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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Probing substrate water access through the O1 channel of Photosystem II by single site mutations and membrane inlet mass spectrometry

Abstract Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO 2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn 4 CaO 5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated fromThermosynechococcus vestitus(T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn 4 CaO 5 cluster during its S 2 →S 3 and S 3 →S 4 →S 0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacteriumSynechocystis sp.PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitusnumbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn 4 CaO 5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn 4 CaO 5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.

Plant Sciences↗
DOE OSTI2020

Extracting meaningful standard enthalpies and entropies of activation for surface reactions from kinetic rates

While analyses based on the Arrhenius kinetic model have been successfully applied since its introduction, the Arrhenius model neglects to describe pre-exponential factor in a scientifically meaningful fashion. Since the 1930s, transition-state theory (TST), has met with success in interpreting the pre-exponential factor’s value, allowing a standard entropy of activation to be estimated. However, analyses based on TST’s assumptions have been applied inconsistently in the literature, particularly in corrosion science, leading to difficulty in comparison of standard entropy of activations from different studies. In this work, the foundational principles of TST and standard states are discussed and a standard method to apply TST in analyzing rates of surface reactions is recommended. When full details are not available, reacting species’ concentrations should be normalized to the concentration of active surface sites. For corrosion reactions, conversion relationships are given to convert from units of corrosion rate to surface reaction rate, consistent with TST. This method is dubbed a surface reactant equi-density approximation. Application of this standard to reported data results in adjustments of the standard entropy of activation between - 65 and +50 J/mol K and brings reported entropies into a narrower range of values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Group 7 and 8 Catalysts for Electrocatalytic CO 2 Conversion

Group 7 and 8 CO 2 reduction electrocatalysts have seen advances in selective product formation (primarily CO and formate) achieved through structural innovation and fine-tuning of coordination chemistry over the last decade. Furthermore, significant improvements have also been made by involving the secondary ligand coordination sphere in CO 2 reduction. Hydrogen bonding interactions with CO 2 and charged groups in the secondary sphere in particular are shown to lower overpotentials, stabilize intermediates or transition states and improve catalytic rates.

14 SOLAR ENERGY↗
DOE OSTI2023

Diffusion, atomic transport, and ordering in Al-Zr alloys: FCC and liquid phases

Additive manufacturing of materials with controlled microstructure demands knowledge of atomic scale properties near the solid-liquid transition state. Many of these properties are not affordable by experimental techniques and computer modeling is the possible solution to the problem. In this paper, we present the results of an extended atomistic study of intrinsic atomic transport due to vacancy diffusion in FCC and L12 solid phases and diffusion in the liquid phase of Al-Zr alloys. A deceleration of the overall self-diffusion was observed when Zr was added to Al. The effect was stronger in the solid and weaker in the liquid. Additionally, the effect was strongly temperature dependent in the solid phases, but not in the liquid. Atomic transport was chemically biased: transport of Zr atoms was significantly slower than that of Al atoms, and this bias effect was stronger in the solid phases. The overall diffusion and chemical ordering processes in the liquid state were five to six orders in magnitude faster than in the solid. Chemical short-range order parameters in the liquid saturated at values close to those in the ordered L12 structure of Al3Zr. Chemical and structural ordering in the solid phases was negligible over the modeled microsecond time scale. Here, the results are discussed in view of optimizing additive manufacturing parameters for the controlled formation of metastable L1 2 precipitates.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Effects of iron carbide crystal phases and dopants on the conversions of CO 2 into ethylene

The density functional theory method was used to investigate the conversions of CO 2 to ethylene formation on two common iron carbide surfaces: Fe 3 C(0 1 0) and Fe 5 C 2 (1 1 1). Based on the structure relaxation of reaction intermediates and the elementary reaction transition states. We deduced the most competitive reaction pathways for ethylene production. The main CO 2 -to-ethylene routes and the competition of side products, CO and CH 4 , are discussed. Our analyses showed that CO 2 conversion is surface structure sensitive, whereas CH 4 and C2+ hydrocarbon formations depend on the reactivity of native C atoms in the carbides. To modify the intrinsic catalyst performance, mixing dopants in Fe catalysts is an effective strategy. Furthermore, we demonstrate that doping Zn and Zr can alter the local electronic structure and enhance CO 2 adsorption on the catalyst surface.

CO2 hydrogenation↗
DOE OSTI2026

Product-promoted acetylene cyclotrimerization to benzene on Ag(111)

Acetylene cyclotrimerization to benzene on Ag(111) has recently been found to be 100% selective. However, it requires monolayer coverages, limiting its practical application due to the high pressure required to attain this surface coverage of acetylene near room temperature. Here, we show that co-adsorbed benzene, the reaction product, promotes cyclotrimerization at submonolayer acetylene coverages without compromising the 100% selectivity of Ag(111) via temperature-programmed desorption experiments. Scanning tunneling microscopy and density functional theory (DFT) calculations elucidate the origin of this effect whereby attractive acetylene–benzene interactions locally compress acetylene domains. DFT calculations further illustrate how co-adsorbed benzene reduces the transition-state energy for formation of the key C 4 intermediate, making cyclotrimerization competitive with desorption. Together, these findings reveal how product-reactant interactions can enhance C–C coupling.

Acetylene cyclotrimerization↗
DOE OSTI2022

Acetate formation on metals via CH 4 carboxylation by CO 2 : A DFT study

Here, density functional theory calculations have been performed to investigate CH 4 activation and coupling to CO 2 forming C 2 carboxylates such as acetate on the close-packed (111) or (0001) surfaces of ten mid-to-late transition and coinage metals (Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au). Consistent with the literature, the activation energy (E a ) for the initial C-H bond scission in CH 4 is mild, being ca. 1 eV or less on all but the coinage metals, of which Ag exhibits the highest E a at 2.13 eV, followed by Au and Cu. E a for the CH 3 -CO 2 coupling step is 0.8 ~ 1.1 eV on Co, Ru, Rh, and Ag, 1.2 ~ 1.5 eV on Ni, Cu, Pd, and Ir, and 1.8 ~ 2.1 eV on Pt and Au. While the two E a are comparable for several metals in terms of DFT total energies, free energy analysis indicates CH 3 -CO 2 coupling to be much more rate-limiting than CH 4 activation. Overcoming it would require over 800 K even on the most active of the metals considered, Ru, which makes the formation of acetate not feasible on the monometallic metal surfaces. Instead, we propose that single atom alloys based on early transition metals doped into a host metal such as Ni(111) could be viable catalysts. The dopant sites serve to stabilize the transition state of C-C coupling while Ni sites continue to activate CH 4 , thereby significantly lowering the required temperature for acetate formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Mechanistic study of direct coupling of CO 2 and C 2 H 4 over atomically dispersed metal at graphene edges

Direct coupling of CO 2 and ethylene (hereinafter DCCE) to acrylic acid is valuable for valorizing CO 2 to manufacture acrylate-derived products. However, previous studies in DCCE have been limited on molecular catalysts with challenges in improving catalytic performance. In this work, we employed density functional theory calculations and ab initio molecular dynamics simulations to investigate the heterogeneous catalysis of DCCE over atomically dispersed metal centers at nitrogen-doped zigzag edge of graphene. Based on competitive adsorption and structural stability, Mo, Cr, V, Ru, and Ni active sites are chosen to explore the reaction kinetics. Here, we find that the activation barriers are determined by the charge redistribution at transition states, which explains the trend of activity for the C-C coupling and the hydrogen transfer, two key steps in DCCE. Furthermore, we show that the intramolecular hydrogen transfer (rate-limiting step) is hindered due to the lack of local coordinate at the active sites. We thus propose to use co-adsorbed water as a “proton-exchanger” following a water-assisted route, and show that the activation barriers are reduced over all metal centers. Particularly, water promotes the hydrogen transfer over metals with strong CO 2 -ethylene co-activation and facile C-C coupling kinetics, which could be considered promising for DCCE. In both mechanisms, the stability of metallactone intermediate can be used to predict the catalytic activity. It is anticipated that the insights from this work can provide guidelines for mimicking well-defined multifunctional active sites in molecular catalysts to design heterogeneous catalysts for such C-C coupling, which advances catalytic utilization of CO 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Theoretical and kinetic modeling study of hydrazine oxidation

The present work constitutes the first theoretical and kinetic modeling study of hydrazine oxidation, which may be important for burnout in ammonia-fueled combustion. The kinetics of the oxidation of N 2 H 4 , N 2 H 3 and tHNNH by molecular oxygen were investigated via a quantum chemistry/canonical transition state theory approach. Geometries and anharmonic frequencies were obtained with density functional theory, and energies from coupled cluster calculations (CCSD(T)) extrapolated to the infinite basis set limit, with corrections for core-valence electron correlation, scalar relativistic effects, and higher level correlation up to lambda coupled cluster, CCSDT(Q) Λ . The key reactions occurred on the N 2 H 4 O 2 potential energy surface, where the results indicated a fast reaction of N 2 H 3 with HO 2 via singlet adducts to yield tHNNH + H 2 O 2 and HNN(H)O + H 2 O, while reaction on the triplet surface proceeds via a bound complex followed by a tight, submerged barrier to yield N 2 H 4 + O 2 . The results were incorporated in a detailed reaction mechanism, which was used to interpret the shock tube results from Michel and Wagner (1965) on the effect of O 2 on hydrazine conversion at 1100–1400 K. The kinetic model captured qualitatively the observed behavior, but underestimated the reaction rate under oxidizing conditions. The hydrazine pyrolysis chemistry dominated conversion at reducing conditions and/or high temperature. At oxidizing conditions and intermediate temperatures (≲ 1400 K), reactions of N 2 -amines with HO 2 and O 2 were important for the oxidation rate.

Ab initio calculations↗
DOE OSTI2024

Familial Alzheimer mutations stabilize synaptotoxic γ-secretase-substrate complexes

Mutations that cause familial Alzheimer’s disease (FAD) are found in amyloid precursor protein (APP) and presenilin, the catalytic component of γ-secretase, that together produce amyloid β-peptide (Aβ). Nevertheless, whether Aβ is the primary disease driver remains controversial. We report here that FAD mutations disrupt initial proteolytic events in the multistep processing of APP substrate C99 by γ-secretase. Cryoelectron microscopy reveals that a substrate mimetic traps γ-secretase during the transition state, and this structure aligns with activated enzyme-substrate complex captured by molecular dynamics simulations. In silico simulations and in cellulo fluorescence microscopy support stabilization of enzyme-substrate complexes by FAD mutations. Neuronal expression of C99 and/or presenilin-1 in Caenorhabditis elegans leads to synaptic loss only with FAD-mutant transgenes. Designed mutations that stabilize the enzyme-substrate complex and block Aβ production likewise led to synaptic loss. Collectively, these findings implicate the stalled process—not the products—of γ-secretase cleavage of substrates in FAD pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Lattice Boltzmann simulation of the dissolution of slag in alkaline solution using real-shape particles

Highlights: • A dissolution numerical model was proposed to capture the real dissolution kinetics of slag in alkaline solution. • The log forward dissolution rate of Si was described as a function of NBO/T and solution pH. • A threshold solid volume fraction of 0.688 was found for a voxel in 3D, 63.8% larger than that for a pixel in 2D. • The proposed dissolution numerical model provides a reliable alternative to study the dissolution kinetics of slag. A dissolution numerical model was proposed in this study to capture the real dissolution kinetics of slag in alkaline solution. It consists of three modules, i.e. (i) simulation of the initial particle parking structure of slag in alkaline solution using real-shape particles of slag, (ii) simulation of the chemical reactions between slag and solution based on the transition state theory, and (iii) simulation of the physical transport of aqueous ions using the lattice Boltzmann method. This dissolution numerical model was verified using experimental results, showing reasonable accuracy. After verification, the dissolution numerical model was implemented to study the influences of temperature and particle shape using a proper recipe of slag in alkaline solution. This recipe was designed to avoid solid phase precipitation or gel formation via thermodynamic analysis. The simulation results showed faster dissolution kinetics of slag when using higher temperatures and more irregular particle shapes.

36 MATERIALS SCIENCE↗
DOE OSTI2021

GeoMicro3D: A novel numerical model for simulating the reaction process and microstructure formation of alkali-activated slag

Highlights: • The GeoMicro3D model was innovatively developed for simulating the reaction process and microstructure formation of AAS. • In GeoMicro3D, the dissolution of slag and reactions of aqueous ions are fundamentally described in the local lattice cell. • A novel approach is proposed to speed up the nucleation simulations. • GeoMicro3D was implemented and verified with the relevant experimental data and thermodynamic calculation results. For the first time, this study developed a novel model, named GeoMicro3D, to simulate the reaction process and microstructure formation of alkali-activated slag. The GeoMicro3D model consists of four modules that are designed to simulate, respectively: (i) the initial spatial distribution of real-shape slag particles in alkaline activator, (ii) the dissolution of slag and diffusion of ions via the transition state theory and lattice Boltzmann method, respectively, (iii) the spatial distribution of reaction products using a nucleation probability theory, and (iv) the chemical reactions with thermodynamic modelling. Afterwards the GeoMicro3D model was implemented and verified. The simulation results were discussed and compared with the relevant experimental data and thermodynamic calculation results using GEMS. A good agreement was found in the comparisons, showing the strong simulation capability of GeoMicro3D.

36 MATERIALS SCIENCE↗
DOE OSTI2022

HȮ 2 + HȮ 2 : High level theory and the role of singlet channels

At low temperatures and high pressures, the HȮ 2 + HȮ 2 reaction is an important reaction in combustion. There are significant unresolved discrepancies between prior theoretical and experimental studies of this reaction. It has generally been presumed to occur as an abstraction on the triplet surface to produce H 2 O 2 + 3 O 2 . Here, we employ a combination of high-level electronic structure theory (the ANL0 composite method or multi-reference methods as appropriate), sophisticated transition state theory (vibrationally adiabatic torsions, variational, and variable reaction coordinate), and master equation analyses to predict the thermal kinetics on the H 2 O 4 surface. Notably, this analysis suggests a significant branching to HȮ 3 + ȮH near 1000 K via reaction on the singlet surface. This channel does not appear to have been considered in prior combustion models. HȮ 3 itself is a metastable complex (bound by only 3 kcal mol -1 ) that rapidly dissociates to ȮH + 3 O 2 . Thus, the net reaction for this channel, HȮ 2 + HȮ 2 → ȮH + ȮH + O 2 , converts two low reactivity HȮ 2 radicals into two highly reactive ȮH radicals. The ramifications of these newly derived rate expressions are highlighted through kinetic modeling studies of H 2 , CH 3 OH, $\textit{n}$-heptane, and isooctane oxidation; all at the high pressures of relevance to combustion devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

An experimental and kinetic modeling study of the pyrolysis of isoprene, a significant biogenic hydrocarbon in naturally occurring vegetation fires

Isoprene dominates the carbon flux emitted by vegetation and constitutes 40% of non-methane biogenic emissions worldwide. Despite pyrolysis experiments at temperatures above 1000 K showing a link between isoprene combustion and aromatic species formation, comprehensive mechanistic research on isoprene is scarce in the literature. Here, in this work, we carry out an experimental and theoretical study to build, for the first time, a chemical kinetic model describing isoprene pyrolysis. The formation of polycyclic aromatic hydrocarbon (PAH) precursor species, often observed in vegetation fire plumes, is partially explained by isoprene pyrolysis experiments and theoretical modeling. Molecular dynamics (MD) simulations unveil reaction pathways from allylic isoprenyl radicals to allene and cyclopentadiene (CPD) intermediates, two relevant species detected in the experiments. Rate constants for these identified pathways are calculated using variational transition state theory to update the kinetic model, which is validated against single-pulse shock tube (SPST), and jet-stirred reactor (JSR) experimental data in the temperature range of 850–1690 K. The kinetic model presents satisfactory agreement with the SPST experimental data, and a reaction pathway analysis shows that association of propargyl radicals results in benzene formation. The JSR pathway analysis also identifies the prominent reactions for CPD, benzene, styrene, and toluene formation. Our model does not reproduce the CPD experimental profiles, indicating that additional studies are necessary. Overall, our findings advance the understanding of isoprene pyrolysis and its related atmospheric pollutants in naturally occurring vegetation fires where smoldering and oxygen-deficient combustion processes are present.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

From electronic structure to model application of key reactions for gasoline/alcohol combustion: Hydrogen-atom abstractions by $CH_3\dot{O}$ radical

H-atom abstraction by methoxy radical ($CH_3\dot{O}$) plays an important role in capturing the kinetics of reactions between gasoline components and alcohols. This study focuses on determining the reaction rates and thermodynamic properties of methoxy radical reactions with five gasoline fuel components: n-heptane, iso-octane, 1-hexene, cyclopentane and toluene. Electronic structure calculations were per-formed for all the stationary points with M06-2X/6 -311 ++ g(d,p) method. G3 composite method with atomization method is used for determining Δ f H 0 of all the closed shell and radical species, using which the necessary thermodynamic data of all the species was determined. Coupled cluster theory QCISD(T)/cc-pVXZ (where X = D and T) and Møller-Plesset perturbation theory MP2/cc-pVXZ (where X = D, T and Q) were used to calculate single point energies. Subsequently, rate constants for all hydrogen atom ab-straction channels have been performed using conventional transition state theory with unsymmetric tunneling corrections. A systematic comparison of rates for abstraction from different sites within the same species and same site from different species is done in order to get insights into this reaction class. Here, the computed thermodynamic properties and rate constants were incorporated into a recent gasoline mechanism to investigate the impact of the calculations performed in this work. A shift in predicted NTC (negative temperature coefficient) behavior and significant reduction in model reactivity is observed upon incorporating the rates calculated herein.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2025

Experimental and modeling study of the autoignition behavior of a saturated heterocycle: Pyrrolidine

Experiments are conducted in both rapid compression machine (RCM) and shock tube (ST) to better quantify autoignition behavior (e.g., ignition delay, heat release) and understand heteroatomic effects in heterocyclic compounds, which are important reference components for the combustion of biomass-derived liquid fuels. These tests focus on the nitrogen-containing, five-membered saturated ring, pyrrolidine, at diluted conditions covering pressures of 20 and 50 bar, temperatures of 720–1450 K and a range of stoichiometries (ϕ = 0.5–2). A chemical kinetic model is developed and coupled to an existing combustion kinetics framework describing key nitrogen containing intermediates (e.g. pyrrole, ammonia and NOx). H-abstraction reactions by OH, H, CH 3 and HO 2 , are determined using ab-initio transition state theory methods, while analogies to cyclopentane are adopted for many other reactions, such as ring-opening. Here, the autoignition measurements reveal the lack of negative temperature coefficient (NTC) behavior and low-temperature chemistry for pyrrolidine, as opposed to its saturated hydrocarbon analogue, cyclopentane. Interestingly, at the lowest temperatures (T < 750 K), the reactivity of cyclopentane is greater than pyrrolidine, while at higher temperatures, pyrrolidine becomes more reactive. Agreement between the experimental measurements and the model is good, and it is found that H-abstraction reactions by HO 2 and ensuing chemistry play key roles in controlling the reactivity of this cyclic amine. Most of the fluxes, i.e., >70 %, are predicted to move through 1- or 2-pyrroline (C 4 H 7 N) and then the cyclic C 4 H 6 N radical, at both lower and higher temperatures, to form either CH 2 CHCHCHNH via ring-opening or pyrrole via β-scission. It appears that the ring opens more easily at lower temperature whereas the C–H β-scission dominates at higher temperature and lower pressure, such that the reaction of the fuel radical intermediate carrying an unpaired electron on the nitrogen atom with HO 2 is the next most notable in promoting oxidation. When comparing pyrrolidine and cyclopentane, which exhibits distinct pathways in different temperature regimes, the pyrrolidine pathways and sensitivity analysis align more closely to the high temperature case of cyclopentane where the important role of HO 2 radicals is seen to provide chain branching through HO 2 reaction with the fuel, accompanied by H 2 O 2 formation and decomposition to OH. The formation of 5-membered diene rings and ring opening reactions are also found to be highly relevant. Of particular note, it is found that there is little influence of small molecule nitrogen-chemistry, e.g., NH 2 , HCN, NO/NO 2 on the reactivity of the pyrrolidine mixtures investigated here where no recirculated combustion gases are included.

Autoignition↗
DOE OSTI2020

An automated cluster surface scanning method for exploring reaction paths on metal-cluster surfaces

Metal-cluster surfaces present a wide variety of unique coordination environments. This complexity makes it difficult to manually probe the surface reactivity of such clusters. Here, we present a simple and automated method to systematically discover reaction pathways on cluster surfaces, based on the automated cluster surface scanning (ACSS) technique for mapping out potential energy surfaces. We showcase our method on 55-atom icosahedral Cu and Ag clusters, where we determine the activation energies of four elementary steps common in heterogeneous catalysis – hydrogen recombination (H* + H* → H 2 * + *), oxygen recombination (O* + O* → O 2 * + *), water formation (OH* + H* → H 2 O* + *), and CO oxidation (CO* + O* → CO 2 * + *) – with density functional theory calculations (DFT-PBE + D3). We show that the ACSS method requires significantly less human effort than the established manually performed climbing-image nudged elastic band (MP + CI-NEB) technique and locates transition states with comparable accuracy (root-mean-squared error of 0.10 eV) and similar computational cost. Rigorous sampling of the potential energy surface with the ACSS method allows one to locate all lowest-energy reaction pathways obtained via the MP+CI-NEB approach, as well as alternative pathways that one may have missed with the MP+CI-NEB approach due to the many possible pathways available on these clusters. The accuracy and efficiency afforded by the ACSS method could enable high-throughput exploration of the diverse reactivity of metal clusters.

36 MATERIALS SCIENCE↗
DOE OSTI2023

QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations

Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. As a result, the adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.

97 MATHEMATICS AND COMPUTING↗