Temperature driven transformations of glycine molecules embedded in interstellar ice.

The formation of glycine amino acid on ice grains in space raises fundamental questions about glycine chemistry in interstellar media. In this work, we studied glycine conformational space and the related tautomerization mechanisms in water media by means of QM/MM molecular dynamics simulations of four glycine conformational isomers (cc, ct, tc, and tt). Interstellar low density amorphous (LDA) ice and T = 20 K were considered as representative for a cold interstellar ice environment, while temperatures of 250 and 450 K were included to model rapid local heating in the ice. In addition to the LDA environment, water clusters with 4, 17, and 27 H2O molecules were subjected to QM/MM dynamics simulations that allowed glycine tautomerization behaviour to be evaluated in water surface-like environments. The tautomerization processes were found to be strongly dependent on the number of water molecules and specific isomer structure. All the glycine isomers mostly preserve their canonical "neutral" conformations under interstellar conditions.

Exploring Spin Distribution and Electronic Properties in FeN4-Graphene Catalysts with Edge Terminations.

Understanding the spin distribution in FeN4-doped graphene nanoribbons with zigzag and armchair terminations is crucial for tuning the electronic properties of graphene-supported non-platinum catalysts. Since the spin-polarized carbon and iron electronic states may act together to change the electronic properties of the doped graphene, we provide in this work a systematic evaluation using a periodic density-functional theory-based method of the variation of spin-moment distribution and electronic properties with the position and orientation of the FeN4 defects, and the edge terminations of the graphene nanoribbons. Antiferromagnetic and ferromagnetic spin ordering of the zigzag edges were considered. We reveal that the electronic structures in both zigzag and armchair geometries are very sensitive to the location of FeN4 defects, changing from semi-conducting (in-plane defect location) to half-metallic (at-edge defect location). The introduction of FeN4 defects at edge positions cancels the known dependence of the magnetic and electronic proper-ties of undoped graphene nanoribbons on their edge geometries. The implications of the reported results for catalysis are also discussed in view of the presented electronic and magnetic properties.

Thermal fluctuation and conformational effects on NMR parameters in ß-O-4 lignin dimers from QM/MM and machine-learning approaches.

Advanced solid-state and liquid-state nuclear magnetic resonance (NMR) approaches have enabled high throughput information about functional groups and types of bonding in a variety of lignin fragments from degradation processes and laboratory synthesis. The use of quantum chemical (QM) methods may provide detailed insight into the relationships between NMR parameters and specific lignin conformations and their dynamics, whereas a rapid prediction of NMR properties could be achieved by combining QM with machine-learning (ML) approaches. In this study, we present the effect of conformations of ß-O-4 linked lignin guaiacyl dimers on 13C and 1H chemical shifts while considering the thermal fluctuations of the guaiacyl dimers in water, ethanol and acetonitrile, as well as their binary 75 wt% aqueous solutions. Molecular dynamics and QM/MM simulations were used to describe the dynamics of guaiacyl dimers. The isotropic shielding of the majority of the carbon nuclei was found to be less sensitive toward a specific conformation than that of the hydrogen nuclei. The largest 1H downfield shifts of 4-6 ppm were established in the hydroxy groups and the rings in the presence of organic solvent components. The Gradient Boosting Regressor model has been trained on 60% of the chemical environments in the dynamics trajectories with the NMR isotropic shielding (σiso), computed with density-functional theory, for lignin atoms. The high efficiency of this machine-learning model in predicting the remaining 40% σiso(13C) and σiso(1H) values was established.

Molecular Insight into the Cosolvent Effect on Lignin-Cellulose Adhesion.

Understanding and controlling the physical adsorption of lignin compounds on cellulose pulp are key parameters in the successful optimization of organosolv processes. The effect of binary organic-aqueous solvents on the coordination of lignin to cellulose was studied with molecular dynamics simulations, considering ethanol and acetonitrile to be organic cosolvents in aqueous solutions in comparison to their monocomponent counterparts. The structures of the solvation shells around cellulose and lignin and the energetics of lignin-cellulose adhesion indicate a more effective disruption of lignin-cellulose binding by binary solvents. The synergic effect between solvent components is explained by their preferential interactions with lignin-cellulose complexes. In the presence of pure water, long-lasting H-bonds in the lignin-cellulose complex are observed, promoted by the nonfavorable interactions of lignin with water. Ethanol and acetonitrile compete with water and lignin for cellulose oxygen binding sites, causing a nonlinear decrease in the lignin-cellulose interactions with the amount of the organic component. This effect is modulated by the water exclusion from the cellulose solvation shell by the organic solvent component. The amount and rate of water exclusion depend on the type of organic cosolvent and its concentration.

P-block single-metal-site tin/nitrogen-doped carbon fuel cell cathode catalyst for oxygen reduction reaction.

This contribution reports the discovery and analysis of a p-block Sn-based catalyst for the electroreduction of molecular oxygen in acidic conditions at fuel cell cathodes; the catalyst is free of platinum-group metals and contains single-metal-atom actives sites coordinated by nitrogen. The prepared SnNC catalysts meet and exceed state-of-the-art FeNC catalysts in terms of intrinsic catalytic turn-over frequency and hydrogen-air fuel cell power density. The SnNC-NH3 catalysts displayed a 40-50% higher current density than FeNC-NH3 at cell voltages below 0.7 V. Additional benefits include a highly favourable selectivity for the four-electron reduction pathway and a Fenton-inactive character of Sn. A range of analytical techniques combined with density functional theory calculations indicate that stannic Sn(IV)Nx single-metal sites with moderate oxygen chemisorption properties and low pyridinic N coordination numbers act as catalytically active moieties. The superior proton-exchange membrane fuel cell performance of SnNC cathode catalysts under realistic, hydrogen-air fuel cell conditions, particularly after NH3 activation treatment, makes them a promising alternative to today's state-of-the-art Fe-based catalysts.

Zeolite Structure Direction: Identification, Strength and Involvement of Weak CH⋠⋠⋠O Hydrogen Bonds.

We demonstrate that weak CH⋅⋅⋅O hydrogen bonds (HBs) are important host-guest interactions in zeolite assemblies involving structure directing organocations. This type of HB is identified between alkyl groups of the organic structure directing agent (OSDA) and the silica framework in as-synthesized silicalite-1 of complex topology (MFI) using a combination of experimental and theoretical data obtained at low and room temperatures. The 28 weak CH⋅⋅⋅O HBs, evidenced along dynamics simulation at room temperature, represent 30 % of the energy of the Coulomb electrostatic interaction between OSDA and the zeolite framework. The strongest and most stable HB found here connects the OSDA to the [41 52 62 ] cage containing F atoms and should contribute to preserve zeolite topology during crystal growth. An inspection of other as-synthesized zeolites of very different framework topology indicates that the directional CH⋅⋅⋅O HBs have to be considered when discussing zeolite structure directing phenomena.

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review.

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.

High performance of PtCu@TiO2 nanocatalysts toward methanol oxidation reaction: from synthesis to molecular picture insight.

The electrocatalytic production of hydrogen from methanol dehydrogenation successfully uses platinum catalysts. However, they are expensive and Pt has the tendency to be poisoned from the intermediate compounds, formed during the methanol oxidation reaction (MOR). For these two reasons, there has been active research for alternative bi- and tri-component Pt-based catalysts. Herein, PtCu nanoparticles deposited on titania were studied and proposed to be efficient MOR catalysts. The catalyst was prepared by photo-deposition of Cu on a high-surface-area TiO2 powder support, followed by a partial galvanic displacement of the Cu deposit by platinum. The morphology and structure of the catalyst were characterized by physicochemical methods. The PtCu@TiO2 electro-catalyst has higher intrinsic catalytic activity and comparable mass specific activity for MOR in comparison with a commercial Pt/C catalyst. The experimental analyses were complemented by density functional theory-based computations. The theoretical results revealed that the most energetically favorable Pt and Cu arrangement in the supported PtCu nanoparticles was core (Cu)-shell (Pt) and/or phase-separated. The inter-atomic interactions responsible for the bimetallic cluster stabilization on titania were highlighted from the computed electronic charge distribution.

Structures, intermolecular interactions, and chemical hardness of binary water-organic solvents: a molecular dynamics study.

The evolution of structural properties, thermodynamics and averaged (dynamic) total hardness values as a function of the composition of binary water-organic solvents, was rationalized in view of the intermolecular interactions. The organic solvents considered were ethanol, acetonitrile, and isopropanol at 0.25, 0.5, 0.75, and 1 mass fractions, and the results were obtained using molecular dynamics simulations. The site-to-site radial distribution functions reveal a well-defined peak for the first coordination shell in all solvents. A characteristic peak of the second coordination shell exists in aqueous mixtures of acetonitrile, whereas in the water-alcohol solvents, a second peak develops with the increase in alcohol content. From the computed coordination numbers, averaged hydrogen bonds and their lifetimes, we found that water mixed with acetonitrile largely preserves its structural features and promotes the acetonitrile structuring. Both the water and alcohol structures in their mixtures are disturbed and form hydrogen bonds between molecules of different kinds. The dynamic hardness values are obtained as the average over the total hardness values of 1200 snapshots per solvent type, extracted from the equilibrium dynamics. The dynamic hardness profile has a non-linear evolution with the liquid compositions, similarly to the thermodynamic properties of these non-ideal solvents. Graphical abstract Computed dynamic total hardness, as a function of the cosolvent mass fraction for water-ethanol (EtOH), water-isopropanol (2PrOH) and water-acetonitrile (AN).

The effect of Pd ensemble structure on the O2 dissociation and CO oxidation mechanisms on Au-Pd(100) surface alloys.

The reactivity of various Pd ensembles on the Au-Pd(100) alloy catalyst toward CO oxidation was investigated by using density functional theory (DFT). This study was prompted by the search for efficient catalysts operating at low temperature for the CO oxidation reaction that is of primary environmental importance. To this aim, we considered Pd modified Au(100) surfaces including Pd monomers, Pd dimers, second neighboring Pd atoms, and Pd chains in a comparative study of the minimum energy reaction pathways. The effect of dispersion interactions was included in the calculations of the O2 dissociation reaction pathway by using the DFT-D3 scheme. The addition of the dispersion interaction strongly improves the adsorption ability of O2 on the Au-Pd surface but does not affect the activation energy barriers of the Transitions States (TSs). As for O2 to dissociate, it is imperative that the TS has lower activation energy than the O2 desorption energy. DFT-D3 is found to favor, in some cases, O2 dissociation on configurations being identified from uncorrected DFT calculations as inactive. This is the case of the second neighboring Pd configuration for which uncorrected DFT predicts positive Gibbs free energy (ΔG) of the O2 adsorption, therefore an endergonic reaction. With the addition of D3 correction, ΔG becomes negative that reveals a spontaneous O2 adsorption. Among the investigated Au-Pd (100) ensembles, the Pd chain dissociates most easily O2 and highly stabilizes the dissociated O atoms; however, it has an inferior reactivity toward CO oxidation and CO2 formation. Indeed, CO strongly adsorbs on the palladium bridge sites and therefore poisoning the surface Pd chain. By contrast, the second neighboring Pd configuration that shows somewhat lower ability to dissociate O2 turns out to be more reactive in the CO2 formation step. These results evidence the complex effect of Pd ensembles on the CO oxidation reaction. Associative CO oxidation proceeds with high energy barriers on all the considered Pd ensembles and should be excluded, in agreement with experimental observations.

ZSM-5 Zeolite: Complete Al Bond Connectivity and Implications on Structure Formation from Solid-State NMR and Quantum Chemistry Calculations.

Al site distribution in the structurally complex and industrially important ZSM-5 zeolite is determined by studying the spectroscopic response of Al(OSi)4 units and using a self-consistent combination of up-to-date solid-state NMR correlations (29Si-27Al and 1H-27Al D-HMQC) and quantum chemistry methods (DFT-D). To unravel the driving forces behind specific Al sitting positions, our approach focuses on ZSM-5 containing its more efficient OSDA, tetrapropylammonium.

Identification of catalytic sites in cobalt-nitrogen-carbon materials for the oxygen reduction reaction.

Single-atom catalysts with full utilization of metal centers can bridge the gap between molecular and solid-state catalysis. Metal-nitrogen-carbon materials prepared via pyrolysis are promising single-atom catalysts but often also comprise metallic particles. Here, we pyrolytically synthesize a Co-N-C material only comprising atomically dispersed cobalt ions and identify with X-ray absorption spectroscopy, magnetic susceptibility measurements and density functional theory the structure and electronic state of three porphyrinic moieties, CoN4C12, CoN3C10,porp and CoN2C5. The O2 electro-reduction and operando X-ray absorption response are measured in acidic medium on Co-N-C and compared to those of a Fe-N-C catalyst prepared similarly. We show that cobalt moieties are unmodified from 0.0 to 1.0 V versus a reversible hydrogen electrode, while Fe-based moieties experience structural and electronic-state changes. On the basis of density functional theory analysis and established relationships between redox potential and O2-adsorption strength, we conclude that cobalt-based moieties bind O2 too weakly for efficient O2 reduction.Nitrogen-doped carbon materials with atomically dispersed iron or cobalt are promising for catalytic use. Here, the authors show that cobalt moieties have a higher redox potential, bind oxygen more weakly and are less active toward oxygen reduction than their iron counterpart, despite similar coordination.

Intermolecular interactions in AST zeolites through 14N NMR and DFT calculations.

The structure of the silica AST zeolites (octadecasil) synthesized in fluoride medium using tetramethylammonium (TMA) as the organic structure-directing agent has been reinvestigated using 14N NMR quadrupolar parameters and DFT calculations. The value of the experimental 14N quadrupolar coupling constant (CQ = 27 kHz) is larger than expected for a TMA cation possessing a high degree of motion. The analysis of a DFT-optimized octadecasil cluster along with the comparison between measured and calculated 14N NMR parameters demonstrate the presence of weak C-H...O hydrogen bonds between the TMA in the [46612] cages and the silica skeleton. These intermolecular interactions can be related to the presence of Si...F tetrel bonds within the [46] cages. These new results provide additional information with regard to the formation mechanisms and structure of the octadecasil zeolites.

Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study.

Application of ab initio molecular dynamics to study free energy surfaces (FES) is still not commonly performed because of the extensive sampling required. Indeed, it generally necessitates computationally costly simulations of more than several hundreds of picoseconds. To achieve such studies, efficient density functional theory (DFT) formalisms, based on various levels of approximate computational schemes, have been developed, and provide a good alternative to commonly used DFT implementations. We report benchmark results on the conformational change FES of alanine dipeptide obtained with auxiliary density functional theory (ADFT) and second- and third-order density functional tight-binding (DFTB) methods coupled to metadynamics simulations. The influence of an explicit water solvent is also studied with DFTB, which was made possible by its lower computational cost compared to ADFT. Simulations lengths of 2.1 and 15 ns were achieved with ADFT and DFTB, respectively, in a reasonably short computational time. ADFT leads to a free energy difference (ΔF eq-ax) of ∼ -3 kcal mol-1 between the two low energy conformers, C7eq and C7ax, which is lower by only 1.5 kcal mol-1 than the ΔF eq-ax computed with DFTB. The two minima in ADFT FES are separated by an energy barrier of 9 kcal mol-1, which is higher than the DFTB barriers by 2-4 kcal mol-1. Despite these small quantitative differences, the DFTB method reveals FES shapes, confor-mation geometries and energies of the stationary points in good agreement with these found with ADFT. This validates the promising applicability of DFTB to FES of reactions occurring in larger-size systems placed in complex environments.

Conversion of Methyl Mercaptan to Hydrocarbons over H-ZSM-5 Zeolite: DFT/BOMD Study.

Methyl mercaptan-a harmful impurity in natural gas-may be selectively converted into H2S and hydrocarbons [methyl mercaptan to hydrocarbon (M2TH) process], using zeolite catalysts. When M2TH is compared with the well-known MTH (methanol to hydrocarbons) process, significant differences emerge, essentially regarding the formation and distribution of products. Density functional theory (DFT) and Born-Oppenheimer molecular dynamics (BOMD) were employed to reveal possible origins for the experimentally observed differences. We established a close similarity between DFT intrinsic (electronic) reaction profiles in the stepwise mechanism of methanol and mercaptan dehydration, although no variance in reactivity was revealed. BOMD simulations at the experimental temperature of 823 K reveal rapid hydrogen abstraction from the methyl group in mercaptan, adsorbed in the zeolite cavity in the presence of the methoxy intermediate. The formation of •CH2SH radical is 10 times faster than that of •CH2OH at the same temperature. The varied reactivity of methanol and mercaptan in MTH and M2TH processes, respectively, can therefore first be attributed to very rapid hydrogen abstraction in mercaptan, which occurs in the zeolite cavity, following the formation of surface methoxy.

Complexation of Trivalent Metal Cations to Mannuronate Type Alginate Models from a Density Functional Study.

Complexation of alginate models, built of ß-d-mannuronic units (M) linked by a 1-4 glycosidic bridge, to Al(3+), Sc(3+), Cr(3+), Fe(3+), Ga(3+), and La(3+) cations was studied by applying the quantum chemical density functional theory (DFT) based method. The binding modes and energies were obtained for complexes with one, two, and three truncated alginate chain(s). In all the hydrated structures a monodentate binding mode is established to be the energetically most favored with shorter M(3+)···O(COO(-)) bonds than M(3+)···O(OH) bonds. Coordination bond lengths are found to be specific to each cation and to depend very little on the water in the coordination sphere and on the number of saccharide units used to model an alginate chain. The binding energy tendency Fe(3+) ≈ Cr(3+) > Al(3+) ≈ Ga(3+) ≫ Sc(3+) ≥ La(3+) is not affected by the alginate models, the coordination to water molecules, and the number of chains. A significant covalent contribution that arises predominantly from a charge donation from the carboxylate oxygen to the metal cation was established from the orbital population analysis. An exothermic chain-chain association is predicted by the computed enthalpy variations. A comparison between the structural features of alginate complexation to trivalent and divalent cations is provided and discussed.

Preferential orientations of structure directing agents in zeolites.

The local structure of as-synthesised silicalite-1 zeolites is modified using asymmetric R(Pr)3N(+) structure directing agents. Using multi-nuclear NMR ((1)H, (13)C, (14)N, (19)F, (29)Si), we show for the first time the ability of these cations to adopt preferential orientations at the zeolite channels' crossing.

Identification of catalytic sites for oxygen reduction in iron- and nitrogen-doped graphene materials.

While platinum has hitherto been the element of choice for catalysing oxygen electroreduction in acidic polymer fuel cells, tremendous progress has been reported for pyrolysed Fe-N-C materials. However, the structure of their active sites has remained elusive, delaying further advance. Here, we synthesized Fe-N-C materials quasi-free of crystallographic iron structures after argon or ammonia pyrolysis. These materials exhibit nearly identical Mössbauer spectra and identical X-ray absorption near-edge spectroscopy (XANES) spectra, revealing the same Fe-centred moieties. However, the much higher activity and basicity of NH3-pyrolysed Fe-N-C materials demonstrates that the turnover frequency of Fe-centred moieties depends on the physico-chemical properties of the support. Following a thorough XANES analysis, the detailed structures of two FeN4 porphyrinic architectures with different O2 adsorption modes were then identified. These porphyrinic moieties are not easily integrated in graphene sheets, in contrast with Fe-centred moieties assumed hitherto for pyrolysed Fe-N-C materials. These new insights open the path to bottom-up synthesis approaches and studies on site-support interactions.

Application of vibrational correlation formalism to internal conversion rate: case study of Cu(n) (n = 3, 6, and 9) and H2/Cu3.

This work reports non-radiative internal conversion (IC) rate constants obtained for Cun with n = 3, 6, and 9 and H2 on Cu3. The Time-Dependent Density Functional Theory (TDDFT) method was employed with three different functionals in order to investigate the electronic structures and the absorption spectra. The performance of the generalized gradient approximation of Perdew, Burke and Ernzerhof (PBE) and the hybrid B3LYP and PBE0 exchange correlation functionals in combination with the SVP and the def2-TZVP basis sets was examined. TDDFT results were used as input data to compute internal conversion rate constants. For this purpose, we have developed a program package. A description of the theoretical background used in our numerical implementation and the program input file is presented. In view of future applications of this program package in photoinduced catalysis, we present the analysis of the IC rate processes for the photodissociation of H2 on Cu3. These results showed the applicability of the method and the computational program to identify the vibrational modes in transition metal clusters giving rise to the largest IC rate constant due to their interactions with the excited electronic states occurring in the hot-electron induced dissociation phenomena.