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Using DFT-based molecular dynamics simulations incorporating explicit water solvent, we elucidate the varying behavior of the ligand pKa of a molecular catalyst for methanol dehydrogenation, using the Ru(PNP) catalytic system as a case study. The pKa of the amido ligand moiety in this catalytic system is highly sensitive to the species adsorbed on the metal center, resulting in a substantial variation in the ligand pKa along the catalytic cycle. Since the ligand pKa is an important characteristic that determines the exact role of the ligand during aqueous methanol dehydrogenation, it has important implications for metal-ligand cooperative pathways.

The understanding of the formation of silicate oligomers in the initial stage of zeolite synthesis is important. The use of organic structure-directing agents (OSDAs) is known to be a key factor in the formation of different silicate species and the final zeolite structure. For example, tetraethylammonium ion (TEA+) is a commonly used organic template for zeolite synthesis. In this study, ab initio molecular dynamics (AIMD) simulation is used to provide an understanding of the role of TEA+ in the formation of various silicate oligomers, ranging from dimer to 4-ring. Calculated free-energy profiles of the reaction pathways show that the formation of a 4-ring structure has the highest energy barrier (97 kJ/mol). The formation of smaller oligomers such as dimer, trimer, and 3-ring has lower activation barriers. The TEA+ ion plays an important role in regulating the predominant species in solution via its coordination with silicate structures during the condensation process. The kinetics and thermodynamics of the oligomerization reaction indicate a more favorable formation of the 3-ring over the 4-ring structure. The results from AIMD simulations are in line with the experimental observation that TEA+ favors the 3-ring and double 3-ring in solution. The results of this study imply that the role of OSDAs is not only important for the host–guest interaction but also crucial for controlling the reactivity of different silicate oligomers during the initial stage of zeolite formation.

Photoelectrochemical (PEC) splitting of water to make hydrogen is a promising clean-energy technology. The oxygen evolution reaction (OER) largely determines the energy efficiency in PEC water-splitting. Hematite, which is a cheap and sustainable semiconductor material with excellent chemical properties, a favourable band gap (2.1 eV) and composed of earth abundant elements is a suitable model photoanode material for studying OER. To understand the design of energy efficient anodes, it is highly desirable to have mechanistic insight into OER at an atomistic level which can be directly connected to experimentally measured quantities. We present a multiscale computational model of OER which connects the thermodynamics and kinetics of elementary charge transfer reactions in OER to kinetics of OER at laboratory length and time scales. We couple density functional theory (DFT) and DFT based molecular dynamics (DFT-MD) simulations with solvent effects at an atomistic level with kinetic Monte Carlo (kMC) simulations at a coarse-grained level in our multiscale model. The time and applied bias potential dependent surface coverage, which are experimentally not known, and the O2 evolution rate during OER at the hematite-water interface are calculated by the multiscale model. Furthermore, the multiscale model demonstrates the effect of explicitly modelling the interaction of water with the electrode surface via direct adsorption. This journal is

Herein we provide mechanistic insights into the dehydrogenation of aqueous methanol catalysed by the [Ru(trop2dae)] complex (which is in‐situ generated from [Ru(trop2dad)], trop2dad=1,4‐bis(5H‐dibenzo[a,d]cyclohepten‐5‐yl)‐1,4‐diazabuta‐1,3‐diene), established by density functional theory based molecular dynamics (DFT‐MD) and static DFT calculations incorporating explicit solvent molecules. The aqueous solvent proved to participate actively in various stages of the catalytic cycle including the catalyst activation process, and the key reaction steps involving C−H activation and hydrogen production. The aqueous solvent forms an integral part of the reactive system for the C−H activation steps in the [Ru(trop2dae)] system, with strong hydrogen bond interactions with the anionic oxygen (RO−, R=CH3, CH2OH, HCO) and hydride moieties formed along the reaction pathway. In contrast to the [Ru(trop2dad)] catalyst, C−H activation and hydrogen production does not proceed via a metal‐ligand cooperative pathway for the [Ru(trop2dae)] system. The pKa of the coordinated amine donors in these complexes provides a rationale for the divergent reactivity, and the obtained mechanistic information provides new guidelines for the rational design of active and additive free catalytic systems for aqueous methanol dehydrogenation., ChemCatChem, 12 (9), ISSN:1867-3880, ISSN:1867-3899

ispartof: FARADAY DISCUSSIONS vol:220 issue:0 pages:144-178 ispartof: location:England status: published

The thermal dissociation of tri-n-octylamine hydrochloride (TOAHCl) in open system was investigated by TGA and DFT methods. The dissociation starts at the temperature of about 120 °C which was predicted with DFT calculations and verified by isothermal TGA. Then a thermodynamic cycle depicting the dissociation process was built. The thermal dissociation which couples with the evaporation of products tri-n-octylamine (TOA) and HCl undergoes two continuous steps due to the evaporation speed difference between the two compounds. Based on the assumption, kinetics analysis was performed by employing isoconversional methods of Friedman, Kissinger-Akahira-Sunose (KAS) and Starink. The activation energies of the two steps fall in the range of 81.1 ± 2.6 kJ mol−1 and 96.8 ± 13.4 kJ mol−1, which are comparable with the enthalpy values from 94.7 ± 5.6 kJ mol−1 to 100.1 ± 5.4 kJ mol−1.The comparability indicates that the dissociation of TOAHCl is a process with no transition state which is in accordance with the DFT prediction. Model-fitting methods were performed by simultaneous treatment of kinetic curves under different temperature programs via reaction-order kinetics mechanism. And the results reveal that the reaction orders are 0.21 and 0.07 respectively for the two steps.

A thermal dissociation process (ideally, 100% atom utilization) to regenerate the amine extractant and to produce gaseous HCl which is the key to realizing the CO2 mineralization with metal chloride waste liquids was investigated. Solvent effects on the thermal dissociation of tri‐n‐octylamine hydrochloride (TOAHCl) were predicted to be prominent via analyzing structure parameters, charge distribution, solvation free energy, apparent basicity, and N‐H frequency with the help of molecular simulation and experiments. Inert solvents with low polarity such as decalin, dodecane were favorable in thermal dissociation experiments. In particular, decalin enhanced the dissociation most effectively which is in agreement with the prediction. In dilute solutions, the thermal dissociation kinetics was shown to be first order. The apparent reaction rate (3.0 × 10−4−1.5 × 10−2 min−1) and activation energy (58.219‐121.827 kJ/mol) differ a lot at 180‐190°C in various solvents, confirming a strong solvent effect. A two‐stage reaction scheme in dilute solutions has been proposed from the experimental study. The overall process is entropically driven, with the removal of HCl into gas phase from the solvated state. The work could offer a fundamental direction for the further actual process.

The thermal dissociation of tri-n-octylamine hydrochloride (TOAHCl) was investigated using both the quantum chemical simulation and experimental methods. The pathway through which a mixture of tri-n-octylamine (TOA) and hydrogen chloride (HCl), rather than di-n-octylamine (DOA) and 1-chlorooctane, are produced has been determined through transition state (TS) search with Intrinsic Reaction Coordinate (IRC) calculations. Particularly, strong agreement between the experimental FTIR spectra and that of TOA demonstrates the same result for the first time. Moreover, the thermal dissociation of TOAHCl proceeds in two continuous steps, which is different from the low molecular mass amine hydrochlorides. The experimental enthalpy of the dissociation was 70.793 $$\hbox {kJ mol}^{-1}$$ with DSC measurement which is very close to the density functional theory (DFT) calculation result 69.395 $$\hbox {kJ mol}^{-1}$$ . Furthermore, with the aid of DFT calculations, some other important thermochemical characteristics such as crystal lattice energy with the value of 510.597 $$\hbox {kJ mol}^{-1}$$ were evaluated by means of Born–Fajans–Haber cycle. The thermal dissociation of tri-n-octylamine hydrochloride was investigated with both the quantum chemical simulation and experimental methods. Intrinsic reaction coordinate (IRC) calculations suggest that the products are tri-n-octylamine and HCl rather than di-n-octylamine and 1-chlorooctane. Furthermore, the dissociation is a two-stage process as determined by experimental analysis.

Aiming at an atomistic mechanism of heavy metal cation complexing on clay surfaces, we carried out systematic first principles molecular dynamics (FPMD) simulations to investigate the structures, free energies and acidity acidity constants of Ni(II) complexes formed on edge surfaces of 2:1 phyllosilicates. Three representative complexes were studied, including monodentate complex on the SiO site, bidentate complex on the Al(OH)2 site, and tetradentate complex on the octahedral vacancy where Ni(II) fits well into the lattice. The complexes structures were characterized in detail. Computed free energy values indicate that the tetradentate complex is significantly more stable than the other two. The calculated acidity constants indicate that the tetradentate complex can get deprotonated (pKa = 8.4) at the ambient conditions whereas the other two hardly deprotonate due to extremely high pKa values. By comparing with the 2 Site Protolysis Non Electrostatic Surface Complexation and Cation Exchange (2SPNE SC/CE) model, the vacant site has been assigned to the strong site and the other two to the weak site, respectively. Thus a link has been built between atomistic simulations and macroscopic experiments and it is deduced that this should also apply to other heavy metal cations based on additional simulations of Co(II) and Cu(II) and previous simulations of Fe(II) and Cd(II)). This study forms a physical basis for understanding the transport and fixation of heavy metal elements in many geologic environments.

Nitrogen-hydrogen (N-H) stretching vibration modes serve as key probes in the identification of the binding strength between amine and hydrogen chloride. Their assignments give us a theoretical viewpoint that could help us select the most suitable solvent for the regeneration of extractant tri-n-octylamine by the thermal dissociation of tri-n-octylamine hydrochloride method. Through a combination of ab initio molecular dynamics (AIMD) and static normal mode analysis (NMA), as well as the experimental infrared spectra, we conclude that the AIMD simulations which include the explicit solvents agree with the thermal dissociation experimental results perfectly, whereas the NMA calculated with implicit solvents could not show the solvent effects on the v(N-H) correctly, although the general trend seems not bad.

ispartof: FARADAY DISCUSSIONS vol:220 issue:0 pages:464-488 ispartof: location:England status: published

In this work, we use density functional theory based molecular dynamics with an explicit description of methanol solvent to study the effect of cations on formic acid dehydrogenation catalyzed by a ruthenium PNP pincer complex (RuPNP). Formic acid dehydrogenation is a two step process that involves the reorientation of the formate moiety bound via its oxygen to a H bound intermediate, followed by the hydride transfer step to form CO2 and the hydrogenated catalyst. We find the reorientation step to proceed with a low barrier in methanol solvent and in the presence of a Li+ cation, while the hydride transfer is significantly hindered by the presence of cations (Li+ and K+). The cation seems to strongly stabilize the negatively charged formate moiety, hindering complete hydride transfer and resulting in a high barrier for this step. This study is a first step towards addressing the exact role of cations in formic acid dehydrogenation reactions.

Designing catalysts for water oxidation (WOCs) that operate at low overpotentials plays an important role in developing sustainable energy conversion schemes. Recently, a mononuclear ruthenium WOC that operates via metal&ndash, ligand radical coupling pathway was reported, with a very low barrier for O&ndash, O bond formation, that is usually the rate-determining step in most WOCs. A detailed mechanistic understanding of this mechanism is crucial to design highly active oxygen evolution catalysts. Here, we use density functional theory based molecular dynamics (DFT-MD) with an explicit description of the solvent to investigate the catalyst activation step for the [Ru(bpy) 2 (bpy&ndash, NO)] 2 + complex, that is considered to be the rate-limiting step in the metal&ndash, ligand radical coupling pathway. We find that a realistic description of the solvent environment, including explicit solvent molecules and thermal motion, is crucial for an accurate description of the catalyst activation step, and for the estimation of the activation barriers.

Aiming to identify the complexing mechanisms of heavy metal cations on edge surfaces of 2:1-type clay minerals, systemic first-principles molecular dynamics (FPMD) simulations were conducted and the microscopic structures and complex free energies were obtained. Taking Cd(II) as a model cation, the structures on both (010) and (110) edges of the complexes were derived for the three possible binding sites (≡SiO, ≡Al(OH)2/≡AlOH≡AlSiO, and vacant sites). The stable complexes adsorbed on the three binding sites on both terminations had similar structures. The free energies of the complexes on (010) edges were calculated by using the constrained FPMD method. The free energies of complexes on the ≡SiO and ≡Al(OH)2 sites were similar and they were both significantly lower than the free energy of the complex on the octahedral vacant site. In association with the concept of high energy site (HES) and low energy site (LES) in the 2 Site Protolysis Non Electrostatic Surface Complexation and Cation Exchange (2SPNE SC/CE) sorption model, the vacant site was assigned to HES and the other two sites to LES, respectively.

Asymmetric transfer hydrogenation of ketones is an important chemical reaction. In aqueous solution, Ru(p-cymene)[TsDPEN] is an efficient catalyst for asymmetric transfer hydrogenation via a metal–ligand bifunctional mechanism with either 2-propanol or formate as hydrogen donors. Here, we provide novel insight for two key steps in the catalytic cycle of transfer hydrogenation cycle, using a computational model of Ru(p-cymene)[TsDPEN] with an explicit aqueous solvent. Employing ab initio molecular dynamics simulations, we model the hydride transfer between formate and the protonated and deprotonated catalyst, and the dissociation of the ruthenium-formato complex. It is shown that the aqueous solvent provides a significant contribution to the reaction barriers, increasing the hydride transfer barrier, while decreasing the dissociation barrier for ruthenium-formato complex, when compared with a gas-phase model. These effects can be attributed to hydrogen-bond structure around the formate, which favors the fo...

For the purpose of revealing the microscopic mechanism of the early stage in the nucleation of heavy metals on clay edges, we performed first principles molecular dynamics (FPMD) simulations systematically to characterize the chemistry of the incipient clustering processes by taking Pb2+ and Ni2+ as the model cations. We found that Pb2+ and Ni2+ have different complexation mechanisms: Pb2+ cations are adsorbed onto different sites with the similar probability whereas Ni2+ cations prefer octahedral vacancy to the other sites. The reason is that Pb2+ does not enter the vacancy due to the large ionic size. pKa calculations indicate that Ni2+ adions can provide available complexing sites (i.e., OH− groups) for the subsequent cations through hydrolysis and free energy calculations show that the complexation of subsequent cations is thermodynamically favored, which can thus result in nucleation and precipitation eventually. In contrast, the first adsorbed Pb2+ cannot provide available complexing sites due to the extremely high pKa, thus making nucleation impossible. Our findings, consistent with the experiment, reveal the role of the surface in heterogeneous nucleation, which should also apply to other similar systems. The results derived in this study are directly useful for understanding the mobility and fate of heavy metals in surficial environments.

UiO‐66, composed by Zr‐oxide inorganic bricks [Zr6(μ3‐O)4(μ3‐OH)4] and organic terephthalate linkers, is one of the most studied metal–organic frameworks (MOFs) due to its exceptional thermal, chemical, and mechanical stability. Thanks to its high connectivity, the material can withstand structural deformations during activation processes such as linker exchange, dehydration, and defect formation. These processes do alter the zirconium coordination number in a dynamic way, creating open metal sites for catalysis and thus are able to tune the catalytic properties. In this work, it is shown, by means of first‐principle molecular‐dynamics simulations at operating conditions, how protic solvents may facilitate such changes in the metal coordination. Solvent can induce structural rearrangements in the material that can lead to undercoordinated but also overcoordinated metal sites. This is demonstrated by simulating activation processes along well‐chosen collective variables. Such enhanced MD simulations are able to track the intrinsic dynamics of the framework at realistic conditions., Bricks and linkers: The UiO‐66 MOF, although very robust, shows an exceptionally dynamic behavior of linkers in presence of a solvent. In this contribution simulations at operating conditions are used to track at the molecular level how solvent triggers processes such as linker exchange and defect formation in the material.

By advanced molecular dynamics simulations, we show that for a highly active ruthenium-based water oxidation catalyst the dangling carboxylate group of the catalyst plays an important role in the crucial O–O bond formation step. The interplay of the flexible group and solvent molecules facilitates two possible pathways: a direct pathway with a single solvent water molecule or a mediated pathway involving two solvent water molecules, which have similar activation barriers. Our results provide an example for which a realistic molecular dynamics approach, incorporating an explicit description of the solvent, is required to reveal the full complexity of an important catalytic reaction in aqueous solvent., By advanced molecular dynamics simulations, we show that for a highly active ruthenium-based water oxidation catalyst the dangling carboxylate group of the catalyst plays an important role in the crucial O−O bond formation step. The interplay of the flexible group and solvent molecules facilitates multiple pathways. Our results provide an example for which a realistic molecular dynamics approach is required to reveal the full complexity of an important catalytic reaction in aqueous solvent.

Insights into the mechanism of the catalytic cycle for methanol dehydrogenation catalyzed by a highly active PNP pincer ruthenium complex in methanol solvent are presented, using DFT-based molecular dynamics with an explicit description of the solvent, as well as static DFT calculations using microsolvation models. In contrast to previous results, we find the amido moiety of the catalyst to be permanently protonated under catalytic conditions. Solvent molecules actively participate in crucial reaction steps and significantly affect the reaction barriers when compared to pure gas-phase models, which is a direct result of the enhanced solvent stabilization of methoxide anion intermediates. Further, the calculations reveal that this system does not operate via the commonly assumed Noyori-type outer-sphere metal-ligand cooperative pathway. Our results show the importance of incorporating a molecular description of the solvent to gain a deeper and accurate understanding of the reaction pathways, and stress on the need to involve explicit solvent molecules to model complex catalytic processes in a realistic manner.

UiO‐66, composed of Zr‐oxide bricks and terephthalate linkers, is currently one of the most studied metal–organic frameworks due to its exceptional stability. Defects can be introduced in the structure, creating undercoordinated Zr atoms which are Lewis acid sites. Here, additional Brønsted sites can be generated by coordinated protic species from the solvent. In this Article, a multilevel modeling approach was applied to unravel the effect of a confined methanol solvent on the active sites in UiO‐66. First, active sites were explored with static periodic density functional theory calculations to investigate adsorption of water and methanol. Solvent was then introduced in the pores with grand canonical Monte Carlo simulations, followed by a series of molecular dynamics simulations at operating conditions. A hydrogen‐bonded network of methanol molecules is formed, allowing the protons to shuttle between solvent methanol, adsorbed water, and the inorganic brick. Upon deprotonation of an active site, the methanol solvent aids the transfer of protons and stabilizes charged configurations via hydrogen bonding, which could be crucial in stabilizing reactive intermediates. The multilevel modeling approach adopted here sheds light on the important role of a confined solvent on the active sites in the UiO‐66 material, introducing dynamic acidity in the system at finite temperatures by which protons may be easily shuttled from various positions at the active sites.

Aqueous solvation of small amphiphilic molecules exhibits a unique and complex dynamics, that is only partially understood. A recent series of studies on the hydration of small organic compounds, such as tetramethylurea (TMU), trimethylamine N-oxide (TMAO) and urea, has provided strong evidence of a slowdown of the dynamics of the hydrating water molecules. However, the mechanism of this slowdown is still a matter of debate. We analyze the slowdown mechanism by combining molecular dynamics (MD) simulations, using ab initio and classical force field methods, with mid-infrared pump-probe spectroscopy. Aqueous solutions of TMU and of urea were studied at a 0.1 solute/solvent ratio, where we decompose the contribution of different solvating groups to the orientational dynamics. Our results reveal that two competing processes govern the H-bond breaking mechanism: H-bond switching through an associative partner exchange and a dissociative breaking characterized by an unbound state. H-bond switches are shown to occur less often near hydrophobic groups, thus creating a subset of OH groups that do not switch and therefore do not significantly reorient within the lifetime of one H-bond, but will require at least a second H-bond to be formed and broken before it may switch. Our results shed new light on the role of hydrophobic solvation in the water orientational dynamics and help to conciliate the controversy regarding the timescale separation, providing a mechanistic explanation for the observed slow component.

The understanding of the formation of silicate oligomers in the initial stage of zeolite synthesis is of fundamental scientific and technological importance. The use of different organic structure directing agents is known to be a key factor in the formation of different silicate species, and the final zeolite structure. Tetramethylammonium (TMA(+)), for example, is indispensable for the formation of the LTA zeolite type. However, the role of a TMA(+) template has not yet been elucidated at the molecular level. In this study, ab initio molecular dynamic simulations were combined with thermodynamic integration to arrive at an understanding of the role of TMA(+) in the formation of various silicate species, ranging from dimer to 4-ring. Free energy profiles show that trimer and 3-ring silicate are less favourable than other oligomers such as linear tetramer, branched tetramer and 4-ring structures. TMA(+) exhibits an important role in controlling the predominant species in solution via its coordination with silicate structures during the reaction process. This can explain that formation of D4R·8TMA crystals, as observed in experiment, is controlled by the single 4-ring formation step.

Silica oligomerization is the key reaction in zeolite synthesis. NaOH is a common additive in the zeolite synthesis that decreases the reaction rate of smaller silica oligomers and also affects the final structure of the zeolite. Here we report a study of the role of sodium in the initial stages of silica oligomerization. We performed ab initio molecular dynamics simulations using ecplicit aqueous solution in order to obtain the free energy profile and study the behavior of sodium during the reaction. Our study confirms that sodium decreases the reaction rates of oligomerization for smaller silica chains. Analysis of the molecular dynamics trajectories shows that sodium does not increase the reaction barriers by direct coordination to the silica. However, sodium is often present in the second solvation shell of the reactive atoms. Correlation between sodium presence in the first or the second shell of the reactive oxygen and a decrease in hydrogen bonding for that oxygen was found for the first reaction step. Therefore, the presence of sodium could contribute to an increase in reaction barriers for silica oligomerization by some rearrangement of the hydrogen bond network of water solution around the reactants.

Acid–base chemistry of clay minerals is central to their interfacial properties, but up to now a quantitative understanding on the surface acidity is still lacking. In this study, with first principles molecular dynamics (FPMD) based vertical energy gap technique, we calculate the acidity constants of surface groups on (0 1 0)-type edges of montmorillonite and kaolinite, which are representatives of 2:1 and 1:1-type clay minerals, respectively. It shows that Si–OH and Al–OH2OH groups of kaolinite have pKas of 6.9 and 5.7 and those of montmorillonite have pKas of 7.0 and 8.3, respectively. For each mineral, the calculated pKas are consistent with the experimental ranges derived from fittings of titration curves, indicating that Si–OH and Al–OH2OH groups are the major acidic sites responsible to pH-dependent experimental observations. The effect of Mg substitution in montmorillonite is investigated and it is found that Mg substitution increases the pKas of the neighboring Si–OH and Si–OH2 groups by 2–3 pKa units. Furthermore, our calculation shows that the pKa of edge Mg–(OH2)2 is as high as 13.2, indicating the protonated state dominates under common pH. Together with previous adsorption experiments, our derived acidity constants suggest that Si–O– and Al–(OH)2 groups are the most probable edge sites for complexing heavy metal cations.

The depletion interactions between two colloidal plates or between two colloidal spheres, induced by interacting polymers in a good solvent, are calculated theoretically and by computer simulations. A simple analytical theory is shown to be quantitatively accurate for case of two plates. A related depletion potential is derived for two spheres; it also agrees very well with direct computer simulations. Theories based on ideal polymers show important deviations with increasing polymer concentration: They overestimate the range of the depletion potential between two plates or two spheres at all densities, with the largest relative change occurring in the dilute regime. They underestimate the well depth at contact for the case of two plates, but overestimate it for two spheres. Depletion potentials are also calculated using a coarse graining approach which represents the polymers as ``soft colloids'': good agreement is found in the dilute regime. Finally, the effect of the polymers on colloid-colloid osmotic virial coefficients is related to phase behavior of polymer-colloid mixtures., Comment: revtex

Using first-principles molecular-dynamics simulations, probable inner-sphere complexes of Fe2+ adsorbed on the edge surfaces of clay minerals were investigated. Ferrous ions are important reductants in natural processes and their properties can be altered significantly by complexation on edge surfaces of clay minerals. However, the microscopic picture of adsorption sites and structures of Fe2+ is difficult to reveal with modern experimental techniques and, therefore, remains unclear. From the results of first-principles molecular-dynamics simulations, evidence has been provided that complexes on ≡Si-O sites were the most stable forms, which should be responsible for the experimentally observed pH-dependent uptake. Such complexation was found to be strong enough to distort the local coordination structures of Si-O tetrahedra in the substrate. Analyses showed that Fe2+-Owater coordination structures were dominated by the solvent with surface groups participating in the complexes via H bonding. The present study provided a microscopic basis for understanding the chemical processes involving surface-complexed Fe2+ ions.

Clathrates are strong, low density, fully sp3 structures that have been found for several elements of the IV group. Carbon clathrates however are, as of now, hypothetical materials. Ab initio calculations at T = 0 K predict carbon clathrates to be metastable with remarkable mechanical and electronic properties. Here we study the behavior and structural stability of the type I C46 carbon clathrates up to high temperature and pressure by means of Monte Carlo simulations based on an accurate model for the interatomic interactions. We find that the clathrate structure remains mechanically stable up to melting and we report the equilibrium structural parameters, thermal expansion, and equation of state.

We report first-principles molecular dynamics (FPMD) studies on the structures of interfaces between phyllosilicate edges and water. Using FPMD, the substrates and solvents are simulated at the same first-principles level, and the thermal motions are sampled via molecular dynamics. Both the neutral and charged silicate frameworks are considered, and for charged cases, the octahedral (Mg for Al) and tetrahedral (Al for Si) substitutions are taken into account. For all frameworks, we focus on the commonly occurring (0 1 0)- and (1 1 0)-type edge surfaces. With constrained FPMD, we calculated the free energy of the leaving processes of coordinated water of octahedral cations; therefore, the coordination states of those edge cations are determined. For (0 1 0)-type edges, both the 5- and 6-fold coordination states of Al are stable and occur with a similar probability, whereas only the 5-fold coordination is stable for Mg cations. For (1 1 0)-type edges, only the 6-fold states of Al cations are stable. However, for Mg cations, both coordination states are stable. In the 5-fold case, the solvent water molecules form H-bonds with the bridging oxygen atoms (i.e., Mg O Si ). The free energy results indicate that there should be a considerable number of 5-fold coordinated octahedral sites (i.e., Mg OH/ Al OH) at the interfaces. The interfacial structures and acid/base groups were determined by detailed H-bonding analyses. (1) Bridging oxygen sites. For (0 1 0) edges, the bridging oxygen atoms are not effective proton-accepting sites because they are inaccessible from the solvent. For (1 1 0) edges, the oxygen atoms of neutral and octahedrally substituted frameworks (i.e., M O Si for M Al/Mg) are proton-accepting sites. For T-sheet substituted cases, the bridging oxygen site becomes a proton-donating group (i.e., Al OH Si ) through the capture of a proton. (2) T-sheet groups. All T-sheet edge groups are M OH (M Si/Al) and act as both proton donors and acceptors. (3) O-sheet groups. For (0 1 0) edges with 6-fold Al, the active surface groups include Al (OH)(H2O) and Al (OH)2, whereas for Mg cations, the edge group is Mg (OH2)2. For 5-fold coordination, the active groups are Al OH. At (1 1 0) edges, proton-donating sites include Al OH, Al OH2 and Mg OH2 groups. Overall, our results reveal the significant effects of isomorphic substitutions on the interfacial structures, and the models provide a molecular-level basis for understanding relevant interfacial processes.

We report an accurate computational study of the role of water in transfer hydrogenation of formaldehyde with a ruthenium-based catalyst using a water-specific model. Our results suggest that the reaction mechanism in aqueous solution is significantly different from that in the gas phase or in methanol solution. Previous theoretical studies have shown a concerted hydride and proton transfer in the gas phase (M. Yamakawa, H. Ito, R. Noyori, J. Am. Chem. Soc. 2000, 122, 1466-1478;J.-W. Handgraaf, J. N. H. Reek, E. J. Meijer, Organometallics 2003, 22, 3150-3157; D. A. Alonso, P. Brandt, S. J. M. Nordin, P. G. Andersson, J. Am. Chem. Soc. 1999, 121, 9580-9588; D. G. I. Petra, J. N. H. Reek, J.-W. Handgraaf, E. J. Meijer, P. Dierkes, P. C. J. Kamer, J. Brussee, H. E. Schoemaker, P. W. N. M. van Leeuwen, Chem. Eur. J. 2000, 6, 2818-2829), whereas a delayed, solvent-mediated proton transfer has been observed in methanol solution (J.-W. Handgraaf, E. J. Meijer, J. Am. Chem. Soc. 2007, 129, 3099-3103). In aqueous solution, a concerted transition state is observed, as in the previous studies. However, only the hydride is transferred at that point, whereas the proton is transferred later by a water molecule instead of the catalyst.

The acid chemistry of confined waters in smectite interlayers have been investigated with first principles molecular dynamics (FPMD) simulations. Aiming at a systematic picture, we establish the model systems to take account of the three possible controlling factors: layer charge densities (0 e, 0.5 e and 1.0 e per cell), layer charge locations (tetrahedral and octahedral) and interlayer counterions (Na+ and Mg2+). For all models, the interlayer structures are characterized in detail. Na+ and Mg2+ show significantly different hydration characteristics: Mg2+ forms a rigid octahedral hydration shell and resides around the midplane, whereas Na+ binds to a basal oxygen atom and forms a very flexible hydration shell, which consists of five waters on average and shows very fast water exchanges. The method of constraint is employed to enforce the water dissociation reactions and the thermodynamic integration approach is used to derive the free-energy values and the acidity constants. Based on the simulations, the following points have been gained. (1) The layer charge is found to be the direct origin of water acidity enhancement in smectites because the neutral pore almost does not have influences on water dissociations but all charged pores do. (2) With a moderate charge density of 0.5 e per cell, the interlayer water shows a pKa value around 11.5. While increasing layer charge density to 1.0 e, no obvious difference is found for the free water molecules. Since 1.0 e is at the upper limit of smectites’ layer charge, it is proposed that the calculated acidity of free water in octahedrally substituted Mg2+-smectite, 11.3, can be taken as the lower limit of acidities of free waters. (3) In octahedrally and tetrahedrally substituted models, the bound waters of Mg2+ show very low pKa values: 10.1 vs 10.4. This evidences that smectites can also promote the dissociations of the coordinated waters of metal cations. The comparison between the two Mg2+-smectites reveals that different layer charge locations do not lead to obvious differences for bound and free water acidities.

In order to identify the influences imposed by Fe substitution, density functional theory-based Car-Parrinello molecular dynamics simulations were employed to study both oxidized and reduced Febearing smectites. The following basic properties were investigated: local structures in the clay layer, hydroxyl orientations, and the vibration dynamics of H and Si. Structural analyses indicated that the average Fe-O bond lengths are ~2.08 A and 2.02 A in the reduced and oxidized models, respectively, and the Fe substitutions did not affect the coordination structures of the Al-O and Si-O polyhedra. For hydroxyl orientations, Fe(III) substitution had no obvious influence but Fe(II) forces the coordinated hydroxyls to present a wide-angle distribution. Furthermore, the present work has shown that both substitutions can red-shift the hydroxyl in-plane bending mode. The analyses also revealed that Fe(III) substitution has no effect on the Si-O stretching, while Fe reduction causes a blue-shift of the out-of-plane stretching mode. The results provide quantitative constraints and clues for future research.

To shed light on the hydration mechanisms of Cu(2+), we carried out simulations in both gas and aqueous phases by using the ab initio molecular dynamics technique equipped with the method of constraint. The simulations provide relatively complete free-energy information, from which the coexisting coordination pictures are clearly revealed. In both phases, the 5-fold complex is the most thermodynamically favorable state whereas the classically-accepted 6-fold occurs as a very weak stable state. In the gas phase, the 4-fold complex is a more reachable state than the 6-fold, but it cannot hold stably in the aqueous phase. The extracted thermodynamic values illustrate that in the gas phase the entropy term dominates the evolution processes to the 5-fold whereas in the aqueous case the energy term is dominant.

We present molecular dynamics simulations of glutamic acid and glutamate solvated in water, using both density functional theory (DFT) and the Gromos96 force field. We focus on the microscopic aspects of the solvation−particularly on the hydrogen bond structures and dynamics−and investigate the influence of the protonation state and of the simulation method. Radial distribution functions show that the hydrogen bonds are longer in the force field systems. We find that the partial charges of the solutes in the force field simulations are lower than the localized electron densities for the quantum simulations. This lower polarization decreases the hydrogen bond strength. Protonation of the carboxylate group renders glutamic acid a very strong and stable hydrogen bond donor. The donated hydrogen bond is shorter and lives longer than any of the other hydrogen bonds. The solute molecules simulated by the force field accept on average three more hydrogen bonds than their quantum counterparts. The life times of these bonds show the opposite result: the residence times are much longer (up to a factor 4) in the ab initio simulations.

We review recent developments in the modelling of the phase diagram and the kinetics of crystallization of carbon. In particular, we show that a particular class of bond-order potentials (the so-called LCBOP models) account well for many of the known structural and thermodynamic properties of carbon at high pressures and temperatures. We discuss the LCBOP models in some detail. In addition, we briefly review the ``history'' of experimental and theoretical studies of the phase behaviour of carbon. Using a well-tested version of the LCBOP model (viz. LCBOPI+) we address some of the more controversial hypotheses concerning the phase behaviour of carbon, in particular: the suggestion that liquid carbon can exist in two phases separated by a first-order phase transition and the conjecture that diamonds could have formed by homogeneous nucleation in Uranus and Neptune., 28 pages, 15 figures. To appear in Mol. Phys. in 2008

pH-Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH-sensitive properties, in particular on the acidity constant (pKa). Obtaining molecular control over the factors that influence the pK(a) value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pK(a) values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules.

We report the first computational study of a fully atomistic model of the ruthenium-catalyzed transfer hydrogenation of formaldehyde and the reverse reaction in an explicit methanol solution. Using ab initio molecular dynamics techniques, we determined the thermodynamics, mechanism, and electronic structure along the reaction path. To assess the effect of the solvent quantitatively, we make a direct comparison with the gas-phase reaction. We find that the energy profile in solution bears little resemblance to the profile in the gas phase and a distinct solvation barrier is found: the activation barriers in both directions are lowered and the concerted hydride and proton transfer in the gas phase are converted into a sequential mechanism in solution with the substrate appearing as methoxide-like intermediate. Our results indicate that besides the metal-ligand bifunctional mechanism, as proposed by Noyori, also a concerted solvent-mediated mechanism is feasible. Our study gives a new perspective of the active role a solvent can have in transition-metal-catalyzed reactions.

The aqueous solvation of hydrochloric acid is studied using density functional theory based molecular dynamics simulations at two concentrations. The large simulation boxes that we use allow us to investigate larger-scale structures such as the water-bridged chloride ion network. We find a strong concentration dependence for almost all structural and dynamical properties. Excess protons are mostly present both as Eigen and Zundel structures, either as a direct hydronium-chloride contact-ion pair or a solvent-separated ion pair. Increasing the concentration has a detrimental effect on the natural hydrogen bonded network of water molecules. This effect is visible in our studies as a decrease in the persistence time of the solvation shells around the chloride ions. Also the number of proton hops, determined by a new and well defined identification procedure, suffers from the breakdown of the natural hydrogen bond network.

The redox potentials of the organic compounds tetrathiafulvalene (TTF) and thianthrene (TH) in an explicit aprotic polar solvent, acetonitrile, have been computed using ab initio molecular dynamics simulation based on a Gaussian basis set methodology. The density functional description of the pure solvent yields a diffuse and mobile liquid, with structural and dynamical properties that are in good agreement with earlier classical models and experiment. Molecular dynamics simulation of both solute species in their neutral and radical cation states combined with free energy difference calculations result in estimates for the redox potentials of the reactions TH*+ + TTF --> TH + TTF*+ and TH2+ + TTF*+ --> TH*+ + TTF2+. The obtained values are 0.95 +/- 0.06 and 1.09 +/- 0.06 V, respectively, in excellent agreement with experimental data of 0.93 and 1.08 V. Our computational approach is based on Marcus theory, assuming quadratic free energy surfaces. We show that this approximation can still be accurate in systems, such as TH, that undergo a significant change in geometry upon oxidation. Furthermore, despite the different localization of the spin density in the radical cations, results based on self-interaction-corrected functionals and on standard generalized gradient approximations are identical to within 10 meV.

We present a density-functional theory based molecular dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data. We observe that, in line with infrared spectroscopic data, the hydroxyl-stretching mode is significantly redshifted in the liquid, whereas the hydroxyl bending mode shows a blueshift. A substantial enhancement of the molecular dipole moment is accompanied by significant fluctuations due to thermal motion. We compute a value of 32 for the relative permittivity, almost identical to the experimental value of 33. Our results provide valuable data for improvement of empirical potentials.

We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen-oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials., Comment: 14 pages, 4 figures, accepted for publication in Chemical Physics Letters

We present a density functional theory based computational study comparing simplified models for the ruthenium(II)- and iridium(I)-catalyzed transfer hydrogenation of ketones. For the ruthenium compound our results confirm earlier findings that the hydrogenation involves a ruthenium hydride and occurs via a concerted hydrogen transfer mechanism with no direct ruthenium−ketone binding along the reaction path. In contrast, for the iridium compound our calculations suggest that the reaction proceeds via direct hydrogen transfer between simultaneously coordinated ketone and alcohol. We find that for both metal complexes the formation of a very stable metal−alkoxide complex plays an important role. For the ruthenium-catalyzed reaction it constitutes a resting state that does not take an active part in the transfer hydrogenation, while for the iridium-catalyzed reaction it is an important intermediate along the reaction path.

The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H-SAPO-34 at 350 degrees C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first-principle molecular dynamics approach enables unprecedented insights into zeolite-catalyzed reactions at the nanometer scale to be obtained.

The surface tension of interacting polymers in a good solvent is calculated theoretically and by computer simulations for a planar wall geometry and for the insertion of a single colloidal hard-sphere. This is achieved for the planar wall and for the larger spheres by an adsorption method, and for smaller spheres by a direct insertion technique. Results for the dilute and semi-dilute regimes are compared to results for ideal polymers, the Asakura-Oosawa penetrable-sphere model, and to integral equations, scaling and renormalization group theories. The largest relative changes with density are found in the dilute regime, so that theories based on non-interacting polymers rapidly break down. A recently developed ``soft colloid'' approach to polymer-colloid mixtures is shown to correctly describe the one-body insertion free-energy and the related surface tension.

We studied the hydration of a single methanol molecule in aqueous solution by first-principle DFT-based molecular dynamics simulation. The calculations show that the local structural and short-time dynamical properties of the water molecules remain almost unchanged by the presence of the methanol, confirming the observation from recent experimental structural data for dilute solutions. We also see, in accordance with this experimental work, a distinct shell of water molecules that consists of about 15 molecules. We found no evidence for a strong tangential ordering of the water molecules in the first hydration shell., Comment: 5 pages, 3 figures, submitted to Chemical Physics Letters

The enantioselective outcome of transfer hydrogenation reactions that are catalysed by ruthenium(II) amino alcohol complexes was studied by means of a systematically varied series of ligands. It was found that both the substituent at the 1-position in the 2-amino-1-alcohol ligand and the substituent at the amine functionality influence the enantioselectivity of the reaction to a large extent: enantioselectivities (ee values) of up to 95 % were obtained for the reduction of acetophenone. The catalytic cycle of ruthenium(II) amino alcohol catalysed transfer hydrogenation was examined at the density functional theory level. The formation of a hydrogen bond between the carbonyl functionality of the substrate and the amine proton of the ligand, as well as the formation of an intramolecular H⋅⋅⋅H bond and a planar H-Ru-NH moiety are crucially important for the reaction mechanism. The enantioselective outcome of the reaction can be illustrated with the aid of molecular modelling by the visualisation of the steric interactions between the ketone and the ligand backbone in the ruthenium(II) catalysts.

This paper reports a first-principles molecular dynamics simulation study of the microscopic mechanism of the base-catalyzed dehydrochlorination of pentachloroethane. So far the nature of the mechanism of this reaction is not understood: the concerted and stepwise mechanisms are under debate. By combining ab initio molecular dynamics with the method of constraints, we determine the reaction mechanism and associated free energy profile. We find that the reaction barrier is in good agreement with experimental findings and reveal that the reaction proceeds via a concerted mechanism. Our simulations provide no evidence for the presence of carbanion intermediate indicative of the stepwise pathway. This microscopic understanding will provide new implications for understanding the reduction of polyhalogenated alkanes and rational design of effective materials to treat these contaminants.

The fluid-β and β-δ coexistence lines for a state of the art intermolecular nitrogen potential [R. D. Etters et al., Phys. Rev. B 33, 8615 (1986)] are located by absolute free energy calculations using Monte Carlo simulations. We have found that the Etters potential provides an accurate description of the fluid-β coexistence line, but significantly overestimates the pressures of the β-δ coexistence line. This suggest that for a more accurate description of the δ phase the Etters potential needs to be improved. The present results constitute, to our knowledge, the first numerical calculation of full coexistence lines of a realistic molecular solid.

The addition of water to sulfur trioxide in liquid water has been studied using the ab initio molecular dynamics (MD) method. The hydration reaction observed in the MD simulation is spontaneous and, within a few hundred femtoseconds, yields a contact ion pair consisting of a hydrogen sulfate anion and a hydronium cation. The reaction mechanism is concerted: sulfur−oxygen bond formation and deprotonation of the hydrating water occur simultaneously. The reaction in solution is compared to two gas-phase additions, namely, the bare reaction with only the two reactants present and the reaction catalyzed by an additional water molecule. Both of these reactions lead to neutral products and require substantial amounts of activation energy. The gas-phase results have also been used to evaluate the accuracy of the BLYP (Becke−Lee−Yang−Parr) functional, which has been used in the ab initio MD to determine the density functional electronic structure. Whereas the calculated geometries of the sulfur trioxide−water com...

We have tested the performance of three frequently used density functionals (LDA, LDA+B, and LDA+B+LYP) in a study of the intermolecular interactions of benzene. Molecular geometries are satisfactory, with the gradient‐corrected density functionals yielding slightly better results. The quadrupole moment is significantly underestimated by all three functionals. LDA performs fortuitously comparatively well for both binding energies and geometries of the dimer and the solid, whereas in LDA+B, and LDA+B+LYP the dimer interaction is purely repulsive, leading to the complete absence of cohesion in the solid. These results are consistent with density‐functional theory calculations for noble gas dimers. However, when the dispersion energy calculated from a model potential is included, LDA fails. Binding energies are overestimated by unacceptable amounts, and intermolecular distances are too small. In contrast, dispersion corrected LDA+B and LDA+B+LYP perform reasonably well, although discrepancies are still large...