Search Results (166)

Anaerobic digestion (AD) has long been valued for producing a biogas–digestate pair, yet its profitability is tightening. Next-generation AD biorefineries now position syngas both as a supplementary feedstock and as a springboard to capture high-value intermediates, hydrogen (H₂) and volatile fatty acids (VFA). This review dissects how complex natural consortia “decide” between hydrogenogenesis and acetogenesis when CO, H₂, and CO₂ co-exist in the feedstocks, bridging molecular mechanisms with process-scale levers. The map of the bioenergetic contest between the biological water–gas shift reaction and Wood–Ljungdahl pathways is discussed, revealing how electron flow, thermodynamic thresholds, and enzyme inhibition dictate microbial “decision”. Kinetic evidence from pure and mixed cultures is integrated with practical operating factors (gas composition and pressure, pH–temperature spectrum, culture media composition, hydraulic retention time, and cell density), which can bias consortia toward the desired product. Full article

Classical thermodynamics omits rigidity, which property distinguishes solids from gases and liquids. By accounting for rigidity (i.e., Young’s elastic modulus, ϒ), we recently amended historical formulae and moreover linked heat capacity, thermal expansivity, and ϒ. Further exploration is motivation by the importance of classical thermodynamics to various applied sciences. Based on heat performing work, we show here, theoretically, that density times sublimation enthalpy divided by the molar mass (ρΔH_sub/M, energy per volume), depends linearly on ϒ (1 GPa = 10⁹ J m⁻³). Data on diverse metals, non-metallic elements, chalcogenides, simple oxides, alkali halides, and fluorides with cubic structures validate this relationship at ambient conditions. Furthermore, data on hcp metals and molecular solids show that ρΔH_sub/M is proportional to ϒ for anisotropic materials. Proportionality constants vary only from 0.1 to 0.7 among these different material types (>100 substances), which shows that the elastic energy reservoir of solids is large. Proportionality constants depend on whether molecules or atoms are sublimated and are somewhat affected by structure. We show that ductility of refractory, high-ϒ metals affect high-temperature determinations of their ΔH_sub. Our results provide information on sublimation processes and subsequent gas phase reactions, while showing that elasticity of solids is the key parameter needed to assessing their energetics. Implications are highlighted. Full article

The nitrogen cycle (N-cycle) is a cornerstone of global biogeochemistry, regulating nitrogen availability and affecting atmospheric chemistry, agricultural productivity, and ecological balance. Central to this cycle is the reversible interplay between nitrate (NO₃⁻) and nitrite (NO₂⁻), mediated by molybdenum-dependent enzymes—Nitrate reductases (NARs) and Nitrite oxidoreductases (NXRs). Despite catalyzing opposite reactions, these enzymes exhibit remarkable structural and mechanistic similarities. This review aims to elucidate the molecular underpinnings of nitrate reduction and nitrite oxidation by dissecting their enzymatic architectures, redox mechanisms, and evolutionary relationships. By focusing on recent structural, spectroscopic, and thermodynamic data, we explore how these two enzyme families represent “two sides of the same coin” in microbial nitrogen metabolism. Special emphasis is placed on the role of oxygen atom transfer (OAT) as a unifying mechanistic principle, the influence of environmental redox conditions, and the emerging evidence of bidirectional catalytic potential. Understanding this dynamic enzymatic interconversion provides insight into the flexibility and resilience of nitrogen-transforming pathways, with implications for environmental management, biotechnology, and synthetic biology. Full article

Markov chain perturbation theory is a rapidly developing subfield of the theory of stochastic processes. This review outlines emerging applications of this theory in the analysis of stochastic models of chemical reactions, with a particular focus on biochemistry and molecular biology. We begin by discussing the general problem of approximate modeling in stochastic chemical kinetics. We then briefly review some essential mathematical results pertaining to perturbation bounds for continuous-time Markov chains, emphasizing the relationship between robustness under perturbations and the rate of exponential convergence to the stationary distribution. We illustrate the use of these results to analyze stochastic models of biochemical reactions by providing concrete examples. Particular attention is given to fundamental problems related to approximation accuracy in model reduction. These include the partial thermodynamic limit, the irreversible-reaction limit, parametric uncertainty analysis, and model reduction for linear reaction networks. We conclude by discussing generalizations and future developments of these methodologies, such as the need for time-inhomogeneous Markov models. Full article

Measurements of the surface tension of aqueous solutions of some trisiloxane surfactants containing various polyether groups (HOL7, HOL9, and HOL12) at 293 K, 303 K, and 313 K were performed. The studied surfactants were synthesized by hydrosilylation reaction and their structural analysis was carried out by the ¹H NMR, ¹³C NMR, ²⁹Si NMR, as well as FT-IR techniques. The thermal stability of HOL7, HOL9, and HOL12, as well as their molecular weight distributions, were also studied. On the basis of the obtained experimental results of the surface tension of aqueous solutions of HOL7, HOL9, and HOL12, the activity of the studied surfactants at the water–air interface was determined and discussed in the light of intermolecular interactions. Using the measured values of the surface tension, the Gibbs surface excess concentration, the area occupied by the surfactant molecule in the adsorption layer, and the standard Gibbs free energy of adsorption of the studied surfactants at the water–air interface were also calculated. Based on the obtained thermodynamic parameters of adsorption of the studied surfactants at the water–air interface, temperature, as well as a number of polyether groups in the hydrophilic part of surfactant, impact on particular surfactant adsorption was deduced. In general, the changes in the standard Gibbs free energy of adsorption of the studied surfactants at the water–air interface indicate that their adsorption tendency decreases with decreasing temperature. In addition, that tendency also diminishes as the number of the polyether groups in the hydrophilic part of the surfactant increases. Full article

Norovirus is a leading cause of viral gastroenteritis worldwide and has been studied extensively from the perspective of life and biomedical sciences. However, no biothermodynamic analysis of Norovirus has been reported in the literature. Such an analysis would provide insights into the role of energetic constraints in the interactions between Norovirus and its host cells and other viruses. In this research, Norovirus was characterized from the aspect of chemistry and chemical thermodynamics, with the determination of its molecular formula, empirical formula, molar mass and thermodynamic properties (enthalpy, entropy, Gibbs energy) of formation. Based on these properties, biosynthesis reactions were formulated that show how Norovirus particles are synthetized inside host cells, and the thermodynamic properties of biosynthesis were determined. Moreover, the thermodynamic properties of the binding of Norovirus to its host cell receptor were determined. These were then used to develop a model of virus–host interactions at the cell membrane (antigen-receptor binding) and inside the cytoplasm (virus multiplication), with the phenomenological equations of nonequilibrium thermodynamics. Based on the model, an analysis of the virus–virus competition between Norovirus and Rotavirus was conducted. Full article

In chemical vapor deposition (CVD)-mediated graphene growth, copper foil serves as both a catalyst for methane decomposition and as a substrate for graphene nucleation and growth. Due to the low solubility of carbon in copper and the ease of transferring graphene from its surface, copper—particularly the Cu(111) facet—is widely favored for high-quality, monolayer graphene synthesis. In this article, the thermodynamic processes involved in methane dissociation and graphene nucleation on the Cu(111) surface were investigated using density functional theory (DFT). Molecular dynamics simulations were performed for structural optimization and to evaluate the reaction energies. Additionally, the average adsorption energies (ΔEad) of carbon clusters with varying atomic numbers on the Cu(111) surface were calculated. The graphene growth process was further modeled using the kinetic Monte Carlo (KMC) method to simulate carbon atom migration and nucleation dynamics. Thermodynamic analysis based on equilibrium component data was conducted to examine the influence of key operational parameters—temperature, pressure, and the CH₄/H₂ partial pressure ratio—on the graphene deposition rate. Full article

Antibiotic pollution, particularly via tetracycline (TC), poses significant environmental risks due to its recalcitrance and potential to induce antibiotic resistance. This study employed density functional theory (DFT) and transition state theory (TST) to investigate TC degradation by hydroxyl radicals (·OH), focusing on hydrogen atom transfer (HAT) and radical adduct formation (RAF) pathways. Geometry optimizations and vibrational analysis validated stationary points, while intrinsic reaction coordinate (IRC) calculations confirmed transition states. Key findings reveal that RAF pathways exhibit lower activation barriers (1.23–30.33 kJ/mol) and greater exothermicity (−164.42 kJ/mol) compared to HAT pathways (3.51–42.04 kJ/mol, −109.58 kJ/mol), making them kinetically and thermodynamically dominant. Frontier molecular orbital (FMO) analysis links HAT to TC’s HOMO (π-orbital character on aromatic rings) and RAF to its LUMO (electrophilic sites). Rate constants calculated at 298 K (TST with Wigner correction) confirm RAF’s kinetic superiority (up to 7.0 × 10¹¹ s⁻¹), surpassing HAT’s fastest pathway (6.2 × 10¹¹ s⁻¹). These insights advance the understanding of TC degradation mechanisms and help with the design of efficient photocatalytic oxidation processes for antibiotic removal. Full article

The challenging problem of chlorine “poisoning” SnO₂ for poorly recoverable detection of dichloromethane has been solved in this work. The materials synthesized by Ni or/and Mo doping SnO₂ were spread onto the micro-hotplates (<1 mm³) to fabricate the MEMS sensors with a low power consumption (<45 mW). The sensor based on Mo·Ni co-doped SnO₂ is evidenced to have the best sensing performance of significant response and recoverability to dichloromethane between 0.07 and 100 ppm at the optimized temperature of 310 °C, in comparison with other sensors in this work and the literature. It can be attributed to a synergetic effect of Mo·Ni co-doping into SnO₂ as being supported by characterization of geometrical and electronic structures. The sensing mechanism of dichloromethane on the material is investigated. In situ infrared spectroscopy (IR) peaks identify that the corresponding adsorbed species are too strong to desorb, although it has demonstrated a good recoverability of the material. A probable reason is the formation rates of the strongly adsorbed species are much slower than those of the weakly adsorbed species, which are difficult to form significant IR peaks but easy to desorb, thus enabling the material to recover. Theoretical analysis suggests that the response process is kinetically determined by molecular transport onto the surface due to the free convection from the concentration gradient during the redox reaction, and the output steady voltage thermodynamically follows the equation only formally identical to the Langmuir–Freundlich equation for physisorption but is newly derived from statistical mechanics. Full article

We address the scientific “time” concept in the context of more general relaxation processes toward the Wärmetod of thermodynamic equilibrium. More specifically, we sketch a construction of a conceptual ladder of chemical reaction steps that can rigorously bridge a description from the microscopic domain of molecular quantum chemistry to the macroscopic materials domain of Gibbsian thermodynamics. This conceptual reformulation follows the pioneering work of Kenichi Fukui (Nobel 1981) in rigorously formulating the intrinsic reaction coordinate (IRC) pathway for controlled description of non-equilibrium passages between reactant and product equilibrium states of an overall material transformation. Elementary chemical reaction steps are thereby identified as the logical building-blocks of an integrated mathematical framework that seamlessly spans the gulf between classical (pre-1925) and quantal (post-1925) scientific conceptions and encompasses both static and dynamic aspects of material change. All modern chemical reaction rate studies build on the apparent infallibility of quantum-chemical solutions of Schrödinger’s wave equation and its Dirac-type relativistic corrections. This infallibility may now be properly accepted as an added“inductive law” of Gibbsian chemical thermodynamics, the only component of 19th-century physics that passed intact through the revolutionary quantum upheavals of 1925. Full article

This study focuses on biochemical pathways of complex biochemical formation, taking into account various thermodynamic parameters that change as the complexity and molecular weight of complex molecules increase. We conducted a study of the co-direction of changes in thermodynamic quantities such as $lg\left[K_d\right]$, $T\Delta S$, $\Delta (\Delta W)$, and $lg\left(\mathrm{cond}\right(W\left)\right)$ during the transition from a monomer to a dimer and then to a trimer and tetramer. In this work, we assume that the co-direction of changes in thermodynamic quantities as the final molecular formation being achieved signals a higher affinity of molecules among themselves than there is for a biochemical formation, which is characterized by the lack of coordination of the biochemical pathway directions of the final molecular compound. As the studied molecular complexes, we took [LGP2-8dsRNA-LGP2], [VP35]₂-dsRNA-[VP35]₂, and MARV NPcore proteins with peptides and the complex of MJ20 with antigens from the Bundibugyo strain of Ebola virus. Calculations of biochemical reaction paths were conducted. Full article

In this work, we studied the main decomposition reactions on the ground state of nitromethane (CH₃NO₂) with the CASPT2 approach. The energetics of the main elementary reactions of the title molecule have been analyzed on the basis of Gibbs free energies obtained from standard expressions of statistical thermodynamics. In addition, we describe a mapping method (orthogonalized 3D representation) for the potential energy surfaces (PESs) by defining an orthonormal basis consisting of two $R^n$ orthonormal vectors (n, internal degrees of freedom) that allows us to obtain a set of ordered points in the plane (vector subspace) spanned by such a basis. Geometries and harmonic frequencies of all species and orthogonalized 3D representations of the PESs have been computed with the CASPT2 approach. It is found that all of the analyzed kinetically controlled reactions of nitromethane are endergonic. For such a class of reactions, the dissociation of nitromethane into CH₃ and NO₂ is the process with the lower activation energy barrier (ΔG); that is, the C-N bond cleavage is the most favorable process. In contrast, there exists a dynamically controlled process that evolves through a roaming reaction mechanism and is an exergonic reaction at high temperatures: CH₃NO₂ → [CH₃^…NO₂]* → [CH₃ONO]* → CH₃O + NO. The above assertions are supported by CASPT2 mappings of the potential energy surfaces (PESs) and classical trajectories obtained by “on-the fly” CASSCF molecular dynamics calculations. Full article

Self-healing technology is an effective method for enhancing the crack resistance of cement-based composites. This study focuses on the impact of the environmentally friendly diluent C12-14 alkyl glycidyl ether (AGE) on the performance of the epoxy resin–polythiol (rimethylolpropane tris (3-mercaptopropionate), TMPMP) self-healing system, examining core fluidity, microcapsule properties, molecular dynamics, and the mechanical properties of cured products. The results show that as the AGE dosage increases, the particle size distribution of microcapsules becomes more concentrated, and the dispersion of particles is improved. Fourier-transform infrared spectroscopy confirms the successful encapsulation of E-51 and AGE. Microcapsules maintain structural integrity at high temperatures of 423.15 K. The onset thermal degradation temperature of the mixture shows an increasing trend with reduced AGE dosage. Specifically, TMPMP_35% exhibits an onset degradation temperature of 370.95 K, while that of TMPMP_20% is increased by 57.57% compared to TMPMP_35%. Conversely, the initial and peak temperatures of the curing reaction decrease with less AGE incorporation. Thermodynamic analysis reveals that activation energy (E) initially increases and then decreases with increasing AGE. The frequency factor (A) correlates positively with the heating rate, indicating that the curing reaction’s reactivity is closely linked to heating rate. Minor variations in the reaction rate constant (k) indicate that the self-healing system maintains stable reactive activity at low temperatures. Notably, the AGE dosage significantly affects the rigidity of the self-healing system; the average Young’s modulus inversely correlates with AGE dosage, with the most substantial decrease of 5.88% occurring when AGE increases from 30% to 35%. This study offers insights into optimizing diluent ratios to balance self-healing and mechanical properties, essential for developing high-performance self-healing cement materials. Full article

Complexation of alkaline earth metal cations with fluorescent tertiary-amide lower-rim calix[4]arene derivative bearing two phenanthridine moieties was studied experimentally (UV spectrophotometry, fluorimetry, isothermal microcalorimetry, NMR spectroscopy) and computationally (classical molecular dynamics and DFT calculations) at 25 °C. The complexation reactions were studied in acetonitrile, methanol, and ethanol, whereby the solvent effect on cation-binding processes was particularly addressed. The complex stability constants and standard reaction thermodynamic quantities (Gibbs energies, enthalpies, and entropies) were determined. The receptor exhibited particularly high affinity towards alkaline earth metal cations in acetonitrile, with peak affinity for Ca²⁺. The stability of all complexes was significantly lower in ethanol and methanol, where the most stable complex was formed with Sr²⁺. The decrease in cation-binding abilities was a consequence of the differences in solvation of the reactants and products of the complexation reactions (involving inclusion of the solvent molecule in the calixarene cone), cation charge density, as well as the cation–ligand binding site compatibility. The reactions were enthalpically controlled in acetonitrile, whereas in methanol and ethanol, the binding processes were endothermic and thus entropy driven. The results of ¹H NMR measurements, MD simulations, and DFT calculations provided an insight into the structure of the complexes and the corresponding adducts with solvent molecules, as well as the structural aspects behind the differences in complexation thermodynamics. Due to the significant increase in its fluorescence upon cation binding, the studied calixarene derivative was proven to be a promising luminescent sensor for alkaline earth metal cations. Full article

Oxalic acid is the most abundant low-molecular-weight dicarboxylic acid in the atmosphere, and it plays a crucial role in the formation of new particles and cloud condensation nuclei. However, most observational studies have focused on particulate oxalate, leaving a significant knowledge gap on oxalic acid vapor. This study investigated the concentrations and formation of oxalic acid vapor and oxalate in PM_2.5 at a rural tropical coastal island site in south China across different seasons, based on semi-continuous measurements using an Ambient Ion Monitor-Ion Chromatograph (AIM-IC) system. We replaced the default 25 μL sampling loop on the AIM-IC with a 250 μL loop, improving the ability to distinguish the signal of oxalic acid vapor from noise. The data revealed clear seasonal patterns in the dependent daytime and nighttime formation of oxalic acid vapor, benefiting from high signal-to-noise ratios. Specifically, concentrations were 0.059 ± 0.15 μg m⁻³ in February and April 2023, exhibiting consistent diurnal variations similar to those of O₃, likely driven by photochemical reactions. These values decreased to 0.021 ± 0.07 μg m⁻³ in November and December 2023, with higher nighttime concentrations likely related to dark chemistry processes, amplified by accumulation due to low mixing layer height. The concentrations of oxalate in PM_2.5 were comparable to those of oxalic acid vapor, but exhibited (3–7)-day variations, superimposed on diurnal fluctuations to varying degrees. Additionally, thermodynamic equilibrium calculations were performed on the coastal data, and independent size distributions of particulate oxalate in the upwind marine atmosphere were analyzed to support the findings. Full article