spectrometry.

Irradiation of the major conformation of duplex DNA found in cells (B form) produces cyclobutane pyrimidine dimers (CPDs) from adjacent pyrimidines in a head-to-head orientation (syn) with the C5 substituents in a cis stereochemistry. These CPDs have crucial implications in skin cancer. Irradiation of G-quadruplexes and other non-B DNA conformations in vitro produces, however, CPDs between nonadjacent pyrimidines in nearby loops with syn and head-to-tail orientations (anti) with both cis and trans stereochemistry to yield a mixture of six possible isomers of the T=T dimer. This outcome is further complicated by formation of mixtures of nonadjacent CPDs of C=T, T=C, and C=C, and successful analysis depends on development of specific and sensitive methods. Toward meeting this need, we investigated whether ion mobility mass spectrometry (IMMS) and MS/MS can distinguish the cis,syn and trans,anti T=T CPDs. Ion mobility can afford baseline separation and give relative mobilities that are in accord with predicted cross sections. Complementing this ability to distinguish isomers is MS/MS collisional activation where fragmentation also distinguishes the two isomers and confirms conclusions drawn from ion mobility analysis. The observations offer early support that ion mobility and MS/MS can enable the distinction of DNA photoproduct isomers.

Ultrasound wavelet spectra enable direct tissue recognition and full-color visualization.

Traditional brightness-mode ultrasound imaging is primarily constrained by the low specificity among tissues and the inconsistency among sonographers. The major cause is the imaging method that represents the amplitude of echoes as brightness and ignores other detailed information, leaving sonographers to interpret based on organ contours that depend highly on specific imaging planes. Other ultrasound imaging modalities, color Doppler imaging or shear wave elastography, overlay motion or stiffness information to brightness-mode images. However, tissue-specific scattering properties and spectral patterns remain unknown in ultrasound imaging. Here we demonstrate that the distribution (size and average distance) of scattering particles leads to characteristic wavelet spectral patterns, which enables tissue recognition and high-contrast ultrasound imaging. Ultrasonic wavelet spectra from similar particle distributions tend to cluster in the eigenspace according to principal component analysis, whereas those with different distributions tend to be distinguishable from one another. For each distribution, a few wavelet spectra are unique and act as a fingerprint to recognize the corresponding tissue. Illumination of specific tissues and organs with designated colors according to the recognition results yields high-contrast ultrasound imaging. The fully-colorized tissue-specific ultrasound imaging potentially simplifies the interpretation and promotes consistency among sonographers, or even enables the applicability for non-professionals.

Kinetic and Mechanistic Modelling of Pyrimethanil Fungicide Adsorption onto Soils of Varying Physico-chemical Properties.

Pesticide transport in the environment is impacted by the kinetics of its adsorption onto soil. The adsorption kinetics of pyrimethanil was investigated in ten soil samples of varying physicochemical properties. The highest adsorption was in the soil having the maximum silt and CaCO3 contents, pH and electrical conductance but the lowest amorphous Fe oxides and CaCl2 extractable Mn. Pseudo-second order kinetics and intra-particle diffusion model best accounted the adsorption kinetics of pyrimethanil. The equilibrium adsorption estimated by pseudo-second order kinetics (q02) was significantly and positively correlated with CaCl2 extractable Cu content (r = 0.709) while rate coefficient (k02) had a negative correlation with crystalline iron oxides content (r = -0.675). The intra-particle diffusion coefficient (ki.d.) had inverse relationship with CaCl2 extractable Mn content in soils (r = -0.689). FTIR spectra showed a significant interaction of pyrimethanil with micronutrient cations. Adsorption kinetic parameters of pyrimethanil could be successfully predicted by soil properties. The findings may help to evolve fungicide management decisions.

Proceedings of the EuBIC-MS developers meeting 2023.

The 2023 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers Meeting was held from January 15th to January 20th, 2023, in Congressi Stefano Franscin at Monte Verità in Ticino, Switzerland. The participants were scientists and developers working in computational mass spectrometry (MS), metabolomics, and proteomics. The 5-day program was split between introductory keynote lectures and parallel hackathon sessions focusing on "Artificial Intelligence in proteomics" to stimulate future directions in the MS-driven omics areas. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts and actively contribute to highly relevant research projects. We successfully produced several new tools applicable to the proteomics community by improving data analysis and facilitating future research.

The Effect of Conjugated Nitrile Structures as Acceptor Moieties on the Photovoltaic Properties of Dye-Sensitized Solar Cells: DFT and TD-DFT Investigation.

A major challenge in improving the overall efficiency of dye-sensitized solar cells is improving the optoelectronic properties of small molecule acceptors. This work primarily investigated the effects of conjugation in nitriles incorporated as acceptor moieties into a newly designed series of D-A-A dyes. Density functional theory was employed to specifically study how single-double and single-triple conjugation in nitriles alters the optical and electronic properties of these dyes. The Cy-4c dye with a highly conjugated nitrile unit attained the smallest band gap (1.80 eV), even smaller than that of the strong cyanacrylic anchor group (2.07 eV). The dyes lacking conjugation in nitrile groups did not contribute to the LUMO, while LUMOs extended from donors to conjugated nitrile components, facilitating intramolecular charge transfer and causing a strong bind to the film surface. Density of state analysis revealed a considerable impact of conjugated nitrile on the electronic properties of dyes through an effective contribution in the LUMO, exceeding the role of the well-known strong 2,1,3-benzothiadiazole acceptor unit. The excited state properties and the absorption spectra were investigated using time-dependent density functional theory (TD-DFT). Conjugation in the nitrile unit caused the absorption band to broaden, strengthen, and shift toward the near-infrared region. The proposed dyes also showed optimum photovoltaic properties; all dyes possess high light-harvesting efficiency (LHE) values, specifically 96% for the dyes Cy-3b and Cy-4c, which had the most conjugated nitrile moieties. The dyes with higher degrees of conjugation had longer excitation lifetime values, which promote charge transfer by causing steady charge recombination at the interface. These findings may provide new insights into the structure of conjugated nitriles and their function as acceptor moieties in DSSCS, which may lead to the development of extremely effective photosensitizers for solar cells.

Probing the interaction between the metallo-ß-lactamase SMB-1 and ampicillin by multispectral approaches combined with molecular dynamics.

Metallo-ß-lactamases (MßLs) hydrolyze and inactivate ß-lactam antibiotics, are a pivotal mechanism conferring resistance against bacterial infections. SMB-1, a novel B3 subclass of MßLs from Serratia marcescens could deactivate almost all ß-lactam antibiotics including ampicillin (AMP), which has posed a serious threat to public health. To illuminate the mechanism of recognition and interaction between SMB-1 and AMP, various fluorescence spectroscopy techniques and molecular dynamics simulation were employed. The results of quenching spectroscopy unraveled that AMP could make SMB-1 fluorescence quenching that mechanism was the static quenching; the synchronous and three-dimensional fluorescence spectra validated that the microenvironment and conformation of SMB-1 were altered after interaction with AMP. The molecular dynamics results demonstrated that the whole AMP enters the binding pocket of SMB-1, even though with a relatively bulky R1 side chain. Loop1 and loop2 in SMB-1 undergo significant fluctuations, and α2 (71-73) and local α5 (186-188) were turned into random coils, promoting zinc ion exposure consistent with circular dichroism spectroscopy results. The binding between them was driven by a combination of enthalpy and entropy changes, which was dominated by electrostatic force in agreement with the fluorescence observations. The present study brings structural insights and solid foundations for the design of new substrates for ß-lactamases and the development of effective antibiotics that are resistant to superbugs.

Binding of single/double stranded ct-DNA with graphene oxide­silver nanocomposites in vitro: A multispectroscopic approach.

The fundamental binding of single-stranded (ssDNA) and double-stranded DNA (dsDNA) with graphene oxide-Ag nanocomposites (GO-AgNCPs) has been systematically investigated by multi spectroscopic methods, i.e. ultraviolet-visible (UV-vis) absorption, fluorescence spectroscopy, and circular dichroism (CD). The experimental and theoretical results demonstrate that both ssDNA and dsDNA can be adsorbed onto the GO-AgNCPs surface. All of the evidence indicated that there were relatively strong binding of ssDNA/dsDNA with GO-AgNCPs. The article compares the differences in binding between the two types of DNA and the nanomaterials using spectroscopic and thermodynamic data. UV-vis absorption spectroscopy experiments indicate that the characteristic absorbance intensity of both ss DNA and ds DNA increases, but the rate of change in absorbance is different. The fluorescence results revealed that ss/dsDNA could interact with the GO-AgNCPs surface, in spite of the different binding affinities. The Ka value of ssDNA binding with GO-AgNCPs is greater than that of dsDNA at each constant temperature, indicating that the affinity of dsDNA toward GO-AgNCPs is comparatively weak. Molecular docking studies have corroborated the mentioned experimental results. The calculated thermodynamic parameters showed that the binding process was thermodynamically spontaneous, van der Waals force and hydrogen bonding played predominant roles in the binding process. The mechanism of ss/ds DNA binding with GO-AgNCPs was also investigated, and the results indicated that GO-AgNCPs directly binds to the minor groove of ss/ds DNA by replacing minor groove binders.

Temporal insights into molecular and cellular responses during rAAV production in HEK293T cells.

The gene therapy field seeks cost-effective, large-scale production of recombinant adeno-associated virus (rAAV) vectors for high-dosage therapeutic applications. Although strategies like suspension cell culture and transfection optimization have shown moderate success, challenges persist for large-scale applications. To unravel molecular and cellular mechanisms influencing rAAV production, we conducted an SWATH-MS proteomic analysis of HEK293T cells transfected using standard, sub-optimal, and optimal conditions. Gene Ontology and pathway analysis revealed significant protein expression variations, particularly in processes related to cellular homeostasis, metabolic regulation, vesicular transport, ribosomal biogenesis, and cellular proliferation under optimal transfection conditions. This resulted in a 50% increase in rAAV titer compared with the standard protocol. Additionally, we identified modifications in host cell proteins crucial for AAV mRNA stability and gene translation, particularly regarding AAV capsid transcripts under optimal transfection conditions. Our study identified 124 host proteins associated with AAV replication and assembly, each exhibiting distinct expression pattern throughout rAAV production stages in optimal transfection condition. This investigation sheds light on the cellular mechanisms involved in rAAV production in HEK293T cells and proposes promising avenues for further enhancing rAAV titer during production.