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Biochars are an exciting class of environmental materials with a wide range of applications, including carbon storage and sequestration, soil enhancement, and pollution remediation. However, the limited knowledge of their molecular structures and compositions and the lack of comprehensive understanding of the relationship between these structures and biochars' diverse functionality, is hindering advancements in their development. In this work, we further advance the approach, first introduced by Wood et al. (2023), to constructing biochar molecular models; and now include control of microporosity (pores ≤ 2 nm size) within the developed models. We construct biochar models representative of woody biochars which are experimentally produced at 600–650 ° C highest heating temperatures. Our models reproduce experimental H/C and O/C atomic ratios, percentage aromatic carbon, true density, cumulative porosity, and pore size distribution. The development of microporous biochar molecular models allows us to identify the importance of chemical structures involved in the assembly of biochar materials, and describe the relationship between these structures and obtained micropores. To facilitate other researchers integrating our approach into their work, we detail the steps taken, including the tests and reasons for each decision, in the construction of the biochar models. Furthermore, we share our developed molecular models in a format that can be easily integrated into other group's work in the form of molecular dynamics simulations. • Molecular models of biochar with controlled pore volumes and pore size distribution. • Models truthful to experimental H/C, O/C, aromaticity, true density and microporosity. • Identification of structural moieties within biochar – key to supporting micropores. [ABSTRACT FROM AUTHOR]

[Display omitted] • Non-idealities at the solid/liquid interface obtained from molecular simulations. • Molecular dynamics simulations maintain a constant solution composition. • NaCl(aq) at graphite and at NaCl(s) surfaces displays asymmetric ion adsorption. • Asymmetric adsorption induces an electric potential at the solid/liquid interface. Solid/liquid interfaces control various processes of technological relevance in the process industry and many fundamental physicochemical phenomena. This work examines the link between the atomistic description of mass transfer at solid/liquid interfaces out of equilibrium and constitutive mass transfer equations which are typically used to model these processes at the mesoscale. In our analyses we discuss the microscopic inconsistencies apparent in simplified models of mass transfer whenever non-idealities dominate the liquid phase in the proximity of solid/liquid interfaces. Using C μ MD – a molecular simulation technique to investigate out-of-equilibrium, concentration-driven processes with pseudo open-boundary conditions – we outline a strategy to capture and quantify non-idealities induced by specific interactions between the solid surface and molecules in the fluid phase. We demonstrate our approach by studying electrolyte solutions in technologically important, multi-component systems where the introduction of a solid/liquid interface induces substantial deviations in the composition and electrochemical properties locally compared to the bulk fluid phase. To this aim, we analyse NaCl(aq) solutions in contact with (i) the graphite basal surface and (ii) {100} NaCl(s) crystalline surfaces. We uncover the tendency of the sodium cation to preferentially adsorb at the surfaces considered, which induces local violations of electroneutrality that leads to the emergence of an electric potential in the fluid phase at the solid/liquid interface. [ABSTRACT FROM AUTHOR]

Approximately 11% of human genes are transcribed by a bidirectional promoter (BDP), defined as two genes with <1 kb between their transcription start sites. Despite their evolutionary conservation and enrichment for housekeeping genes and oncogenes, the regulatory role of BDPs remains unclear. BDPs have been suggested to facilitate gene coregulation and/or decrease expression noise. This review discusses these potential regulatory functions through the context of six prospective underlying mechanistic models: a single nucleosome free region, shared transcription factor/regulator binding, cooperative negative supercoiling, bimodal histone marks, joint activation by enhancer(s), and RNA-mediated recruitment of regulators. These molecular mechanisms may act independently and/or cooperatively to facilitate the coregulation and/or decreased expression noise predicted of BDPs. • 11% of human genes are transcribed by a bidirectional promoter (BDP). • BDPs are proposed to facilitate gene coregulation and decrease transcriptional noise. • Discussion of six mechanistic models for BDP transcriptional regulation. [ABSTRACT FROM AUTHOR]

Construction of atomic-scale three-dimensional (3D) molecular models of unoxidized and oxidized activated carbon fiber (ACF) nanoregions is of substantial scientific and technological interest as it allows in-depth analysis of complex interfacial process. The influence of oxygen functionalities on the specific interactions with guest particles is an important factor that controls wettability, competitive adsorption of fluid mixtures, interfacial transport, reactions, or nucleation processes. We combine experimental techniques of wide-angle X-ray scattering and nitrogen adsorption porosimetry with advanced molecular modelling to construct reliable 3D molecular models of unoxidized and oxidized pitch-based ACF-5 nanoregions. ACF-5 is a ultramicroporous carbon molecular sieve with an average pore size of 0.46 ± 0.2 nm. Narrow hydrophobic nanospaces are formed between defective and slightly curved graphene-like sheets. By atomistic-scale modelling of formaldehyde adsorption at room temperature and different values of the relative humidities, we show that oxygen functionalities and water co-adsorption impact the mechanism and uptake of formaldehyde. Our simulation data indicate that hydrophobic nanopores are preferable to adsorb formaldehyde efficiently in the presence of humidity. Image 1 [ABSTRACT FROM AUTHOR]

• The Mono/Multi molecular models of LHG jet coal were constructed and verified. • The pyrolysis process of LHG jet coal was simulated by the ReaxFF MD method. • The pyrolysis process was divided into 3 stages including 3 key pyrolysis paths. • The formation mechanisms and reaction pathways of CO, H 2 S were revealed. • The detail chemical reactions of LHG jet coal pyrolysis were shown. Zhundong coalfield is the largest coalfield in China and the unclear stage evolution mechanism of Zhundong coal pyrolysis is the key factor restricting its coal fire control. Here, the monomolecular model (299 atoms) and large-scale multimolecular model (5083 atoms) were constructed for Liu huanggou (LHG) coal from Zhundong coalfield. The pyrolysis processes of the two models were calculated by ReaxFF MD method. Based on the reaction consistency analysis, the reaction paths tracing on pyrolysis stage evolution and toxic gases formation mechanisms were obtained. The LHG coal pyrolysis process is mainly because of the breakages of the ether oxygen bridge bonds, thioether bridge bonds and aliphatic hydrocarbon bridge bonds. It begins with the shedding of small molecules and then undergoes the thermal decomposition of the main structure and pyrolytic fragments. During the pyrolysis process, the LHG coal has constantly broken out tars, gases and other key products, accompanied by a large number of free radicals and intermediates produced. The main sources of CO are the active reaction sites where the carbonyl group and the carboxyl group located; H 2 S is directly produced from the sulfhydryl group. The research results will guide the staged control and directional transformation of coal fire. [ABSTRACT FROM AUTHOR]

Highlights: [•] Material molecular models are claimed to be cognitive augmentations. [•] The material and representational properties of such models are examined. [•] The use of these models as research tools is compared to paper-and-pencil strategies. [•] The modeling strategy exploiting the materiality of these models is analyzed as a form of haptic reasoning. [•] The cognitive enhancements allowed by the intelligent use of these models are examined. [Copyright &y& Elsevier]

Despite its biochemical importance, a complete Raman analysis of arachidonic acid (AA, 20:4n-6) has never been reported. Gradient temperature Raman spectroscopy (GTRS) applies the temperature gradients utilized in differential scanning calorimetry (DSC) to Raman spectroscopy, providing a straightforward technique to identify molecular rearrangements that occur near and at phase transitions. Herein we utilize the GTRS technique for AA and 1 -18:0, 2 -20:4n-6 phosphatidyl choline (AAPC) from cryogenic to mammalian body temperatures. 20 Mb three-dimensional data arrays with 0.2 °C increments and first/second derivatives allowed complete assignment of solid, liquid and transition state vibrational modes. The AA DSC shows a large exothermic peak at −60 °C indicating crystallization or a similar major structural change. No exothermic peak of this magnitude was observed in six other unsaturated lipids (DHA, n-3DPA, n-6DPA, LA, ALA, OA). Melting in AA occurs over a large range: (−60 to −35 °C): very large frequency offsets and intensity changes correlate with premelting initiating circa −60 °C, followed by melting (−37 °C). Novel, unique 3D structures for both molecules reveal that AA is not symmetric as a free fatty acid, and it changes significantly when in the sn-2 phospholipid position. Further, different CH and CH 2 sites are unequally elastic and nonequivalent. [ABSTRACT FROM AUTHOR]

Abstract: For years, conventional drug design at G-protein coupled receptors (GPCRs) has mainly focused on the inhibition of a single receptor at a usually well-defined ligand-binding site. The recent discovery of more and more physiologically relevant GPCR dimers/oligomers suggests that selectively targeting these complexes or designing small molecules that inhibit receptor–receptor interactions might provide new opportunities for novel drug discovery. To uncover the fundamental mechanisms and dynamics governing GPCR dimerization/oligomerization, it is crucial to understand the dynamic process of receptor–receptor association, and to identify regions that are suitable for selective drug binding. This minireview highlights current progress in the development of increasingly accurate dynamic molecular models of GPCR oligomers based on structural, biochemical, and biophysical information that has recently appeared in the literature. In view of this new information, there has never been a more exciting time for computational research into GPCRs than at present. Information-driven modern molecular models of GPCR complexes are expected to efficiently guide the rational design of GPCR oligomer-specific drugs, possibly allowing researchers to reach for the high-hanging fruits in GPCR drug discovery, i.e. more potent and selective drugs for efficient therapeutic interventions. [Copyright &y& Elsevier]

Abstract: By assessing a large number of binary systems, it is shown that molecular modeling is a reliable and robust route to vapor–liquid equilibria (VLE) of mixtures. A set of simple molecular models for 78 pure substances from prior work is taken to systematically describe all 267 binary mixtures of these components for which relevant experimental VLE data is available. The mixture models are based on the modified Lorentz–Berthelot combining rule. Per binary system, one state independent binary interaction parameter in the energy term is adjusted to a single experimental vapor pressure. The unlike energy parameter is altered usually by less than 5% from the Berthelot rule. The mixture models are validated regarding the vapor pressure at other state points and also regarding the dew point composition, which is a fully predictive property in this work. In almost all cases, the molecular models give excellent predictions of the mixture properties. [Copyright &y& Elsevier]

Abstract: There are a large number (>125) of molecular representations for coals that span the rank range over seven decades. However, their utility has mostly been in representing chemical structural features, rather than in probing physical structure or exploring the structure–behavior relationship. This paper examines the utility of coal models and reviews the existing and emerging opportunities for coal models to contribute to coals effective utilization via demystification of the structure–behavior relationship. Coal models have been used to explore the coalification pathway, including contraction with water removal. Physical evaluations have probed the density of models as a check on their accuracy. Pore size distribution and sorption have been explored in simple pores and more recent work with carbon dioxide, water and methane sorption within the porous structure of large-scale (<20,000 atoms) model. Pair distribution frequency and small angle X-ray scattering simulations have also been compared with experimental observations and offer an additional check on the constitution of the model structure. Simulated HRTEM and simulated (calculated) NMR spectra also exist. Models have been disassembled in efforts to represent the pyrolysis process, char formation, and char reactivity (including the role of ion-exchangable ions). Similar to the pyrolysis models, direct liquefaction has been explored with a pyrolysis style approach. Coal-solvent swelling, and coal-solvent solubility have also been explored. While considerable progress has accompanied improvements in computational power and software advances, it is the generation of the model that is the most significant barrier to the meaningful utility of these models. The ability to generate large-scale models (incorporation of molecular weight diversity and structural diversity) with new automation approaches, coupled with new dynamic force-fields that can simulate reactive events in complicated materials like coals, offers a new hope for the utility of coal or char molecular models to probe our understanding and aid in the scientific method rather than our current informed trial and error approach. [Copyright &y& Elsevier]

Abstract: Molecular models of inorganic solution species, brown coal and brown coal containing inorganic species have been optimised using the computer-aided molecular package for Windows, CAChe, and the general-purpose semi-empirical molecular package MOPAC. The coal models were based on elemental composition and the experimentally measured distribution of aliphatic carbon, aromatic carbons, and oxygen functional groups. The calculated partial charges and bond polarities of the model are consistent with the hydrophilic properties of brown coal. Water molecules within the model exert the major stabilisation through H-bonds and electrostatic interactions. Calculated values of bond lengths and angles of the inorganic models were in good agreement with reported values, but variations occur because they are modelled as isolated structures. Brown coal models with NaCl, Na+, Mg2+ and Ca2+ are stabilised when the respective cations have been located in spaces that reduce steric hindrance and are surrounded by oxygen functional groups, carboxyl anions and water molecules. Coal models with octahedral Fe(III) or Ni(II) complexes may form stable structures bonded to carboxyl groups, but mono-nuclear complexes with bi-dentate carboxyl ligands usually form distorted structures. Polynuclear complexes form energetically favoured structures in coal, especially when carboxyl ligands form mono-dentate bonds to the metal centres. Reported experimental data on iron and nickel complexes, and for polymeric iron species in brown coal, are consistent with the modelling results. [Copyright &y& Elsevier]