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Molecular titanosilicates {(tBuO3)3SiO}2Ti(NR2)2 (1, R=Et; 2, R=Me) and {(tBuO3)3SiO}3TiNR2 (TSA1, R=Et; 3, R=Me) were obtained from the reaction between silanol (tBuO3)3SiOH (S1) and titanium amides Ti(NR2)4 (R=Et, R=Me). Additionally, the reaction of 3 and TSA1 with CO2 led to the exclusive formation of carbamates {(tBuO)3SiO}3Ti(O2CNR2) (4, R=Et; 5, R=Me). The molecular structure of 5 confirmed the proposed connectivity and presence of SiO4 and Ti(O2CNR2) units. In compound 4, titanium is coordinated to five oxygen atoms belonging to one bidentate carbamate group and three silicate ligands in a distorted square‐base pyramidal geometry. Also, we have performed DFT calculations and QTAIM analysis to study the distribution of the electron density in the carbamate {(tBuO)3SiO}3Ti(O2CNEt2) (4) and salt {(tBuO)3SiO}3TiO(H2NMe2) 6 which was obtained by the hydrolysis of compound 5. [ABSTRACT FROM AUTHOR]

Amyloid-associated neurodegenerative diseases, including Alzheimer's disease (AD), are characterized by the in-brain accumulation of β-sheet structured protein aggregates called amyloids. However, neither a disease model nor therapy is established. We review past data and present new, preliminary data and opinions to help solve this problem. The following is the data-derived model/hypothesis. (1) Amyloid-forming proteins have innate immunity functions implemented by conversion to another sheet conformation, α-sheet. (2) In health, α-sheet structured, amyloid-forming proteins inactivate microbes by co-assembly with microbe α-sheets. Amyloid-forming proteins then undergo α-to-β-sheet conversion. (3) In disease, α-sheet-structured, amyloid-forming proteins over-accumulate and are neuron-toxic. This hypothesis includes formation by virus capsid subunits of α-sheets. In support, we find that 5–10 mM methylene blue (MB) at 54 °C has a hyper-expanding, thinning effect on the phage T4 capsid, as seen by negative stain- and cryo-electron microscopy after initial detection by native gel electrophoresis (AGE). Given the reported mild anti-AD effect of MB, we propose the following corollary hypothesis. (1) Anti-AD MB activity is, at least in part, caused by MB-binding to amyloid α-sheet and (2) MB induces the transition to α-sheet of T4 capsid subunits. We propose using AGE of drug incubated T4 to test for improved anti-AD activity. [ABSTRACT FROM AUTHOR]

A Kratzer‐Fues potential is coupled with its self to form a double Kratzer‐Fues potential. The solutions of the radial Schrödinger equation with the combined potential are obtained via two different methodologies. Using the supersymmetric approach, the energy equation for a non‐approximated centrifugal term is obtained. The energy equation for the approximated centrifugal term is obtained using the parametric Nikiforov‐Uvarov method. Numerical results are computed for five molecules using MATLAB software program. The computed numerical values are compared with the experimental values and the ground state energy obtained from Herzberg's energy level equation. The study revealed that the results of the approximated centrifugal term are better than the results of the non‐approximated centrifugal term for four molecules. [ABSTRACT FROM AUTHOR]

Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an "atypical diatom" displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well‐known physiology, alongside the steady increase in genome‐enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology. [ABSTRACT FROM AUTHOR]

Commercially available molecular models are elaborately made but generally expensive, which hinders their distribution to all classroom students. Aiming at developing an affordable molecular model, we developed a structure model kit consisting of inexpensive electronic components including transistors and colored light-emitting diodes (LEDs) with a total cost of ca. 2 USD. The structure model kit was designed for building a family of environmental pollutant molecules known as dioxins, in which transistor, white LED, red LED, and yellow LED components are used to represent sp2 carbon, hydrogen, oxygen, and chlorine atoms, respectively. Herein, we report an activity directed to nonchemistry majors studying environmental science and electronic engineering to help them gain insight into the molecular structure of dioxins using the newly developed structure model kit. The activity was well received by many students, some of whom came to understand the relationship between the structure and nomenclature of dioxins, mainly 2,3,7,8-tetrachlorinated dibenzo-p-dioxin (2,3,7,8-TCDD) and its isomers.

The infrastructure features of the spent mushroom substrate (SMS) were detected and explored based on experimental data acquired from Fourier Transform Infrared Spectroscopy, Pyrolysis–Gas Chromatography/Mass Spectrometry as well as Thermogravimetric Analysis. Further, molecular simulation methods were combined with diverse testing technologies to build the 2D and associated 3D models from cellulose, hemicellulose, and lignin. Eventually, a rational 3D model was constructed for SMS using geometry optimization calculations and annealing dynamics simulations. According to the Mulliken population analysis and electron density analysis, the π-π conjugation effect of the aromatic ring structures was influenced by the oxygen atoms, thus, resulting in the electron accumulation on these oxygen atoms. At the same time, oxygen exhibited a greater electronic charge density and reactivity in the Furan ring and pyran ring structures in contrast to other atoms. Furthermore, the molecular orbitals for HOMO and LUMO were computed to check the chemical reaction characteristics of the SMS. According to the HOMO–LUMO energy gap, the structure of the polycyclic aromatic hydrocarbons provided reaction sites for the reaction and played a key role in chemical bond breaking. [ABSTRACT FROM AUTHOR]

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Siglecs are important lectins found in different types of immune cells and function as regulatory molecules by recognizing self-associated glycans and converting extracellular interactions into signals for inhibiting immune cell functions. Although many Siglecs have been found to show broad specificities and recognize different types of sulfated oligosaccharides, Siglec-8 and Siglec-9 displayed a high degree of specificity for sialyl N-acetyllactosamine (sLacNAc) with sulfations at O6-positions of the galactose (6’-sulfation) and N-acetylglucosamine (6-sulfation), respectively. Siglec-3 was recently discovered to bind sLacNAc both sulfations. In addition to a conserved arginine residue for binding to sialic acid residue, the sequence variety in the CC’ loop may provide binding specificities to sulfated oligosaccharides in Siglecs. Thus, the present study employed molecular models to study the impact of different residues in the CC’ loops of Siglec-8/9/3 to the recognitions of 6-sulfations in Gal and/or GlcNAc of sLacNAc. The negatively charged residues in the CC’ loop of Siglec-9 formed unfavorable electrostatic repulsions with the 6-sulfate in Gal and resulted no recognitions, in contrast to the favorable interactions formed between the positively charged residues in the CC’ loop of Siglec-8 and the 6-sulfate in Gal resulting strong specificity. A two-state binding model was proposed for Siglec-3 recognizing 6-sulfations in Gal and GlcNAc of sLacNAc, as the neutral residues in the CC’ loop of Siglec-3 could not form strong favorable interactions to lock the 6-sulfate in Gal within a single binding pose or strong unfavorable interactions to repel the 6-sulfate in Gal. The oligosaccharide adopted two distinctive binding poses and oriented the sulfate groups to form interactions with residues in the CC’ loop and G-strand. The present study provided a structural mechanism for the sequence variety in the CC’ loop of Siglec-8/9/3 determining the recognitions to the sulfated oligosaccharides and offered insights into the binding specificities for Siglecs.

A representative molecular model of kerogen is the prerequisite to the study on molecular interaction of fluid molecules with organic nanopores of shale. The molecular kerogen model in Silurian deep gas shale from southern China remains to be developed. In this work, the chemical structure of the targeted deep shale kerogen is characterized by organic geochemical measurements. The derived structural parameters are utilized to build the molecular structure of the kerogen unit. The kerogen unit shows a good representation of realistic kerogen structure in shale reservoir in terms of carbon skeleton, heteroatomic compositions and groups. The kerogen matrix and a extended kerogen slit model are constructed based on the kerogen unit, which match well with the experimental results in matrix density and kerogen porosity, respectively. The kerogen matrix is overall disordered with gentle stacking of polyaromatic fragments, due to the bendable aliphatic linkages and large-size aromatic units. The kerogen nanopores are not saturated with methane at deep shale reservoir conditions. At high pressure, the absolute adsorption tends to reach a maximum, while the excess adsorption shows a decreasing trend. The effect of pressure on the dissolved gas density is not pronounced. The generated kerogen model can serve as a starting point for further theoretical investigations on fluid storage and transport in organic nanopores of deep shale reservoir at microscopic scale.

Interferon induced with helicase C domain-containing protein 1 (IFIH1) gene encodes a cytoplasmic RNA helicase otherwise known as melanoma differentiation-associated 5 (MDA5), a RIG-1-like RNA helicase that recognizes viral RNA and is involved in innate immunity through recognition of viral RNA. Upon binding to double-stranded (ds) RNA, MDA5 forms a filamentous assembly along the length of dsRNA and utilizes molecular signatures to discriminate self, versus non-self on the basis of dsRNA length and methylation. Its missense variant rs35667974 is protective for type 1 diabetes, psoriasis, and psoriatic arthritis, but is also found to be associated with an increased risk for ankylosing spondylitis, Crohn's disease, and ulcerative colitis. To gain insight into the complex role of this variant we performed a structural analysis of MDA5 in complex with dsRNA using molecular dynamics simulations. Our data suggest that while the Ile923Val mutation of the rs35667974 variant does not affect binding to native dsRNA significantly, it displays a destabilizing effect in the presence of 2′-O uridine methylation. Thus, the presence of 2′-O-methylation at the dsRNA introduces a sensing signature that leads to selective reduction of the overall MDA catalytic activity. This study represents an evaluation of the role of the shared rs35667974 variant of autoimmune locus IFIH1, reported to lead to selectively reduced catalytic activity of the modified MDA5 phenotype and, as a consequence, reduced negative feedback on cytokine and chemokine signaling and selectively protection against autoimmunity. [ABSTRACT FROM AUTHOR]

Carbon nanotubes (CNTs) are nanometer-sized structures that can be used to reinforce cement matrices. The extent to which the mechanical properties are improved depends on the interfacial characteristics of the resulting materials, that is, on the interactions established between the CNTs and the cement. The experimental characterization of these interfaces is still impeded by technical limitations. The use of simulation methods has a great potential to give information about systems lacking experimental information. In this work, molecular dynamics (MD) and molecular mechanics (MM) were used in conjunction with finite element simulations to study the interfacial shear strength (ISS) of a structure formed by a pristine single-walled CNT (SWCNT) inserted in a tobermorite crystal. The results show that, for a constant SWCNT length, ISS values increase when the SWCNT radius increases, while for a constant SWCNT radius, shorter lengths enhance ISS values. [ABSTRACT FROM AUTHOR]

The spontaneous combustion of coal is a disaster associated with coal mining. In this study, the authors investigated the characteristics of spontaneous combustion of coal at different temperatures (room temperature, 50–500 °C with 50 °C interval) using Fourier transform infrared spectroscopy (FTIR), high-resolution transmission electron microscopy (HRTEM), etc. The results showed the aromatic structure was mainly naphthalene. The aliphatic hydrocarbons were long chain. Oxygen, nitrogen, and sulphur existed as C-O, pyridine, pyrrole nitrogen, aliphatic sulphur, and sulfone. The molecular structural formula is C142H112N2O22. The stable 3D structural was obtained through optimization. Thermogravimetric analysis results showed the critical and dry-cracking temperatures of coal samples showed downward trends overall, whereas the acceleration and thermal-decomposition temperatures varied greatly with increase in oxidation temperature. The activation energy change pattern of 4 stages is not obvious. The FTIR results showed the contents of self-associated OH changed greatly. The aliphatic hydrocarbons changed greatly at 30–150 °C and 300–500 °C. The C-O showed increasing trends, whereas the C=O decreased consistently. The HRTEM results showed the aromatic fringes in coal samples were dominated by 1 × 1 and 2 × 2, the contents of which accounted for more than 80% of the total fringes. [ABSTRACT FROM AUTHOR]

• The mechanism of secondary regenerated asphalt was analyzed through molecular dynamics (MD). • The fusion behaviors of new and aged asphalts during secondary regeneration were dynamically characterized and analyzed. • The viscosity and modulus of secondary regeneration were predicted using MD. With the use of recycled asphalt pavement, numerous recycled pavements will suffer from damages which needs to be regenerated for the second time (i.e. secondary regeneration). The mechanism and impact of secondary regeneration may diverge from those observed during primary regeneration. To study the aging and regeneration mechanism of secondary regenerated asphalt, the molecule models of regenerant and asphalts under different aging states were established through the molecular dynamics (MD). The double-layer diffusion models were constructed to examine the fusion behavior of new and aged asphalts. Based on this, the dynamic viscosity, rotational viscosity, bulk modulus, and shear modulus of secondary regenerated asphalt were predicted. The findings indicate that the established molecular models have a strong correlation with real asphalt molecules. During secondary regeneration, the deepening of asphalt aging reduces the fusion velocity and efficiency between aged and new asphalts. The introduction of regenerant can enhance the diffusion velocity between the aged and new asphalts, yet it does not necessarily improve their fusion degree. During the process of secondary regeneration, the shear modulus of secondary aged asphalt can be effectively restored by adding regenerant, but the recovery of dynamic viscosity, rotational viscosity and bulk modulus presents poor trends when compared to the primary regeneration. [ABSTRACT FROM AUTHOR]

• Bulky silanol (Ph 3 CO)(i PrO) 2 Si(OH) was prepared as an alternative to (tBuO)3SiOH. • It was converted into three metalosilicates with lithium, aluminum and gallium. • All compounds were characterized by single-crystal X-ray diffraction. • Their electronic structure was studied using Hirshfeld atom refinement and QTAIM. • Ring-opening polymerization was used to compare the steric bulk of the silanols. The molecular silanol (Ph 3 CO)(i PrO) 2 Si(OH) was designed to evaluate the degree of steric bulk the trityl moiety imposes on the Si–OH group. The reactivity of the silanol was evaluated by the formation of three metallosilicates with lithium, aluminum, and gallium, and their molecular structures and the degree of association were determined. Hirshfeld atom refinement or DFT calculation, and QTAIM analysis of the electron density in all compounds were used to analyze the bonding situation in the metallosilicate moieties and determine the strength of the intermolecular hydrogen bonds formed by the silanol. Finally, ring-opening polymerization of ε-caprolactone was used as another criterion for the evaluation of the steric bulk imposed by the trityl group. [Display omitted] [ABSTRACT FROM AUTHOR]

[Display omitted] • The information of lattice fringes in TEM images is effectively extracted by Python. • The amorphous carbon molecular model suitable for molten salt electrolysis process was constructed firstly. • The influence of electric field on the configuration and charge distribution of the system is investigated. • This study provides a molecular insight into the graphitization process of amorphous carbon. Molten salt electrolysis graphitization is a novel method for the electrochemical graphitization, offering significant technological advantages. Researchers have shown keen interest in preparing graphite materials through molten salt strategies. However, there is still a lack of comprehensive research methodologies at the molecular scale for the removal of heteroatoms and rearrangement of carbon atoms in different amorphous carbon conversion systems. To address the above issue, the deposited carbon (DC, a coking byproduct) was converted into graphitized material (electrolysis products, EP) through the electrochemical method in this study. By processing Transmission Electron Microscope images with Python programming, aromatic skeleton structure information was quantitatively extracted. The evolution of the structure of DC was studied using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. Based on information about elemental content, aromatic skeletal structure, and heteroatom functional groups, average chemical structure models were constructed for DC and EP, and relevant chemical bond parameters were statistically analyzed. Then, the influence of the electric field on the structural transformation of amorphous carbon in molten salts was investigated. The research results show that the electric field significantly affects the graphitization transformation process of amorphous carbon in molten salts, enhancing the interaction between calcium ions and DC molecules, increasing the diffusion coefficient of particles in the system, and promoting the formation of more sp2-hybridized carbon atoms, thus forming a more compact aromatic ring network. This study provides a new research method and molecular/atomic-level insights for a deeper understanding of the mechanism of graphitization transformation of amorphous carbon. [ABSTRACT FROM AUTHOR]

The lack of clarity in characterizing the chemical structure model of lignin waste hinders the comprehensive understanding of its pyrolysis reaction mechanism. The characterization results revealed that the de–alkalized lignin sample contained larger amounts of aliphatic and aromatic carbons compared to carbonyl carbons. Additionally, the aliphatic carbon molecules exhibited a higher presence of oxygenated carbons. The degree of aromaticity (f a) was determined to be 63.93 %. The resulting single–molecule structural model exhibited a molecular formula of C 33 H 26 O 11 and a molecular weight of 598.56. Furthermore, the evolutions patterns and formation pathways of primary volatile components (H 2 , CH 4 , CO, and CO 2) in pyrolysis reactions were revealed. The number of H 2 molecules exhibited a positive correlation with the rise in pyrolysis reaction temperature. CH 4 molecules exhibited a pattern of initially increasing and subsequently decreasing. The number of CO molecules exhibited a positive correlation with the rise in pyrolysis temperature. Conversely, the number of CO 2 molecules demonstrated an initial increase followed by a decrease as the pyrolysis temperature increased. Finally, the generation pathway analysis of pyrolysis products shows that the H 2 molecule is composed of two hydrogen atoms bonded together that have been dissociated from the carboxyl group. Alternatively, it can be produced through hydrogenation reactions involving hydrogen atoms detached from the carboxyl group and methyl groups. CH 4 is primarily generated through the reaction between –CH 3 and free hydrogen ions. CO is primarily produced through the cleavage of the carbonyl group. CO 2 is primarily produced through the cleavage of carboxyl and ester groups. • The molecular structure of lignin waste was constructed by characterization experiments. • The ReaxFF MD method was employed to investigate the pyrolysis of lignin waste. • The effects of different heating strategies on the pyrolysis products were studied. • Micro mechanisms of lignin waste pyrolysis were revealed at the molecular level. [ABSTRACT FROM AUTHOR]

1,2-bis(triethoxysilyl)ethane (BTESE)-derived membranes are of great interest in gas-/liquid-phase separations, while the interplay between their chemical structure, pore topology, and permeability remains unexplored. This highlights the need for a realistic molecular model that captures the BTESE's nanostructure and the complex transport within its pores. By considering the two important ingredients (atomic chemical composition and physical density), we first employ the simulated annealing procedure to reconstruct a database of the BTESE models of different densities. By comparing the X-ray diffraction pattern with the experimental data, the reactive force field used in our molecular simulations strategy is found to capture the amorphous nature of the BTESE's nanostructure. In particular, the molecular texture parameters are screened to match the experimental density. We then turn to extract our BTESE models using the radial distribution function, bond order, and atomic partial charge. The chemical bonding features show that our BTESE model consists of the carbon–silicon–oxygen backbone with a few small molecules formed. Moreover, the pore size distribution of our BTESE model is found to be in good agreement with the experimental data. The sieving effect of the pore topology on the gas permanence observed in experiments is found to be well explained by such a molecular picture. These findings for the realistic molecular model and pore topology provide a means to probe the relationship between chemical structure and the gas transport within pores of the BTESE-derived membranes, as well as other organosilica membranes. [Display omitted] • Towards realistic molecular models of BTESE-derived nanostructures. • Extracted chemical structure, atomic charge, and pore topology support experimental expectations. • Experimental gas permanence can be well explained by theoretical pore size distributions. [ABSTRACT FROM AUTHOR]

Flowering time is crucial for the survival and reproduction. Prunus genus belongs to the Rosaceae family and includes several hundred species of flowering trees and shrubs with important ornamental and economic values. However, the molecular mechanism underlying early flowering in Prunusgenus isunclear.Here,weutilizedthe genome and transcriptome of P. mume and P. persica to explore the transcriptional regulation mechanism of early flowering. Comparative genomics found that genes accounting for 92.4% of the total P. mume genome and 91.2% of the total P. persica genomebelonged to orthogroups. A total of 19,169 orthogroupswere found between P. mume and P. persica, including 20,431 corresponding orthologues and 20,080 collinearity gene pairs. A total of 305 differentially expressed genes (DEGs) associated with early floweringwere found, among which FT, TLI65, andNAP57 were identified as hub genes in the early flowering regulation pathway. Moreover, we identified twenty- five transcription factors (TFs) from nine protein families, including MADS-box, AP2/ ERF, and MYB. Our results provide insights into the underlying molecular model of flowering time regulation in Prunus genus and highlight the utility of multi-omics in deciphering the properties of the inter-genus plants. [ABSTRACT FROM AUTHOR]

Dengue virus (DENV) is one of the most geographically distributed mosquito-borne flaviviruses, like Japanese encephalitis virus (JEV), and Zika virus (ZIKV). In this study, a library of the known and novel Glycyrrhizic acid (GL) derivatives bearing amino acid residues or their methyl/ethyl esters in the carbohydrate part were synthesized and studied as DENV inhibitors in vitro using the cytopathic effect (CPE), viral infectivity and virus yield assays with DENV1 and DENV-2 in Vero E6 and A549 cells. Among the GL conjugates tested, compound hits GL-D-ValOMe 3, GL-TyrOMe 6, GL-PheOEt 11, and GL-LysOMe 21 were discovered to have better antiviral activity than GL, with IC50 values ranging from <0.1 to 5.98 μM on the in vitro infectivity of DENV1 and DENV2 in Vero E6 and A549 cells. Compound hits 3, 6, 11, and 21 had a concentration-dependent inhibition on the virus yield in Vero E6, in which GL-D-ValOMe 3 and GL-PheOEt 11 were the most active inhibitors of DENV2 yield. Meanwhile, the time-of-addition assay indicated that conjugates GL-D-ValOMe 3 and GL-PheOEt 11 exhibited a substantial decrease in the DENV2 attachment stage. Subsequently, chimeric single-round infectious particles (SRIPs) of DENV2 C-prM-E protein/JEV replicon and DENV2 prM-E/ZIKV replicon were utilized for the DENV envelope I protein-mediated attachment assay. GL conjugates 3 and 11 significantly reduced the attachment of chimeric DENV2 C-prM-E/JEV and DENV2 prM-E/ZIKV SRIPs onto Vero E6 cells in a concentration-dependent manner but did not impede the attachment of wild-type JEV CprME/JEV and ZIKV prM-E/ZIKV SRIPs, indicating the inhibition of Compounds 3 and 11 on DENV2 E-mediated attachment. Molecular docking data revealed that Compounds 3 and 11 have hydrophobic interactions within a hydrophobic pocket among the interfaces of Domains I, II, and the stem region of the DENV2 envelope (E) protein. These results displayed that Compounds 3 and 11 were the lead compounds targeting the DENV E protein. Altogether, our findings provide new insights into the structure–activity relationship of GL derivatives conjugated with amino acid residues and can be the new fundamental basis for the search and development of novel flavivirus inhibitors based on natural compounds. [ABSTRACT FROM AUTHOR]

Introduction. The mineral resource base of Russia has effective sorption substances that meet pharmaceutical requirements. Promising mineral raw materials are Zeolites, which combine the properties of an adsorbent and a "molecular sieve" due to the porous structure. In addition to the enterosorption direction, natural Zeolites are a source of macro-and microelements, which determines their use as biologically active food additives.Aim. Study of the physical and chemical characteristics of the Zeolites of the Kholinsky deposit.Materials and methods. The zeolite mineral raw materials of the Kholinsky deposit were used as objects of research. Optical microscopy was performed using a Leica DM direct microscope (Microsystems, Germany). Energy dispersion analysis was performed using an electron scanning microscope JSM-5300 (Jeol Ltd, Japan). The sorption characteristics were studied using the ASAP 2400 device (Micromeritics, USA) according to the method. The construction of a virtual three-dimensional molecular model of the Zeolite was carried out using the program Java Applet Jmol.Results and discussion. The physicochemical properties of Zeolites are investigated. It is established that morphologically the particles of the zeolite phase have a size of 5-30 microns, they are evenly distributed over the entire area of the site and represent the first structural level. Particles of the zeolite phase with a size of 5-6 microns form the second structural level due to Clinoptilolite crystals, microcracks and microgeodes. Based on the energy-dispersion spectral analysis, an increased content of the elements K, Na was revealed, which indicates the alkaline composition of the cation exchange complex. The studied Zeolite samples have micropores (volume 0.0031 cm3/g), mesopores (volume 0.0675 cm3/g), and a specific surface area of 29.1840 m2/g. A virtual three-dimensional molecular model of the Zeolite of the Kholinsky deposit has been developed. According to the molecular model, the sorption characteristics of the Kholinsky deposit Zeolite were: specific surface area - 1096.31 m2/g (1916.34 m2/cm3), the average diameter of the spherical molecule for adsorption in the pores is 5.97 Å.Conclusion. The analysis of the sorption characteristics of the Zeolite revealed the following features: the pores occupy half the volume of the entire Zeolite, which are available for the sorption of water and low-molecular substances. Each pore in three mutually perpendicular directions communicates with the neighboring ones through "windows". A system of intracrystalline pores and cavities is formed, in which the occlusion and adsorption of molecules of the appropriate size easily occurs.

In order to reuse waste resources (waste engine oil and waste asphalt mixture), the regeneration process of waste oil on aged asphalt is systematically explained. The BA was treated by aging test, and the basic mechanical properties, molecular dynamics simulation, and infrared spectrum test were carried out on this basis. The results showed that the WEO can restore the physical properties of the aged asphalt, and the recommended amount of WEO is 3%. The density of the asphalt model corresponds to the actual situation of the asphalt. The aged asphalt components are more aggregated. After the WEO was added, the components of asphalt aggregation were reduced and the diffusion ability was improved. Finally, infrared spectroscopy tests were conducted on asphalt specimens, and the results showed that the process of rejuvenated asphalt was dominated by physical reactions. Consequentially, the results of this study build a bridge between the performance and simulation of aged asphalt rejuvenated by WEO. Consequentially, the results of this research promote the recycling of WEO and waste asphalt pavement materials, ultimately advocating the sustainability of pavement construction. [ABSTRACT FROM AUTHOR]

Protein amyloid-β (Aβ) oligomers with β-sheet-like backbone (β-structured) form extracellular amyloid plaques associated with Alzheimer's disease (AD). However, the relationship to AD is not known. Some investigations suggest that the toxic Aβ component has α-sheet-like backbone (α-structured) subsequently detoxified by intracellular α-to-β conversion before plaque formation. Our objective is to compare this latter hypothesis with observations made by electron microscopy of thin sections of AD-cerebral cortex. We observe irregular, 200-2,000 nm, intracellular, lipofuscin-like inclusions. Some are light-staining and smooth. Others are dark-staining and made granular by fibers that are usually overlapping and are sometimes individually seen. Aspects unusual for lipofuscin include 1) dark and light inclusions interlocking as though previously one inclusion, 2) dark inclusion-contained 2.6 nm thick sub-fibers that are bent as though α-structured, and 3) presence of inclusions in lysosomes and apparent transfer of dark inclusion material to damaged, nearby lysosomal membranes. These data suggest the following additions to α-structure-based hypotheses: 1) Lipofuscin-associated, α-structured protein toxicity to lysosomal membranes is in the chain of AD causation; 2) α-to-β detoxification of α-structured protein occurs in lipofuscin and causes dark-to-light transition that, when incomplete, is the origin of cell-to-cell transmission essential for development of AD. [ABSTRACT FROM AUTHOR]

Building students' spatial ability to assist them in understanding molecular geometry requires proper multimedia. This study investigated the effectiveness of 3D molecular interactive multimedia (3D-MIM) in improving chemistry students' spatial ability. Thirty chemistry education students of a public university in East Java, Indonesia, participated in this study. This pre-experimental pretest-posttest design employed a set of spatial ability tests referring to the three main dimensions of spatial abilities (spatial relationship, spatial orientation, spatial visualization) and semi-structured interview. Our finding showed that students' spatial abilities for the three domains after experiencing the 3DMIM fall in the strong and large effects category. The values of N-gain falling in the moderate category and effect size (d) in the high category confirm the effectiveness of the 3D-MIM. [ABSTRACT FROM AUTHOR]

• The molecular structure characterization of Luling10 coal was realized. • The macromolecular model of Luling10 coal was constructed. • The micro-wetting mechanism of Luling10 coal is revealed. The physicochemical structure and energy composition of coal macromolecules are the major factors affecting coal wettability. This study thus employed 13C NMR, FTIR, and XPS to determine the chemical structure of coal in the No. 10 coal seam of the Luling coal mine and gain insights into the molecular mechanisms of coal wetting. The results showed that the molecular formula of the Luling 10 model was C 290 H 223 O 25 N 5 S. Through molecular dynamics simulation, upon the stable adsorption of sodium dodecyl sulfate (SDS) on the coal surface, both the mobility of water molecules and the water molecule content in the interfacial adsorption layer increased. After SDS was added, except for the hydrogen bond energy, the increase rate of each potential energy increased, and van der Waals energy and bond length energy changed the most. The reason for the decrease of hydrogen bond energy is that more atoms in coal macromolecules form hydrogen bonds with polar water molecules. The increase of SDS promoted the significant changes of bond length energy, bond angle energy and van der Waals force of coal, thus increasing the wettability of coal. Taken together, our findings provide important insights into the molecular mechanisms through which surfactants improve chemical wetting. [ABSTRACT FROM AUTHOR]

• A Mesoproterozoic kerogen molecular model is established for the first time. • This kerogen is mainly short-branched chains or alicyclics rather than long chains. • This kerogen model resembles Paleozoic kerogen, yet differs from Mesozoic kerogen. In the southeastern Xuanlong sag of Northern China, the organic-rich black shale of the Mesoproterozoic Xiamaling Formation holds significant potential as a source rock. Through advanced analytical techniques including elemental analysis, 13C NMR, XPS, FTIR, and XRD, the elemental composition and chemical structure were thoroughly characterized, and the molecular structure of the Xiamaling shale kerogen was established. The 13C NMR analysis revealed the carbon composition of kerogen, indicating 75.19 % aliphatic carbon, 22.06 % aromatic carbon, and 2.75 % carbonyl carbon, with quantitative support from FTIR and XRD spectra. The dominant methylene carbons exhibited a low average methylene chain length (Cn) of 3.87, suggesting that they are primarily short-branched or alicyclic compounds rather than long straight chains. This conclusion was verified by the absence of a sharp peak at a wavenumber of 719.95 cm−1 in the FTIR spectrum. Oxygen-containing functional groups observed in 13C NMR spectra were also identified in FTIR spectra at a wavenumber range of 3500–1000 cm−1. XPS analysis indicated that nitrogen-containing groups were amino, quaternary, pyridine, and primary pyrrole groups, and sulfur existed as sulfoxide, aromatic sulfur, aliphatic sulfur, and sulfone. Finally, a relatively rational 2D molecular structure with the chemical formula of C 278 H 346 N 6 O 26 S 2 was established by comparing the predicted and experimental 13C NMR spectra. Using MD simulation, five optimized 2D molecules were combined to construct a robust 3D kerogen model with a physical density of 1.067 g/cm3. Comparatively, the aliphatic structure of the Mesoproterozoic Xiamaling kerogen model consists of some monocyclic alkanes and polycyclic saturated structures, resembling Paleozoic kerogen models but differing from Mesozoic counterparts. The constructed kerogen model addresses the gap in the Precambrian kerogen modeling and sets the stage for in-depth exploration of pyrolysis mechanisms in the future. [ABSTRACT FROM AUTHOR]

With the advent of atomic resolution transmission electron microscopy (AR-TEM) achieving sub-Ångstrom image resolution and submillisecond time resolution, an era of cinematic molecular science where chemists can visually study the time evolution of molecular motions and reactions at atomistic precision has arrived. However, the appearance of experimental TEM images often differs greatly from that of conventional molecular models, and the images are difficult to decipher unless we know in advance the structure of the specimen molecules. The difference arises from the fundamental design of the molecular models that represent atomic connectivity and/or the electronic properties of molecules rather than the nuclear charge of atoms and electrostatic potentials that are felt by the e-beam in TEM imaging. We found a good correlation between the atomic number (Z) and the atomic size seen in TEM images when we consider shot noise in digital images. We propose Z-correlated (ZC) atomic radii for modeling AR-TEM images of single molecules and ultrathin crystals with which we can develop a good estimate of the molecular structure from the TEM image much more easily than with conventional molecular models. Two parameter sets were developed for TEM images recorded under high-noise (ZCHN) and low-noise (ZCLN) conditions. The molecular models will stimulate the imaginations of chemists planning to use AR-TEM for their research. [ABSTRACT FROM AUTHOR]

Abstract Objective The application of molecular graphics software as a simple and free alternative to molecular model sets for introductory-level chemistry learners is presented. Results Based on either Avogadro or IQmol, we proposed four sets of tasks for students, building basic molecular geometries, visualizing orbitals and densities, predicting polarity of molecules and matching 3D structures with bond-line structures. These topics are typically covered in general chemistry for first-year undergraduate students. Detailed step-by-step procedures are provided for all tasks for both programs so that instructors and students can adopt one of the two programs in their teaching and learning as an alternative to molecular model sets.

Fourier transform infrared spectroscopy (FTIR) and Carbon-13 nuclear magnetic resonance (13C NMR) techniques were applied to establish the molecular models of anthracite combusted at 490 °C and 690 °C (490-C and 690-C). The evolution laws of functional groups were investigated based on the constructed models and quantitative changes calculated by FTIR results. The content of aromatic groups kept decreasing before 500 °C; –CH3/–CH2– showed a rising trend during combustion; and the content of oxygen functional groups kept declining before 400 °C. The chemical formulas of 490-C and 690-C were C217H106O12N2S2 and C201H59O8N3S2, respectively. 690-C model was more compact than that of original anthracite and 490-C due to the spilt of carbon skeleton and the shedding of aliphatic chains during combustion. Total sulfur content in anthracite showed a sudden rise at 690 °C which could be attributed to the generation of organic thiophene; one more pyrrole in 690-C model resulted from the conversion of pyridine at such high temperature.

Carbon nanotubes (CNTs) are nanometer-sized structures that can be used to reinforce cement matrices. The extent to which the mechanical properties are improved depends on the interfacial characteristics of the resulting materials, that is, on the interactions established between the CNTs and the cement. The experimental characterization of these interfaces is still impeded by technical limitations. The use of simulation methods has a great potential to give information about systems lacking experimental information. In this work, molecular dynamics (MD) and molecular mechanics (MM) were used in conjunction with finite element simulations to study the interfacial shear strength (ISS) of a structure formed by a pristine single-walled CNT (SWCNT) inserted in a tobermorite crystal. The results show that, for a constant SWCNT length, ISS values increase when the SWCNT radius increases, while for a constant SWCNT radius, shorter lengths enhance ISS values.

Polymers bearing associative groups (APs) are characterized by their fantastic viscoelastic behaviors. In a work recently published by our group [Jiang et al., Macromolecules53, 3438–3451 (2020)], a single chain sticky Rouse model (SRM) is proposed to describe the linear viscoelasticity of APs without the entanglement effect. In this work, equilibrium molecular dynamics simulation of an unentangled melt of an AP with uniformly distributed stickers is carried out, and the dynamic properties are simultaneously analyzed from the SRM. A chain model with capped stickers is proposed so that a well-defined association chemistry is promised in the simulation system. The relative effective frictional coefficient of stickers, which is the key parameter in the SRM, is extracted from the chain center-of-mass diffusion, and it is found to be consistent with the dynamics of associative reaction in the fully gelated network. Based on this, a linear relaxation modulus and segmental diffusion functions are predicted from the SRM without fitting parameters, and these are found to quantitatively agree with the simulation results, showing the effectiveness of the SRM in connecting the dynamic properties at different molecular levels. The change in relaxation modes and the definition of the effective chain center are found to be crucial in the scenario of the SRM. Finally, the above analysis from the SRM is successfully extended to the simulation system with asymmetric chains. All these simulation results strongly support the SRM as a molecular model for the linear rheology of AP. [ABSTRACT FROM AUTHOR]

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This study aims to investigate the debonding damage behaviors in rubber asphalt-aggregate interfaces under different rubber degradation degrees from a molecular-scale perspective. The pull-off test was simulated using molecular dynamics (MD) to determine the damage patterns at the asphalt-aggregate interface. The digital image processing (DIP) technique was employed to quantify the percentages of cohesive debonding, and the radial distribution function (RDF) and mean square displacement (MSD) was performed to explain the adhesion and cohesion damage mechanisms. In addition, the pull-out test results were compared with the simulated values to verify the reliability of the asphalt-aggregate molecular model. The findings of this study reveal that the presence of rubber powder molecules enhances the cohesion among asphalt molecules and mitigates damage to the cohesion at the asphalt-aggregate molecular interface. As rubber degradation progresses, the damage mode undergoes a gradual transition from adhesive damage to cohesive damage at the asphalt-aggregate interface. At lower temperatures, there is an increase in the internal aggregation of asphalt molecules, and the debonding rate of asphalt molecules at the mineral-aggregate interface rises from 7.67% to 35.67% following complete rubber degradation. Conversely, at higher temperatures, the asphalt-aggregate molecular system is primarily governed by the bonding of "double bond" and "single bond" groups, with cohesive damage dominating the asphalt matrix. The pull-out test results showed similar trends with the simulated values, indicating that the asphalt-aggregate molecular model in this study was relatively reasonable. The present study provides some guidance on the damage behavior of degraded rubberized asphalt-aggregate interface. [ABSTRACT FROM AUTHOR]

Understanding the structural features of coal and its reactive behaviors in thermal processing is the fundamental to achieve high-efficiency utilization of coal. However, the molecular structural features and the evolution characteristics at atomic scales in thermal processing remain unclear in the microscopic views, particularly for the low-rank coals, which usually exhibits high oxygen content with a variety of oxygen-containing organic functional groups and gets lots of CO/CO 2 release during pyrolysis. This research provides a comprehensive analysis of the ZaoQuan vitrinite (ZQV) bituminous coal's structural attributes and its pyrolysis-induced reactivity, which is crucial for optimizing the thermal conversion of low-rank coals. The structural parameters characteristics and molecular structures of ZQV have been revealed based on series of materials characterizations and molecular modeling calculations. The single molecular description of ZQV was conceptualized to be C 209 H 132 O 41 N 2 under the average molecular approximation, and the particle models with size about 10 nm was also been obtained. Based on the built molecular models, reactive force field molecular dynamics (ReaxFF MD) simulations then provided insights into the dynamic behavior of molecular structures under pyrolysis conditions. Experimental validation corroborates the computational predictions, revealing a strong coherence between observed gas products and those derived from simulation data. Crucially, this study vividly captures the dynamic migration patterns of oxygen-containing groups during coal's thermal decomposition, thus contributing to the understanding of gasification processes. The release mechanisms for CO and CO 2 are systematically dissected, proposing three and two distinct pathways respectively. These findings not only consolidate the molecular narrative of coal's structure and pyrolysis reactivity but also serve as a reliable foundation for interpreting the COx evolution of low-rank coals. Our integrated approach propels the scientific comprehension of coal pyrolysis and is anticipated to inform the development of more effective coal utilization pathways and thermal treatment technologies. [Display omitted] • Obtained characteristics for structural parameters and molecular structures of ZQV coal. • Conceptualized single molecular description of ZQV as C 209 H 132 O 41 N 2. • Elucidated gas release behaviors of ZQV with oxygen-containing functional groups during pyrolysis. • Visualized and summarized CO and CO 2 release pathways from ZQV pyrolysis. [ABSTRACT FROM AUTHOR]

For an in-depth understanding of China's low-rank coal's organic structure and pyrolysis process, Meihuajing (MHJ) coal was typically studied. Firstly, the organic structures of MHJ coal were obtained, and its molecular model was constructed based on various physical characterizations. Then, the constructed molecular model was well verified, and the pyrolysis processes of this model under heat-up and isothermal conditions were explored using ReaxFF. The results indicated that the primary organic structure of MHJ coal was aromatic skeleton (76.03%). Naphthalene was more abundant in the aromatic skeleton than benzene and anthracene. Moreover, the chemical formula of the constructed molecular model was C 388 H 259 O 89 N 5 , which was well-validated regarding physical characterizations, thermogravimetric analysis, and ReaxFF simulations. As for pyrolysis simulation, increasing the heating rate primarily suppressed the secondary cracking reactions of tar while further raising the heating rate mainly slowed down the cracking reactions of coke. Besides, the pyrolysis process of MHJ coal was divided into three steps: the rapid cracking stage, the secondary reaction stage of tar, and the basic completion stage of pyrolysis. [Display omitted] • Low-rank MHJ coal in China's Ningxia was selected as the research object. • The organic properties of MHJ coal were obtained using XRD, XPS, 13C NMR, and FTIR. • A reliable MHJ coal molecular model was built and well-validated. • The pyrolysis mechanism of MHJ coal was clarified using TGA and ReaxFF MD. [ABSTRACT FROM AUTHOR]

Objective: The application of molecular graphics software as a simple and free alternative to molecular model sets for introductory-level chemistry learners is presented. Results: Based on either Avogadro or IQmol, we proposed four sets of tasks for students, building basic molecular geometries, visualizing orbitals and densities, predicting polarity of molecules and matching 3D structures with bond-line structures. These topics are typically covered in general chemistry for first-year undergraduate students. Detailed step-by-step procedures are provided for all tasks for both programs so that instructors and students can adopt one of the two programs in their teaching and learning as an alternative to molecular model sets. [ABSTRACT FROM AUTHOR]

As monoclonal antibodies have become a vital resource in medicine, knowledge of their complex molecular structures has increased in importance. Thousands of antibody components (Fab and Fc fragments) are described in the Protein Data Bank [1]. Whole antibodies have been imaged by electron microscopy methods [2, 3] and in a few cases, crystallized [4-6]. The central hinge lacks a unique stable conformation and its dynamic properties are important to antibody function. Monte Carlo and molecular dynamics simulations and small-angle scattering methods have been used to analyze the wide range of configurations that are accessible to antibodies in solution [7, 8]. In order to support the development of antibody-based medicines, the National Institute of Standards and Technology (NIST) has released an extensively characterized IgG1κ monoclonal antibody (mAb), called the NISTmAb Reference Material 86711 [9-14]. To facilitate modeling of whole antibodies we now report the construction of an all-atom 3-D model of the NISTmAb. [ABSTRACT FROM AUTHOR]

The structure of coke affects its reactivity and strength, which directly influences its performance in the blast furnace. This review divides coke structures into chemical structure, physical structure, and optical texture according to their relevant characteristics. The focuses of this review are the current characterization methods and research status of the coke structures. The chemical structures (element composition and functional group) can be characterized by elemental analysis, Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy (Raman), X-ray photoelectron spectroscopy (XPS), and nuclear magnetic resonance imaging technology (13C NMR). The physical structures (pore structure and micro-crystallite structure) can be characterized by image method, X-ray CT imaging technique, mercury intrusion method, nitrogen gas adsorption method, X-ray diffraction method (XRD), and high-resolution transmission electron microscopy (HRTEM). The optical textures are usually divided and counted by a polarizing microscope. In the end, this review provides an idea of the construction of a coke molecular structural model, based on the above characterization. With the coke model, the evolution principles of the coke can be calculated and simulated. Hence, the coke performance can be predicted and optimized.

This study examined the ability of 103 undergraduate chemistry students to understand how to illustrate and name monocyclic organic compounds using molecular models in a case study that employed the action research approach. The theory that underpinned the study was constructivism. The model proved to be a powerful tool that allowed participants to build cognition and develop the necessary symbolisation and representational skills to interpret IUPAC rules for the nomenclature and structures of monocyclic organic compounds through engaging activities. They also demonstrated higher order thinking and reflective skills. [ABSTRACT FROM AUTHOR]

The combination of Reactive molecular dynamics (RMD) simulations and a reactive force field (ReaxFF) was employed to investigate the chemical mechanisms and product distribution in the process of oil shale kerogen pyrolysis. A large-scale reactive system based on five structural models used in the simulation was constructed according to the analysis results of a series of detection about kerogen extracted from Longkou oil shale to investigate the reaction processes of oil shale. The characteristics observed in the simulation agree well with the known characteristics of the oil shale structure and reactions. The simulation results proved the importance of temperature exert on the product distributions, intermolecular interactions and elementary reactions in the process of pyrolysis. A conclusion was made about the suitable temperature range for producing useful organic gases and the highest yield of shale oil. The detailed chemical reaction process of Longkou oil shale pyrolysis was described in this work as well. This work is an intensive study on the pyrolysis mechanism and the formative path of the typical products especially shale gases at different temperatures at the atomic level and will be of great significance for the development and utilisation of oil shale mineral resources. [ABSTRACT FROM AUTHOR]

In the community of computational materials science, one of the challenges in hierarchical multiscale modeling is information-passing from one scale to another, especially from the molecular model to the continuum model. A machine-learning-enhanced approach, proposed in this paper, provides an alternative solution. In the developed hierarchical multiscale method, molecular dynamics simulations in the molecular model are conducted first to generate a dataset, which represents physical phenomena at the nanoscale. The dataset is then used to train a material failure/defect classification model and stress regression models. Finally, the well-trained models are implemented in the continuum model to study the mechanical behaviors of materials at the macroscale. Multiscale modeling and simulation of a molecule chain and an aluminum crystalline solid are presented as the applications of the proposed method. In addition to support vector machines, extreme learning machines with single-layer neural networks are employed due to their computational efficiency. [ABSTRACT FROM AUTHOR]

One member of the polychlorinated biphenyls that is linked to a number of human diseases is 3,3′,4,4′,5-pentachlorobiphenyl. Here, density functional theory calculation, molecular simulations and multi-spectroscopic techniques were utilized to evaluate the interaction mechanism of 3,3′,4,4′,5-pentachlorobiphenyl with the pepsin, the digestive enzyme. The results of density functional theory and molecular simulations demonstrated that 3,3′,4,4′,5-pentachlorobiphenyl could be a good candidate for its availability toward pepsin with a frontier orbital gap of 0.18109 eV, and bound to the hydrophobic cavity of pepsin. The steady-state fluorescence and time-resolved fluorescence revealed that the quenching was initiated by complexation of pepsin and 3,3′,4,4′,5-pentachlorobiphenyl with the binding constant of 105 order. The UV-absorption, synchronous fluorescence spectroscopy, Fourier transform infrared spectroscopy, circular dichroism spectroscopy, and three-dimensional fluorescence data further confirmed that the changes in the secondary structure of pepsin were induced on the presence of 3,3′,4,4′,5-pentachlorobiphenyl, and a quantitative analysis of the secondary structure elements in pepsin was obtained. [ABSTRACT FROM AUTHOR]

Pentavalent plutonium is the most abundant form of soluble, mobile, and oxidized Pu in natural systems. The incorporation of Pu into environmentally abundant mineral hosts can strongly influence the transport and concentration of contaminants in both aqueous environments and the subsurface. This study determines the incorporation energy (ΔE, ΔH, and ΔG) of (PuO 2)+(HSO 4)− and (PuO 2)+(HCO 3)− from solid Pu 2 O 5 and aqueous (PuO 2)+ as sources of Pu(V), as well as the adsorption with subsequent surface incorporation, in a step-by-step approach onto/into different sulfate and carbonate minerals using ab initio computational methods. Solid source and sink reaction energies are calculated for carbonate and sulfate mineral hosts as (MCO 3) 4 + ½(Pu 2 O 5) + (H 2 CO 3) ⇌ ½(H 2 O) + (MCO 3) 3 (PuO 2)(HCO 3) + (MCO 3) for carbonate structures and (MSO 4) 4 + ½(Pu 2 O 5) + (H 2 SO 4) ⇌ ½(H 2 O) + (MSO 4) 3 (PuO 2)(HSO 4) + (MSO 4) for sulfate structures, where "M" denotes the metal cation being replaced by PuO 2 + (M = Ba, Sr, Pb, Ca). For Pu(V) from solid sources, sulfate group host minerals with the largest cations result in the most favorable incorporation energies; for aqueous sources and sinks, this effect is more than compensated by smaller host cations gaining more hydration energy when released. Thus, incorporation favorability using aqueous sources and sinks vs. solids are nearly reversed, with the smallest cationic radii corresponding to the lowest incorporation energy. While previous studies have used a similar methodology for calculating the thermodynamics of incorporation into bulk minerals, what is new in this study is that the method was extended to observe the rate-controlling steps from a species in solution (e.g. , PuO 2 + and HSO 4 − or HCO 3 −), to their co-adsorbed state on the mineral surface, followed by their co-incorporation (by replacing divalent cations and anions from the surface of the host mineral), and finally being incorporated into the bulk, mimicking the stability of co-precipitated or overgrown plutonyl defects. As the plutonyl ion approaches the surface, a small activation barrier has to be overcome (∼0.2 eV), followed by adsorption which is exothermic (∼–2.6 eV) with potential subsequent surface incorporation (endothermic ∼1.2 eV). Combining these steps results in a surface incorporation of plutonyl that is energetically downhill (∼–1.2 eV), which can sequester plutonyl without the addition of any external energy. Keeping the substituted host ions above the incorporation site is more energetically favorable than releasing them, generating a metastable plutonyl overgrowth site where continued growth is more favorable than re-releasing the plutonyl. These findings, with this more process-oriented and environmentally-relevant approach of surface interactions, considering mineral bulk and surfaces, hydration, and enthalpy, entropy, and Gibbs free energy of individual reaction, facilitate the evaluation of incorporation reactions and narrows the list of minerals favorable for the incorporation of actinides to complement (particularly resource-limited) experimental study. In addition, it may serve as a model for future semi-kinetic studies where a full computational treatment of the kinetics is prohibitively computationally expensive. [ABSTRACT FROM AUTHOR]