Bidentate Configuration Research Articles

Immobilization of gaseous As2O3 on γ-Fe2O3 (001) surface by forming monodentate and bidentate complexes: Insight from DFT study

Coal combustion is one primary anthropogenic emission source of atmospheric arsenic. Ferromagnetic γ-Fe2O3 has been regarded as an effective and promising immobilization sorbent for As2O3(g) in flue gas with good magnetic properties. The reported mechanism explorations about gaseous arsenic capture in flue gas by density functional theory (DFT) are mainly based on forming one chemical bond between arsenic and sorbent. Recent studies demonstrated that multidentate arsenic complexes could be formed with iron oxides in solution. However, the possible formation pathway of multidentate complexes between gaseous As2O3 and γ-Fe2O3 was not been reported yet. This is the first study to investigate the thermodynamics and quantum mechanics of bidentate complexes between As2O3(g) and γ-Fe2O3 (001) by DFT. Three kinds of arsenic bidentate complexes were discovered at γ-Fe2O3 (001) surface, including “2 O to 2 Feoct”, “2 O to Fetet & Feoct,” and “As & O to 2 Feoct,” which were named as configuration A, B and C, respectively. Configuration B, “2 O to Fetet & Feoct”, showed the lowest adsorption energy (Eads) among the three kinds of bidentate complexes. The Mulliken population analysis further confirmed the electron transfer between the atoms of newly formed chemical bonds in bidentate configurations. In addition, the projected density of states (PDOS) analysis exhibiting resonance peaks also showed the formation of hybrid orbitals. The criteria for the determination of bidentate complexes were also proposed. The results evidence a convincing conclusion that monodentate and bidentate complexes with stable chemical bonds can be formed when As2O3(g) is immobilized by γ-Fe2O3 (001).

Ab Initio Electronic, Magnetic, and Optical Properties of Fe Phthalocyanine on Cr2O3(0001).

The organic molecules adsorbed on antiferromagnetic surfaces can produce interesting interface states, characterized by charge transfer mechanisms, hybridization of molecular-substrate orbitals, as well as magnetic couplings. Here, we apply an ab initio approach to study the adsorption of Fe phthalocyanine on stoichiometric Cr2O3(0001). The molecule binds via a bidentate configuration forming bonds between two opposite imide N atoms and two protruding Cr ones, making this preferred over the various possible adsorption structures. In addition to the local modifications at these sites, the electronic structure of the molecule is weakly influenced. The magnetic structure of the surface Cr atoms shows a moderate influence of molecule adsorption, not limited to the atoms in the close proximity of the molecule. Upon optical excitation at the onset, electron density moves toward the molecule, enhancing the ground state charge transfer. We investigate this movement of charge as a mechanism at the base of light-induced modifications of the magnetic structure at the interface.

Distinct photochemistry of adsorbed and coprecipitated dicarboxylates with ferrihydrite: Implications for iron reductive dissolution and carbon stabilization

Although ligand-promoted photodissolution of ferrihydrite (FH) has long been known for low molecular weight organic acids (LMWOAs), such as oxalate (Oxa) and malonate (Mal), photochemistry of coprecipitated FH with Oxa and Mal remains unknown, despite the importance of these mineral-organic associations in carbon retention has been acknowledged recently. In this study, ferrihydrite-LMWOAs associations (FLAs) were synthesized under circumneutral conditions. Photo-dissolution kinetics of FLAs were compared with those of adsorbed LMWOAs on FH surface and dissolved Fe-LMWOAs complexes through monitoring Fe(II) formation and organic carbon decay. For aqueous Fe(III)-LMWOAs complexes, Fe(II) yield was controlled by the initial concentration of LMWOAs and nature of photochemically generated carbon-centered radicals. Inner-sphere mononuclear bidentate (MB) configuration dominated while LMWOAs were adsorbed on the FH surface. MB complex of FH-Oxa was more photoreactive, leading to the rapid depletion of Oxa. Oxa can be readsorbed but in the form of binuclear bidentate and outer-sphere complexation, with much lower photoreactivity. While LMWOAs was coprecipitated with FH, the combination mode of LMWOAs with FH includes surface adsorption with a mononuclear bidentate structure and internal physical inclusion. Higher content of LMWOAs in the FLAs promoted the photo-production of Fe(II) as compared to pure FH, while it was not the case for FLAs containing moderate amounts of LMWOAs. The distinct photochemistry of adsorbed and coprecipitated Fe-LMWOAs complexes is attributed to ligand availability and configuration patterns of LMWOAs on the surface or entrapped in the interior structure. The present findings have significant implications for understanding the photochemical redox cycling of iron across the interface of Fe-organic mineral associates.

Photoinduced Dynamic Ligation in Metal-Organic Frameworks.

Metal organic frameworks (MOFs), a class of porous crystalline materials consisting of metal-based nodes and organic linkers, have emerged as a promising platform for photocatalysis due to their ultrahigh functional surface area, customizable topologies, and tunable energetics. While interesting photochemistry has been reported, the related photoinduced structural dynamics of MOFs remains unclear. The consensus is that the coordination bonds between MOF nodes and linkers are considered static during photoexcitation, while the open-metal sites on the nodes are taken as the key active sites for catalysis. In this work, through a complementary time-resolved visible and infrared (IR) spectroscopic investigation, along with computational studies, we report for the first time light-induced structural bond dissociation (COO-M) and reformation in an iron-oxo framework, MIL-101(Fe). The probed excited state displayed ligand-to-metal charge transfer (LMCT) characteristics and exhibited a ca. 30 μs lifetime. The incredibly long excited-state lifetime led us to probe potential structural rearrangements that facilitated charge separation in MIL-101(Fe). By probing the vibrational fingerprints of the carboxylate linker upon LMCT photoexcitation, we observed the reversible transition of the carboxylate-Fe bond from a bidentate bridging mode to a monodentate mode, indicating the partial dissociation of the carboxylate ligand. Importantly, the bidentate configuration is recovered on the same time scale of the excited state lifetimes as probed via visible transient absorption spectroscopy. The elucidated photoinduced configurational dynamics provides a foundation for an in-depth understanding of MOF-based photocatalytic mechanisms.

Facet-dependent adsorption of aromatic organoarsenicals on hematite: The mechanism and environmental impact

Aromatic organoarsenic feed additives have been extensively used in poultry and livestock farming; however, a risk of releasing toxic inorganic arsenic exists when they are exposed to the environment. An in-depth understanding of the adsorption -migration behavior of aromatic organoarsenicals on environmental media is limited. In this study, p-arsanilic acid (p-ASA) and roxarsone (ROX) were considered as examples to systematically study their adsorption behaviors on the surface of hematite, a representative iron oxide in soil. By comparing the adsorption abilities and adsorption kinetics of hematite exposed with different facets (hexagonal nanoplates, HNPs, mainly exposed with {001} facets and hexagonal nanocubes, HNCs, exposed with {012} facets), combined with in situ shell-isolated nanoparticle enhanced Raman spectroscopy characterization and density functional theory simulation, the facet-dependent adsorption performance was observed and the mechanism revealed. The results showed that p-ASA formed a bidentate binuclear complex on HNCs and HNPs, whereas ROX formed monodentate mononuclear and bidentate binuclear configurations on the {001} and {012} facets, respectively. These differences not only lead to facet-dependent adsorption capacities but also affect their stability, as verified by sequential extraction experiments, affecting the environmental behavior and fate of aromatic organoarsenicals. This study not only provides insights into the environmental behavior of aromatic organoarsenicals but also offers theoretical support for the development of functional adsorbents and remediation strategies.

Unraveling the role of polysaccharide-goethite associations on glyphosate’ adsorption–desorption dynamics and binding mechanisms

HypothesisGlyphosate retention at environmental interfaces is strongly governed by adsorption and desorption processes. In particular, glyphosate can react with organo-mineral associations (OMAs) in soils, sediments, and aquatic environments. We hypothesize mineral-adsorbed biomacromolecules modulate the extent and rate of glyphosate adsorption and desorption where electrostatic and noncovalent interactions with organo-mineral surfaces are favored. ExperimentsHere we use in-situ attenuated total reflectance Fourier-transform infrared, X-ray photoelectron spectroscopy, and batch experiments to characterize glyphosate’ adsorption and desorption mechanisms and kinetics at an organo-mineral interface. Model polysaccharide-goethite OMAs are prepared with a range of organic (polysaccharide, PS) surface loadings. Sequential adsorption–desorption studies are conducted by introducing glyphosate and background electrolyte solutions, respectively, to PS-goethite OMAs. FindingsWe find the extent of glyphosate adsorption at PS-goethite interfaces was reduced compared to that at the goethite interface. However, increased polysaccharide surface loading resulted in lower relative glyphosate desorption. At the same time, increased PS surface loading yielded slower glyphosate adsorption and desorption kinetics compared to corresponding processes at the goethite interface. We highlight that adsorbed PS promotes the formation of weak noncovalent interactions between glyphosate and PS-goethite OMAs, including the evolution of hydrogen bonds between (i) the amino group of glyphosate and PS and (ii) the phosphonate group of glyphosate and goethite. It is also observed that glyphosate’ phosphonate group preferentially forms inner-sphere monodentate complexes with goethite in PS-goethite whereas bidentate configurations are favored on goethite.

Modeling Uranyl Adsorption on MoS2/Mo2CTx Heterostructures Using DFT and BOMD Methods.

Uranium-bearing wastewaters exert a great threat to the ecological environment due to its high radiotoxicity level. The designing and fabrication of novel adsorption materials can be promoted for radionuclide elimination from wastewater. In this work, results from density functional theory and Born-Oppenheimer molecular dynamics simulations are reported for the uranyl adsorption behavior on the MoS2/Mo2CTx heterostructure in the gas phase and in an aqueous environment. Uranyl ions prefer to be adsorbed at deprotonated O sites on the Mo2COH surface and S sites on the MoS2 side of the heterojunctions, resulting in the formation of bidentate configurations. In addition to coordination interaction, H-bond and van der Waals interactions can also play an important role in binding configurations. More importantly, the oxidation state U(VI) can be reduced to U(V) and then to U(IV) caused by the strong reducibility of the Mo2COH surface at room temperature, whereas the uranyl complex can move freely on the MoS2 surface. However, the coordination number of U with respect to H2O in the first hydration shell on the Mo2COH surface remains unchanged and is found to be 3, which is similar to that on the MoS2 surface. This work provides novel nanosorbents for the removal of uranyl from wastewater. The present viewpoint provides valuable mechanistic interpretations for uranyl adsorption and will give a supplement to the experimental research.

Adsorption study of potential collector polyoxyethylene ether phosphate on magnesite

The anionic-nonionic surfactant polyoxyethylene ether phosphate exhibits several advantages, as the surfactant is a potential collector for magnesite flotation, is easy to prepare and exhibits high surface activity. In this work, the flotation performance of fatty alcohol polyoxyethylene ether phosphate (AEOP) on magnesite was investigated and compared with that of dodecyl phosphonic (DP) and dodecyl phosphonate (DOP), and the results show that AEOP can be used at lower concentrations and a wider range of pH values. Zeta potential tests, Fourier transform infrared spectroscopy tests, and X-ray photoelectron spectroscopy tests demonstrated that AEOP was chemisorbed on the surface of magnesite by acting on the Mg sites. DFT calculations further demonstrated that both AEOP−1 and AEOP−2 were adsorbed on magnesite surfaces via mononuclear monodentate and binuclear bidentate configurations, which were similar to DP and DOP. In addition, the nonionic EO groups were not involved in the adsorption process.

Acidity-activity relationships in the solvent-free tert-butylation of phenol over sulfated metal oxides

Sulfated metal oxides have long been reported to exhibit enhanced acidity properties, which in turn affect reactivity. In this study, sulfated SnO2, TiO2 and ZrO2 of varying acidic properties were synthesized and utilized for the solvent-free alkylation of phenol with tert-butyl alcohol. Herein, it was observed that tert-butylation of phenol could be carried out at 120 °C with significant yield towards alkylated products; the majority was accounted for by the mono-alkylated products. Among the catalysts studied, SnO2 with high content of sulfation was found to be the more active. In-situ DRIFTS in the range of 25–500 °C was used to investigate the temperature evolution of sulfate species and differentiate between bidentate and tridentate configurations. By combining temperature-programmed desorption, in-situ DRIFTS and catalytic performance measurements a correlation between the ratio of Lewis to Brønsted acids and overall reactivity was observed.

Controlling product selectivity in oxidative desulfurization using an electrodeposited iron oxide film.

Sulfur-containing compounds must be removed from raw fuel oils before use and recently, there has been an effort to identify and optimize a more energy efficient method of oil processing. One promising route is electrochemical oxidative desulfurization (ODS), and in this work, we investigate an electrodeposited iron oxide film (FeOx(OH)y) as a working electrode to catalyze the oxidation of dibenzothiophene (DBT). The FeOx(OH)y film displays unexpected selectivity for the DBT sulfoxide (DBTO)-departing from the catalytic behavior of gold, which favors the dimerization of DBT. In addition, we observe a morphological change within our FeOx(OH)y film from γ-FeOOH to γ-Fe2O3. This change provides insight to the activity of each structure for ODS as the rate of oxidation increases after the incorporation of γ-Fe2O3. Our experimental observations are corroborated with DFT calculations, which suggest that the adsorption energy of DBT on Au is significantly greater than on the FeOx(OH)y, favoring the formation of dimeric and oligomeric products. Calculations also demonstrate that DBT binds preferably in a monodentate configuration but that oxidation occurs via DBT bound via a bidentate configuration. Monodentate binding on γ-FeOOH is significantly stronger than binding on γ-Fe2O, resulting in easier conversation to bidentate binding on γ-Fe2O3.

Carbon dioxide activation by discandium dioxide cations in the gas phase: a combined investigation of infrared photodissociation spectroscopy and DFT calculations.

We present a combined computational and experimental study of CO2 activation at the Sc2O2+ metal oxide ion center in the gas phase. Density functional theory calculations on the structures of [Sc2O2(CO2)n]+ (n = 1-4) ion-molecule complexes reveal a typical end-on binding motif as well as bidentate and tridentate carbonate-containing configurations. As the number of attached CO2 molecules increases, activated forms tend to dominate the isomeric populations. Distortion energies are unveiled to account for the conversion barriers from molecularly bound isomers to carbonate structures, and show a monotonically decreasing trend with successive CO2 ligand addition. The infrared photodissociation spectra of target ion-molecule complexes were recorded in the 2100-2500 cm-1 frequency region and interpreted by comparison with simulated IR spectra of low-lying isomers representing distinct configurations, demonstrating a high possibility of carbonate structure formation in current experiments.

Adsorption of croconic acid anions at silver electrodes in sodium fluoride solutions. Interplay of DFT calculations and in situ ATR-SEIRAS measurements for the interpretation of experimental spectra of adsorbed species

The adsorption of species coming from the disodium salt of croconic acid (4,5-dihydroxy-4-cyclopentene-1,2,3-trione, H2C5O5) at chemically deposited silver electrodes was studied in aqueous sodium fluoride solutions by combining in situ ATR-SEIRAS (Surface-Enhanced Infrared Reflection Absorption Spectroscopy experiments under Attenuated Total Reflection conditions) and Density Functional Theory (DFT) calculations. Voltammetric experiments suggest the existence of reversible adsorption processes in the potential range between −0.55 and −0.20 V vs Ag/AgCl (KCl 1 M), whereas irreversible reduction is observed for potentials below-0.55 V. ATR-SEIRA spectra show potential-dependent adsorbate bands in the potential range for reversible adsorption, that were assigned according to DFT calculations. Calculated optimized geometry of adsorbed croconate and bicroconate correspond to bonding to the silver surface in a bidentate configuration through two oxygen atoms with the molecular plane perpendicular to the metal surface. The broadening and splitting at high electrode potentials of the CO stretching bands for adsorbates coming from croconic acid can be explained by invoking the existence of collective vibrational modes appearing at high coverage. In overall, the ATR-SEIRA spectra obtained with Ag thin layer electrodes resembles that reported for Au thin layers. As a difference, higher adsorbate coverage seems to be obtained in the case of silver. Moreover, a strong feature at ca. 1580 cm−1 is experimentally observed, that was much weaker on gold samples. The calculated frequencies for adsorbed croconate and bicroconate do not change significantly with the adsorption bonding sites for the optimized geometries. Taking into account the calculated frequencies of both types of species, a better agreement with the experimental behavior (including the splitting/shifting caused by dipole–dipole coupling in high-coverage collective modes) is obtained in the case of bicroconate. The coexistence with some adsorbed croconate species cannot be ruled out.

Bulk-to-nano regulation of layered metal oxide gears H2O2 activation pathway for its stoichiometric utilization in selective oxidation reaction

H2O2 has been widely used as a green oxidant in many heterogeneous reactions. However, its disproportionation accelerated by either Brønsted acid (BA) or redox metal sites often results in low H2O2 utilization. Given this, metals less able to redox have been used because the formation of surface metal-peroxo species exhibits a certain degree of selectivity towards substrates. However, those catalysts often bear BA sites on their surface for charge balance, making it imperative to study H2O2 activation pathway in the presence of both sites. Herein, layered HNb3O8 with structurally preserved BA sites was used for this purpose. We found that the exposure of Nb sites via bulk-to-nano regulation of this material hinders H2O2 disproportionation promoted by BA sites. Among various Nb-peroxo species, its bidentate configuration formed on highly distorted NbOx was found to provide the best reactivity in alkene epoxidation with a near stoichiometric H2O2 utilization.

Unraveling the adsorption behaviors of uranium and thorium on the hydroxylated titanium carbide MXene

Hydroxylated titanium carbide Ti3C2(OH)2, a representative of MXenes, is employed to investigate adsorption behaviors for uranium and thorium using density functional theory based simulation methods. The structural analysis of the complexes compares very well to existing computational and experimental literatures. A closer look at the adsorption configurations and energies indicates that the main adsorption sites are deprotonated Os atoms of the OH groups terminated on the Ti3C2(OH)2 MXene surface. The most stable models for U(VI) and Th(IV) adsorbed on the Ti3C2(OH)2 MXene in the gas phase are bidentate and tridentate configurations, respectively. The adsorption ability of Th(IV) on the Ti3C2(OH)2 MXene is stronger than that of U(VI). More importantly, the aqueous solution has a remarkable effect on the coordinated environment of uranyl and Th4+ ions in the binding configurations. Uranyl and Th4+ ions adsorbed on the Ti3C2(OH)2 MXene in the aqueous environment form pentavalent coordinated structures. Extra OH– ligands from water molecules are found to interact with U and Th atoms compared with the adsorption configurations in the gas phase. Moreover, U-Oax double bonds in the uranyl break to form U-OH bonds in the adsorption model. For all the stable adsorption configurations, the coordinating interaction is the dominant factor, and Th-Os bonds present more covalent nature than U-Os bonds due to the larger charge transfers between Th and Os atoms. This work gives supplement to the experimental observations and will provide deeper insights into the physical chemistry behind the removal of uranium and thorium by using MXenes.

Plasmonic Photoelectrochemical Coupling Reactions of para-Aminobenzoic Acid on Nanostructured Gold Electrodes.

Surface plasmon resonance (SPR) bridges photonics and photoelectrochemistry by providing an effective interaction between absorption and confinement of light to surface electrons of plasmonic metal nanostructures (PMNs). SPR enhances the Raman intensity enormously in surface-enhanced Raman spectroscopy (SERS) and leads to the plasmon-mediated chemical reaction on the surface of nanostructured metal electrodes. To observe variations in chemical reactivity and selectivity, we studied the SPR photoelectrochemical reactions of para-aminobenzoic acid (PABA) on nanostructured gold electrodes. The head-to-tail coupling product "4-[(4-imino-2,5-cyclohexadien-1-ylidene)amino]benzoic acid (ICBA)" and the head-to-head coupling product p,p'-azodibenzoate (ADBA) were obtained from PABA adsorbed on PMN-modified gold electrodes. In particular, under acidic and neutral conditions, ICBA was obtained as the main product, and ADBA was obtained as the minor product. At the same time, under basic conditions, ADBA was obtained as the major product, and ICBA was obtained as the minor product. We have also provided sufficient evidence for the oxidation of the tail-to-tail coupling reaction product that occurred in a nonaqueous medium rather than in an aqueous medium. The above finding was validated by the cyclic voltammetry, SERS, and theoretical calculation results of possible reaction intermediates, namely, 4-aminophenlylenediamine, 4-hydroxyphenlylenediamine, and benzidine. The theoretical adsorption model and experimental results indicated that PABA has been adsorbed as para-aminobenzoate on the gold cluster in a bidentate configuration. This work offers a new view toward the modulation of selective surface catalytic coupling reactions on PMN, which benefits the hot carrier transfer efficiency at photoelectrochemical interfaces.

Spectroelectrochemical and DFT approaches to the study of croconic acid adsorption at gold electrodes in acidic solutions

• Croconate anions adsorb at Au electrodes in croconic acid-containing solutions. • Croconate species bons in a bidentate configuration with O atoms on top positions. • Adsorption occurs with the molecular plane (quasi) normal to the metal surface. • Adsorption causes significant changes on the geometry and symmetry of croconate. • Collective vibrations broaden and split croconate bands at high coverage. The adsorption of species coming from croconic acid (4,5-dihydroxy-4-cyclopentene-1,2,3-trione, H 2 C 5 O 5 , CA) at gold electrodes was studied spectroelectrochemically in aqueous perchloric acid solutions. Voltammetric experiments suggest the existence of reversible adsorption processes in the potential range between 0.30 and 0.80 V vs RHE. Surface-Enhanced Infrared Reflection Absorption Spectroscopy experiments under Attenuated Total Reflection conditions (ATR-SEIRA) show potential-dependent adsorbate bands in the latter potential range that, according to Density Functional Theory calculations, can be assigned to adsorbed croconate. Calculated optimized geometry corresponds to bonding of croconate species to the gold surfaces involving two oxygen atoms in a bidentate configuration, with the molecular plane perpendicular to the metal surface for low and high crocoanate coverage. For intermediate coverage, lateral repulsions between neighbor croconate adsorbates give rise to the tilting of the molecular plane. The broadening and splitting at high electrode potentials of the C O stretching bands for adsorbed croconate can be explained by invoking the existence of collective vibrational modes appearing at high coverage. The cyclic voltammograms recorded in the CA-containing solutions also show the existence of reversible redox processes at potentials below 0.30 V involving adsorbed species, which are detected in the collected ATR-SEIRA spectra.

Glutamate adsorption on gold electrodes at different pH values

Advanced medical applications of gold nanoparticles can use amino acids as surface modifiers. For this reason, understanding the adsorption of amino acids on gold is crucial to improve these applications. Here, the adsorption of glutamate (Glu) on Au(1 0 0) and Au(1 1 0) electrodes has been studied using a combination of electrochemical experiments, and DFT calculations. The adsorption properties have been examined in two different regions, the double layer region, and the OH adsorption/oxide formation region. In the first one, the combined results from the electrochemical experiments and the DFT calculations indicate that Glu is adsorbed in acidic solutions by the two terminal carboxylate groups, each one in a bidentate configuration, and exchanges two electrons upon adsorption. The comparison with the results obtained for the Au(1 1 1) electrode and other molecules containing carboxylic groups confirms this adsorption mode. Glu adsorption also affects the reconstruction process of the Au(1 1 0) and Au(1 0 0) surfaces. On the other hand, in alkaline solutions, glutamate is not adsorbed because the negative charge of the surface prevents its adsorption. In the OH adsorption/oxide formation region, Glu is oxidized when OH is adsorbed, and the results indicate that OH is consumed in this oxidation process. The formation of gold surface oxides inhibits the Glu oxidation reaction.

Influence of a Cu-zirconia interface structure on CO2 adsorption and activation.

CO2 adsorption and activation on a catalyst are key elementary steps for CO2 conversion to various valuable products. In the present computational study, we screened different Cu-ZrO2 interface structures and analyzed the influence of the interface structure on CO2 binding strength using density functional theory calculations. Our results demonstrate that a Cu nanorod favors one position on both tetragonal and monoclinic ZrO2 surfaces, where the bottom Cu atoms are placed close to the lattice oxygens. In agreement with previous calculations, we find that CO2 prefers a bent bidentate configuration at the Cu-ZrO2 interface and the molecule is clearly activated being negatively charged. Straining of the Cu nanorod influences CO2 adsorption energy but does not change the preferred nanorod position on zirconia. Altogether, our results highlight that CO2 adsorption and activation depend sensitively on the chemical composition and atomic structure of the interface used in the calculations. This structure sensitivity may potentially impact further catalytic steps and the overall computed reactivity profile.

Magnesium Coordination of ATP - Force Field Evaluation and Structure-Driven Correction

In the numerous molecular recognition and catalytic processes across biochemistry involving adenosine triphosphate (ATP), the common bioactive form is its magnesium chelate, ATP.Mg2+. In aqueous solution, two chelation geometries predominate, with Mg contacting either the terminal beta and gamma phosphate groups (bidentate) or all three (tridentate). These subforms are approximately isoenergetic, but separated by a high energy barrier. Force field-based atomistic simulation studies of this complex require an accurate representation of its structure and energetics. Here we focused on the energetics of ATP.Mg2+ coordination. With unbiased molecular dynamics simulation showing prohibitively slow interconversion, we devised an enhanced sampling scheme to calculate free energy differences between different Mg2+-phosphate configurations. We observed striking contradictions between Amber and CHARMM force field descriptions, most prominently in opposing predictions of the favoured coordination mode. Through further configurational free energy calculations, conducted against a diverse set of ATP.Mg2+-protein complex structures to supplement otherwise limited experimental data, we observed systematic biases for each force field. However, the force field calculations were strongly predictive of experimentally observed coordination modes, enabling additive corrections to the coordination free energy that deliver close agreement with experiment. Reassessing the applicability of the corrected force field descriptions of ATP.Mg2+ for biomolecular simulation, we observe that calculated properties broadly agree with experimental measurements of solution geometry and the distribution of ATP.Mg2+ structures found in the Protein Data Bank. However, while the corrected Amber force field appears to reproduce both bidentate and tridentate configurations, CHARMM displays an erroneous preference triphosphate overextension. This will affect the interpretation of simulations of bidentate ATP.Mg2+, which comprises the majority of PDB structures.

Global refinery catalysts markets, 2014-2019: 2020-2025 - increasing adoption of zeolites as an effective refinery catalyst driving market growth

We investigated the adsorption and decomposition of formaldehyde (HCHO) molecule on stoichiometric rutile TiO2(110) surface using first principles-calculations. By comparing the adsorption energy of one bidentate and two monodentate configurations, we found the bidentate configuration is the most stable one because of an additional C-O bond formation. The monodentate configuration can change into the bidentate configuration by overcoming a small barrier less than 0.1 eV. Then, we investigated the decomposition of HCHO which involves two deprotonation processes starting from different adsorption structures. The energy barrier of the first deprotonation is 1.3 eV and 1.1 eV for bidentate and monodentate configurations. After the first deprotonation, an adsorbed formate HCOO specie is formed. The second deprotonation needs 1.74 eV and 1.64 eV for bidentate and monodentate configurations, respectively. After that, an adsorbed CO2 is formed. It can desorb from the surface after overcoming a small barrier of 0.12 eV. In principle, it is also possible to obtain a CO molecule from the surface. Yet a large energy barrier higher than 1.74 eV needs to be overcome. By analyzing the energy level alignment of molecular orbitals with TiO2 energy band edges, we discussed the photocatalytic activity of the reactants and intermediates during the decomposition process. Our results give a clear description of the adsorption structure and thermal decomposition process of HCHO on rutile TiO2(110) surface. The discussion of photocatalytic reactivity based on energy level alignment provides valuable insights to understand the combined photocatalytic and thermally catalytic reactions.