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.

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 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.

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.

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.

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.

DFT-D study of 14N nuclear quadrupolar interactions in tetra-n-alkyl ammonium halide crystals.

The density functional theory-based method with periodic boundary conditions and addition of a pair-wised empirical correction for the London dispersion energy (DFT-D) was used to study the NMR quadrupolar interaction (coupling constant CQ and asymmetry parameter ηQ) of (14)N nuclei in a homologous series of tetra-n-alkylammonium halides (C(x)H(2x+1))4N(+)X(-) (x = 1-4), (X = Br, I). These (14)N quadrupolar properties are particularly challenging for the DFT-D computations because of their very high sensitivity to tiny geometrical changes, being negligible for other spectral property calculations as, for example, NMR (14)N chemical shift. In addition, the polarization effect of the halide anions in the considered crystal mesophases combines with interactions of van der Waals type between cations and anions. Comparing experimental and theoretical results, the performance of PBE-D functional is preferred over that of B3LYP-D. The results demonstrated a good transferability of the empirical parameters in the London dispersion formula for crystals with two or more carbons per alkyl group in the cations, whereas the empirical corrections in the tetramethylammonium halides appeared to be inappropriate for the quadrupolar interaction calculation. This is attributed to the enhanced cation-anion attraction, which causes a strong polarization at the nitrogen site. Our results demonstrated that the (14)N CQ and ηQ are predominantly affected by the molecular structures of the cations, adapted to the symmetry of the anion arrangements. The long-range polarization effect of the surrounding anions at the target nitrogen site becomes more important for cells with lower spatial symmetry.

Theoretical and experimental local reactivity parameters of 3-substituted coumarin derivatives.

Local reactivity descriptors, such as atomic charges, atomic electrostatic potential and atomic Fukui indices were computed for a series of 3-substituted coumarin (2-oxo-2H-1-benzopyran) derivatives, using density functional theory (DFT) and Möller-Plesset methods (MP2). The variation of those properties as a function of the substituents was compared with the variation of the measured XPS binding energies. The atomic electrostatic potentials and XPS binding energies serves as indicators of the electrophilicity of a given center within a molecule, while the atomic Fukui indices describe its degree of electronic localization, known as atomic softness. The correlation between those theoretical and experimental properties allowed us to follow the effect of electron withdrawing substituents on the electrophilicity of a given atomic center. The Fukui indices provided additional information about the softening/hardening of the center of interest due to presence of different substituents to the coumarin system. On the basis of these analysis, the 1,2-addition would be favored for 3-acetyl, 3-phosphono, and 7-diethylamino substituents, while 3-carboxyl, 3-ethoxycarbonyl, and 3-nitro substituent would favor 1,4-addition. The substituted coumarins would preferably react with soft nucleophiles at position 2 and with hard nucleophiles at position 4.

14N solid-state NMR: a sensitive probe of the local order in zeolites.

Local order in as-synthesised zeolites templated by tetraalkylammonium cations is proven from solid-state (14)N NMR and related quadrupolar parameters, opening new perspectives in the study of porous materials.

Structure of alginate gels: interaction of diuronate units with divalent cations from density functional calculations.

The complexation of (1→4) linked α-L-guluronate (G) and ß-D-mannuronate (M) disaccharides with Mg(2+), Ca(2+), Sr(2+), Mn(2+), Co(2+), Cu(2+), and Zn(2+) cations have been studied with quantum chemical density functional theory (DFT)-based method. A large number of possible cation-diuronate complexes, with one and two GG or MM disaccharide units and with or without water molecules in the inner coordination shells have been considered. The computed bond distances, cation interaction energies, and molecular orbital composition analysis revealed that the complexation of the transition metal (TM) ions to the disaccharides occurs via the formation of strong coordination-covalent bonds. On the contrary, the alkaline earth cations form ionic bonds with the uronates. The unidentate binding is found to be the most favored one in the TM hydrated and water-free complexes. By removing water molecules, the bidentate chelating binding also occurs, although it is found to be energetically less favored by 1 to 1.5 eV than the unidentate one. A good correlation is obtained between the alginate affinity trend toward TM cations and the interaction energies of the TM cations in all studied complexes, which suggests that the alginate affinities are strongly related to the chemical interaction strength of TM cations-uronate complexes. The trend of the interaction energies of the alkaline earth cations in the ionic complexes is opposite to the alginate affinity order. The binding strength is thus not a limiting factor in the alginate gelation in the presence of alkaline earth cations at variance with the TM cations.

Drug nano-domains in spray-dried ibuprofen-silica microspheres.

Silica microspheres encapsulating ibuprofen in separated domains at the nanometre scale are formed by spray-drying and sol-gel processes. A detailed (1)H and (13)C NMR study of these microspheres shows that ibuprofen molecules are mobile and are interacting through hydrogen bonds with other ibuprofen molecules. (1)H magnetisation exchange NMR experiments were employed to characterize the size of the ibuprofen domains at the nanometre scale. These domains are solely formed by ibuprofen, and their diameters are estimated to be ∼40 nm in agreement with TEM observations. The nature and formation of these particular texture and drug dispersion are discussed.

Investigation of the interface in silica-encapsulated liposomes by combining solid state NMR and first principles calculations.

In the context of nanomedicine, liposils (liposomes and silica) have a strong potential for drug storage and release schemes: such materials combine the intrinsic properties of liposome (encapsulation) and silica (increased rigidity, protective coating, pH degradability). In this work, an original approach combining solid state NMR, molecular dynamics, first principles geometry optimization, and NMR parameters calculation allows the building of a precise representation of the organic/inorganic interface in liposils. {(1)H-(29)Si}(1)H and {(1)H-(31)P}(1)H Double Cross-Polarization (CP) MAS NMR experiments were implemented in order to explore the proton chemical environments around the silica and the phospholipids, respectively. Using VASP (Vienna Ab Initio Simulation Package), DFT calculations including molecular dynamics, and geometry optimization lead to the determination of energetically favorable configurations of a DPPC (dipalmitoylphosphatidylcholine) headgroup adsorbed onto a hydroxylated silica surface that corresponds to a realistic model of an amorphous silica slab. These data combined with first principles NMR parameters calculations by GIPAW (Gauge Included Projected Augmented Wave) show that the phosphate moieties are not directly interacting with silanols. The stabilization of the interface is achieved through the presence of water molecules located in-between the head groups of the phospholipids and the silica surface forming an interfacial H-bonded water layer. A detailed study of the (31)P chemical shift anisotropy (CSA) parameters allows us to interpret the local dynamics of DPPC in liposils. Finally, the VASP/solid state NMR/GIPAW combined approach can be extended to a large variety of organic-inorganic hybrid interfaces.

Vibrational characterization of ethylene adsorption and its thermal evolution on Si(001)-(2 x 1): identification of majority and minority species.

The vibrational and structural properties of a single-domain Si(001)-(2 x 1) surface upon ethylene adsorption have been studied by density functional cluster calculations and high-resolution electron energy loss spectroscopy. The detailed analysis of the theoretically and the experimentally determined vibrational frequencies reveals two coexisting adsorbate configurations. The majority species consist of ethylene molecules which are di-sigma bonded to the two Si atoms of a single Si-Si dimer. The local symmetry of this adsorption complex is reduced to C(2) for ethylene saturation coverage as determined by surface selection rules for the vibrational excitation process. The symmetry reduction includes the rotation of the C-C bond around the surface normal and the twist of the methylene groups around the C-C axis. Experimentally, 17 ethylene-derived modes are found and assigned for the majority and the minority species based on a comparison with calculated vibrational frequencies. The minority species which can account up to 14% of the total ethylene coverage is spectroscopically identified for the first time. It is assigned to ethylene molecules di-sigma bonded to two adjacent Si-Si dimers (in an end-bridge configuration). One part of the minority species desorbs molecularly at 665 K, about 50 K higher than the majority species, whereas the remaining part dissociates to adsorbed acetylene at temperatures around 630 K. For the latter, a di-sigma end-bridge like bonding configuration is proposed based on a comparison with vibrational data for adsorbed acetylene on Si(100)-(2 x 1).

14N and 81Br quadrupolar nuclei as sensitive NMR Probes of n-alkyltrimethylammonium bromide crystal structures. An experimental and theoretical study.

This is the first time a comprehensive study has been carried out on n-alkyltrimethylammonium bromide salts using (14)N and (81)Br solid state NMR, X-ray diffraction, and theoretical calculations. The investigation represents a necessary step toward further (14)N and (81)Br NMR characterization of the environment of cationic and anionic groups in materials, accounting for the amphiphilic properties of cationic surfactants. The NMR spectra of five C(x)H(2x+1)(CH(3))(3)N(+)Br(-) polycrystalline samples with different n-alkyl chain lengths (x = 1, 12, 14, 16, 18) were recorded and modeled. The (14)N and (81)Br quadrupolar coupling interaction parameters (C(Q), eta(Q)) were also estimated from spectrum modeling and from computer simulation. The obtained results were discussed in depth making use of the experimental and reoptimized crystal structures. In the study, both (14)N and (81)Br nuclei were found to be sensitive probes for small structural variations. The parameters which influence the NMR properties the most are mobility, deviation of C-N-C bond angles from T(d) angles, and variations in r(N-Br) distances.

Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters.

The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.