Chemical Potential Research Articles

DiDBiT-TMT: A Novel Method to Quantify Changes in the Proteomic Landscape Induced by Neural Plasticity.

Direct detection of biotinylated proteins (DiDBiT) is a proteomic method that can enrich and detect newly synthesized proteins (NSPs) labeled with bio-orthogonal amino acids with 20-fold improved detectability compared to conventional methods. However, DiDBiT has currently been used to compare only two conditions per experiment. Here, we present DiDBiT-TMT, a method that can be used to quantify NSPs across many conditions and replicates in the same experiment by combining isobaric tandem mass tagging (TMT) with DiDBiT. We applied DiDBiT-TMT to brain slices to determine changes in the de novo proteome that occur after inducing chemical long-term potentiation (cLTP) or treatment with the neuromodulator norepinephrine. We successfully demonstrated DiDBiT-TMT's capacity to quantitatively compare up to 9 samples in parallel. We showed that there is a minimal overlap among NSPs that are differentially expressed in cLTP-treated organotypic brain slices, norepinephrine-treated organotypic brain slices, and organotypic slices undergoing combinatorial treatment with norepinephrine and cLTP. Our results point to the possible divergence of the molecular mechanisms underlying these treatments and showcase the applicability of DiDBiT-TMT for studying neurobiology.

On the Functionalization of C60 with Vinylallenes Generated in situ by Rhodium Catalysis

The functionalization of fullerenes is important for several reasons, primarily related to enhancing their chemical reactivity, solubility, and potential of applications in optoelectronics and biomedicine. In this study, we present a novel approach to functionalize C60 through a cascade process encompassing an unprecedented Rh‐catalyzed cycloisomerization of 1,6‐allenynes to in situ generate a vinylallene that is followed by a Diels‐Alder reaction with pristine fullerene, resulting in the formation of 6,6‐fused bicyclic fullerene derivatives. The mechanism governing this process was elucidated by DFT calculations and confirmed by deuterium labelling and control experiments, demonstrating the critical role of traces of water in the reaction medium to mediate the observed reactivity.

Towards a high-rate operation of contact stabilization process: A microscopic view of carbon capture properties

Carbon capture performance is a key factor determining the chemical energy recovery potential of the high-rate contact stabilization (HiCS) process. However, the mechanisms of organic carbon capture are complex, involving surface adsorption, extracellular adsorption, and intracellular storage. A unique characteristic of the HiCS process is its low sludge residence time (SRT). Unfortunately, the influence of SRT on carbon capture has not been thoroughly studied, especially in terms of the underlying mechanisms. In this study, the microscopic changes in carbon capture performance during the transition from a conventional contact stabilized (CS) system to a high-rate mode of operation were demonstrated using intracellular carbon sources, extracellular polymeric substances (EPS), signaling molecules, and microbial community assays. The results showed that the extracellular carbon adsorption and intracellular carbon storage performance increased, and the microbial community structure changed significantly with converting the CS system to the high-rate operation mode. The enhancement of extracellular carbon adsorption performance mainly relied on the growth of EPS, which was accomplished by the strong growth of the relative abundance of the dominant bacterial group Cloacibacterium within the HiCS system, offsetting the negative effect produced by the decline of acyl-homoserine lactones. 98 mgCOD/gSS, 343 mgCOD/gSS, and 500 mgCOD/gSS of polyhydroxyalkanoates (PHAs) per sludge unit were obtained at SRT-24d, 8d, and 2d, respectively, suggesting that the HiCS system is more advantageous for rapid PHAs production.

Comparative genomics unravels a rich set of biosynthetic gene clusters with distinct evolutionary trajectories across fungal species (Termitomyces) farmed by termites

The use of compounds produced by hosts or symbionts for defence against antagonists has been identified in many organisms, including in fungus-farming termites (Macrotermitinae). The obligate mutualistic fungus Termitomyces plays a pivotal role in plant biomass decomposition and as the primary food source for these termites. Despite the isolation of various specialized metabolites from different Termitomyces species, our grasp of their natural product repertoire remains incomplete. To address this knowledge gap, we conducted a comprehensive analysis of 39 Termitomyces genomes, representing 21 species associated with members of five termite host genera. We identified 754 biosynthetic gene clusters (BGCs) coding for specialized metabolites and categorized 660 BGCs into 61 biosynthetic gene cluster families (GCFs) spanning five compound classes. Seven GCFs were shared by all 21 Termitomyces species and 21 GCFs were present in all genomes of subsets of species. Evolutionary constraint analyses on the 25 most abundant GCFs revealed distinctive evolutionary histories, signifying that millions of years of termite-fungus symbiosis have influenced diverse biosynthetic pathways. This study unveils a wealth of non-random and largely undiscovered chemical potential within Termitomyces and contributes to our understanding of the intricate evolutionary trajectories of biosynthetic gene clusters in the context of long-standing symbiosis.

Signature of pressure-induced topological phase transition in ZrTe5

The layered van der Waals material ZrTe5 is known as a candidate topological insulator (TI), however its topological phase and the relation with other properties such as an apparent Dirac semimetallic state is still a subject of debate. We employ a semiclassical multicarrier transport (MCT) model to analyze the magnetotransport of ZrTe5 nanodevices at hydrostatic pressures up to 2 GPa. The temperature dependence of the MCT results between 10 and 300 K is assessed in the context of thermal activation, and we obtain the positions of conduction and valence band edges in the vicinity of the chemical potential. We find evidence of the closing and re-opening of the band gap with increasing pressure, which is consistent with a phase transition from weak to strong TI. This matches expectations from ab initio band structure calculations, as well as previous observations that CVT-grown ZrTe5 is a weak TI in ambient conditions.

Functionalization of single-walled aluminum nitride nanotube with amino acids using the first principle's study

In this study, we investigate the functionalization of aluminum nitride nanotube (AlNNT) with amino acids (Phenylalanine, Arginine, and Glutamine) using first-principle density functional theory (DFT) calculations. DFT methods were applied to model the interactions between amino acids and AlNNT, exploring the structural and electronic features of the functionalized systems, and examining various aspects of the structures, including their geometry and electronic properties, such as bond lengths, bond angles, total energy, formation energy, band structure, chemical potential, density of states (DOS), projected density of states (PDOS), charge transfer, and electron difference density. The (5, 5) AlNNT exhibits an energy bandgap value of 3.31 eV, implying its semiconducting nature. Furthermore, the pure system's chemical potential was -4.12 eV. The DOS examination shows that the pristine system's band structure profile and energy states match well. Notably, the valence band displays a more pronounced level of energy hybridization compared to the conduction band, which is reflected in the band structure. Functionalization of AlNNT with amino acids enhances the p character and polar covalency, thereby increasing the percentage ionic character and Gibb's free energy of solvation which are essential parameters to determine the aqueous solubility.

Finite temperature fermionic condensate and energy–momentum tensor in cosmic string spacetime

Here we analyze the expectation value of the fermionic condensate and the energy–momentum tensor associated with a massive charged fermionic quantum field with a nonzero chemical potential propagating in a magnetic-flux-carrying cosmic string in thermal equilibrium at finite temperature T. The expectation values of the fermionic condensate and the energy–momentum tensor are expressed as the sum of vacuum expectation values and the finite temperature contributions coming from the particles and antiparticles excitation. The thermal expectations values of the fermionic condensate and the energy–momentum tensor are even periodic functions of the magnetic flux with period being the quantum flux, and also even functions of the chemical potential. Because the analyses of vacuum expectation of the fermionic condensate and energy–momentum tensor have been developed in literature, here we are mainly interested in the investigation of the thermal corrections. In this way we explicitly study how these observable behaves in the limits of low and high temperatures, and also for points near the string. Besides the analytical discussions, we included some graphs that exhibit the behavior of these observable for different values of the physical parameters of the model.

Deconfinement and chiral phase transitions in quark matter with chiral imbalance

We study the thermodynamics of the Polyakov-Nambu-Jona-Lasinio model considering the effects of an effective chiral chemical potential. We offer a new parametrization of the Polyakov-loop potential depending on temperature and the chiral chemical potential which, when used together with a proper regularization scheme of vacuum contributions, predicts results consistent with those from lattice simulations. Published by the American Physical Society 2024

Real-time chiral dynamics at finite temperature from quantum simulation

In this study, we explore the real-time dynamics of the chiral magnetic effect (CME) at a finite temperature in the (1+1)-dimensional QED, the massive Schwinger model. By introducing a chiral chemical potential μ5 through a quench process, we drive the system out of equilibrium and analyze the induced vector currents and their evolution over time. The Hamiltonian is modified to include the time-dependent chiral chemical potential, thus allowing the investigation of the CME within a quantum computing framework. We employ the quantum imaginary time evolution (QITE) algorithm to study the thermal states, and utilize the Suzuki-Trotter decomposition for the real-time evolution. This study provides insights into the quantum simulation capabilities for modeling the CME and offers a pathway for studying chiral dynamics in low-dimensional quantum field theories.

Information theoretic measures for Lifshitz system

In this work, we have studied various mixed state information theoretic quantities for an excited state of Lifshitz spacetime in 3 + 1-dimensions. This geometry is the gravity dual to a class of 2 + 1-dimensional quantum field theories having Lifshitz symmetry. We have holographically calculated mutual information, entanglement wedge cross section, entanglement negativity and mutual complexity for strip like subsystems at the boundary. For this we have used the results of holographic entanglement entropy and complexity present in the literature. We first calculate all of these mentioned quantities for the pure state of Lifshitz spacetime. Then we have moved on to calculate all these quantities for excited state of the Lifshitz spacetime. The gravity dual of excited state of Lifshitz systems in field theory can be obtained by applying constant perturbations along the boundary direction. Further, we would like to mention that for the simplicity of calculation we are only considering results up to the first order in perturbation. The change in the obtained holographic information theoretic quantities are then related to entanglement entropy, entanglement pressure, entanglement chemical potential and charge using the stress tensor complex. These relations are analogous to the first law of entanglement thermodynamics given earlier in the literature. All the calculations are carried out for both values of dynamical scaling exponent (z) present in the Lifshitz field theory.

Unleashing the Power of Domino Reactions on Carbohydrates: State of the Art

AbstractThe intricate nature of carbohydrate structures has prompted the scientific community to seek efficient protocols for their manipulation. Lengthy synthetic pathways, often necessary to achieve complex sugar structures, pose challenges not only in terms of time and cost but also regarding environmental sustainability. Consequently, domino transformations serve as valuable tools in streamlining drug discovery processes. Sequential procedures involving fewer steps and minimal isolation/purification steps are particularly appealing to organic chemists in the field of carbohydrate chemistry. This review highlights several examples of domino transformations applied to carbohydrates, aiming to summarize their chemical potential in delivering sugar‐based compounds with significant applications in the generation of new chemical scaffolds for drug discovery and chemical biology.

Development of new sustainable pyridinium ionic liquids: From reactivity studies to mechanism-based activity predictions.

This study addresses the development of sustainable pyridinium ionic liquids (ILs) because of their potential applications in agriculture and pharmaceuticals. Pyridinium-based ILs are known for their low melting points, high thermal stability, and moderate solvation properties. We synthesized three novel pyridinium-based ILs: 1-(2-(isopentyloxy)-2-oxoethyl)pyridin-1-ium chloride, 1-(2-(hexyloxy)-2-oxoethyl)pyridin-1-ium chloride, and 1-(2-(benzyloxy)-2-oxoethyl)pyridin-1-ium chloride. The biological activities of these compounds were evaluated through plant growth promotion, herbicidal, and insecticidal assays. Our results show that the benzyloxy derivative significantly enhances wheat and cucumber growth, whereas the isopentyloxy compound has potent herbicidal effects. Computational methods, including DFT calculations and molecular docking, were applied to understand the structure‒activity relationships (SARs) and mechanisms of action. The computational techniques involved dispersion-corrected density functional theory (DFT) with the B3LYP functional and the 6-311G** basis set. Grimme's D3 corrections were included to account for dispersion interactions. The calculations were performed via GAMESS-US software. Quantum descriptors of reactivity, such as ionization potential, electron affinity, chemical potential, and electrophilicity index, were derived from the HOMO and LUMO energies. Molecular docking studies were conducted via the CB-Dock server via AutoDock Vina software to predict binding affinities to cancer-related proteins. Petra/Osiris/Molinspiration (POM) analysis was used to predict the drug likeness and other pharmaceutical properties of the synthesized ILs.

Machine Learning-Based Toxicological Modeling for Screening Environmental Obesogens.

The emerging presence of environmental obesogens, chemicals that disrupt energy balance and contribute to adipogenesis and obesity, has become a major public health challenge. Molecular initiating events (MIEs) describe biological outcomes resulting from chemical interactions with biomolecules. Machine learning models based on MIEs can predict complex toxic end points due to chemical exposure and improve the interpretability of models. In this study, a system was constructed that integrated six MIEs associated with adipogenesis and obesity. This system showed high accuracy in external validation, with an area under the receiver operating characteristic curve of 0.78. Molecular hydrophobicity (SlogP_VSA) and direct electrostatic interactions (PEOE_VSA) were identified as the two most critical molecular descriptors representing the obesogenic potential of chemicals. This system was further used to predict the obesogenic effects of chemicals on the candidate list of substances of very high concern (SVHCs). Results from 3T3-L1 adipogenesis assays verified that the system correctly predicted obesogenic or nonobesogenic effects of 10 of the 12 SVHCs tested, and identified four novel potential obesogens, including 2-benzotriazol-2-yl-4,6-ditert-butylphenol (UV-320), 4-(1,1,5-trimethylhexyl)phenol (p262-NP), 2-[4-(1,1,3,3-tetramethylbutyl)phenoxy]ethanol (OP1EO) and endosulfan. These validation data suggest that the screening system has good performance in adipogenic prediction.

Exploring Tsallis thermodynamics for boundary conformal field theories in gauge/gravity duality

Inspired by AdS/CFT interpretation Karch and Robinson (2015), we analyze thermodynamics for thermal boundary conformal field theories (CFT) that are dual to four-dimensional charged anti-de Sitter (AdS) black holes embedded in 11-dimensional M-theory-inspired models with AdS4×S7 space–time, employing the framework of Tsallis entropy. The latter is recognized as a nonadditive extension of the Boltzmann–Gibbs entropy that can satisfy the thermodynamic extensivity for black holes. Specifically, we consider AdS black holes in AdS4×S7 spacetime, interpreting the number of M2-branes as a thermodynamic variable. Using the Tsallis entropy enables us to highlight peculiar thermodynamic features, resorting to essential tools such as the chemical potential and Gibbs energy while examining phase transitions along iso-charge partitions. Then, we leveraged a class of geometrothermodynamic formalisms, including Weinhold, Ruppeiner, Quevedo I, and II metrics. Quevedo’s formulations provide richer information about phase transitions than the first two methods. Our study sheds new light on AdS black holes in a thermodynamically proper context, deepening our understanding of the role of non-extensivity in the critical behavior of such complex systems.

Synthesis, Characterization, Bioactivity Evaluation, and POM/DFT/Docking Analysis of Novel Thiazolidine Derivatives as Potent Anticancer and Antifungal Agents

AbstractA series of 2,2′‐(1,4‐phenylene)bis(N‐substituted phenylthiazolidine‐4‐amide) derivatives, denoted as (A3–9), were synthesized, and characterized for their potential applications against prostate cancer cells (PC3), and Candida albicans fungi. These compounds incorporate various substituents on the phenyl ring such as 4‐NO2, 3‐NO2, 4‐COCH3, 4‐H, 4‐OCH3, 4‐OCH2CH3, and 4‐Cl. The chemical structures of these derivatives were confirmed by NMR, FTIR, and mass spectroscopy. Biological assays, utilizing the MTT assay for prostate cancer cells (PC3) and the disk diffusion assay for Candida albicans fungi, were conducted to evaluate the bioactivity of these compounds. The results revealed promising cytotoxic and antifungal activities. Specifically, compounds A3 (IC50=69.74±0.96), A4 (IC50=63.64±0.950), and A9 (IC50=57.14±0.88 μg/mL) exhibited notable potency against PC3 cells, while A7 and A8 exhibited considerable antifungal efficacy against Candida albicans with MIC of 312 μg/mL. Moreover, density functional theory (DFT) simulations were used to study electronic properties and reactivity descriptors such as energy gap (Eg), ionization potential (IP), electron affinity (EA), chemical potential (μ), chemical hardness (η), global softness (σ), electronegativity (χ), and electrophilicity (ω) to gain a better understanding of the Structure‐Activity Relationship (SAR). Molecular docking analysis against DNA Gyrase and EGFR tyrosine kinase enzymes revealed strong binding interactions of the investigated molecules within their active sites, making them valuable candidates for further development as therapeutic agents against prostate cancer and fungal infections. POM analysis indicates the presence of two antifungal pharmacophore sites (O1δ−, O2δ−) and (O3δ−, O4δ−), as well as two antitumor pharmacophore sites (O1δ−, NH1δ+) and (O4δ−, NH2δ+).

Structural Modified Coumarin Fused Triazole Analogues for Fe3+ Metal Ion Detection: A Comprehensive Photophysical and Fluorescent Chemosensor Study

This study investigates the potential of coumarin fused thiadiazole (CTR-1 and CTR-2) derivatives as chemosensors for Fe3+ ions detection. The photophysical and solvatochromic properties were examined using spectroscopic and theoretical techniques. Key parameters such as the energy bandgap, chemical hardness, softness, electronegativity, chemical potential, and electronic charge of electrophilic groups were computed using frontier molecular orbitals and compared with experimental results. Molecular electrostatic potential map studies indicated a strong electrophilic site in the molecules. Fluorescence quenching techniques demonstrated that both CTR-1 and CTR-2 exhibit strong, selective, and sensitive interactions with Fe3+ ions, with detection limits of 4.15 μM for CTR-1 and 5.02 μM for CTR-2, and rapid detection times of less than 6.5 minutes. Intramolecular interactions between the chemosensors and Fe3+ ions were analyzed using density functional theory and spectroscopic techniques, revealing a 1:1 binding ratio. These findings suggest that CTR-1 and CTR-2 are effective chemosensors for detecting Fe3+ ions.

On Theoretical Aspect of Photons Emission From Quark-Gluon Interaction Upon Hard Collision

Abstract This work applies a quantum chromodynamics theory QCD to photon emission from heavy quark-gluon scattering in the strong interaction quark-gluon to study and calculate photon flow in hard interaction processes. The photon flow from the dense quark-gluon interaction was calculated using critical temperature, quantum chromodynamic coupling and fugacity at chemical potential μq (500 MeV) for the anti-top with gluon interaction in t ¯ g → s ¯ γ system. The photon flow spectrum in hard collisions is described under the first leading order approximation for QCD theory at finite chemical potential and critical temperature using various photon energy values dependent on the fugacity of quark and gluon. Photon flux calculation provided valuable insights into QGP conditions. The coupling strength αc (T) calculation is a strongly decreasing function of critical temperature ranging 107MeV ≤ Tc ≤ 145MeV and also find appreciable increasing as a result of increasing temperature of system ranging 180MeV ≤ T ≤ 360MeV. The photon flow produced in the t ¯ g → s ¯ γ system was observed in the low range of photon energy with two critical temperatures. The total photon emission strongly decreases marginally as a function of the increase in photon energy. The photon flow emission was found to have appreciable enhancement at the anti-top quark interaction with gluon and it increases highly as a result of the increased temperature of the system and reaches to maximum near 360 MeV at minimum strength coupling in the energy of the photon 1GeV≤E≤2 GeV.

Investigation of aluminum nitrate nanotube as the smart carriers for targeted delivery of gemcitabine anti-lung cancer drug

The potential of aluminum nitrate nanotube as a drug carrier for anti-lung cancer drug gemcitabine is examined based on the density functional theory (DFT) calculations. The adsorption geometries of gemcitabine drug onto the surface of nanotube are investigated for various orientation in order to attain the most stable configuration. Significant interaction is observed between the double bonded oxygen atom of the gemcitabine drug and aluminum atom of the nanocage. The charge transfer analysis indicates that there is significant interaction along with considerable charge transfer between gemcitabine and the aluminum nitrate nanotube. The electronic properties such as highest occupied molecular orbital, lowest unoccupied molecular orbitals energy levels, energy gap, chemical hardness, chemical potential, electrophilicity index, and dipole moment for the best three configurations of the complexation are examined. The recovery time calculations are also performed at 298.15 K temperature in order to study the drug desorption process on the targeted site. The stability of the complex is compared in both gas and aqueous medium. Eventually, this work interprets that aluminum nitrate nanotube can be considered to be suitable candidates for delivering gemcitabine anti-lung cancer drug in a biological system.

Comparing phase sensitive detection and Fourier analysis of modulation excitation spectroscopy data exemplified by Ambient Pressure X-ray Photoelectron Spectroscopy

Dynamic processes in catalysis are gaining increased attention and could very well be one of the next frontiers in surface science. One way to study such processes is to induce chemical changes on the surface for example by periodically adjusting the (electro)chemical potential in situ and identify the resulting spectral changes. Often this is referred to as Modulation Excitation Spectroscopy (MES). Using Ambient Pressure Photoelectron Spectroscopy data, we here discuss and compare the analysis of MES data using both Phase Sensitive Detection (PSD) and Fourier analysis. We discuss that PSD determines the component magnitude at a user-defined phase value while Fourier analysis provides the maximum oscillation amplitude and respective phase value of oscillating spectral features. We discuss advantages and disadvantages of the different analysis schemes and explore how the full time-evolution can be obtained.

An integrated In-Silico-In-Chemico-In-Vitro (iSiCiV) Approach to identify biomarkers to predict the skin sensitisation potential of phytochemicals

BackgroundSkin sensitisation is one of the important regulatory endpoints used to determine whether a given test chemical can elicit an allergic response in susceptible individuals. The in-vitro approaches for predicting skin sensitisation potential for chemicals have been well-developed and widely accepted. Continuous efforts are being made to identify novel solutions to overcome the limitations of the existing approaches. PurposeThe herbal preparations used in dermal therapeutics are frequently found to elicit skin sensitisation, requiring caution. The herbal preparations tend to contain more than one phytochemical. The expected active ingredient may not possess skin sensitisation. However, the other phytochemical traces could pose synergistic and potentiating effects towards enhanced/suppressed skin sensitisation. In this regard, isolation, purification, yield, and in-vitro / in-vivo evaluation of skin sensitisation for all the traces would be time, cost, and animal-consuming. Hence, the regulatory agencies appreciate using computational tools to substantiate in-vitro methods. The regulators have also endorsed using in-silico approaches like quantitative structure-activity relationships (QSAR) and read-across. These approaches are limited to structure-based predictions and in combination with system-level approaches, which comprehensively facilitate a better understanding of complex biological systems. Study designIn the present study, 603 phytochemicals were screened in-silico using OECD QSAR Toolbox. The limitations of the QSAR Toolbox in predicting skin sensitisers were identified. MethodThe systems biology-based approach to complement the QSAR-based prediction was developed, and 41 biomarkers were identified as a determinant of skin sensitisation. The molecules attributed to these biomarkers were predicted as skin sensitisers. ResultsAs a result, 31 phytochemicals were predicted as skin sensitisers. Acrolein, eugenol, formaldehyde, and glycerol were selected for experimental validation of the in-silico predictions using direct peptide reactivity assay (DPRA), KeratinoSens™, and h-CLAT assays representing each key event in skin sensitisation. Further, identified biomarkers were validated in THP-1 and KeratinoSens cell lines using qRT-PCR. Among all genes, IL-8 and CCL4 were upregulated by 6.4 and 5.6 folds, respectively, in THP-1, while AKR1C2 and AKR1C3 were upregulated by 7.8 and 11.1 folds, respectively, in KeratinoSens. IL-8 level was analysed by ELISA and found to be in line with qRT-PCR results. ConclusionThe study proposes a possible strategy based on the “iSiCiV” approach to enhance the prediction of the dermal sensitisation potential of a test compound. The approach offers a robust platform and highlights an opportunity to shift the paradigm of skin sensitisation assay with a better understanding of toxicology mechanisms.