Connection between water's dynamical and structural properties: Insights from ab initio simulations.

SignificanceFirst-principles calculations, which explicitly account for the electronic structure of matter, can shed light on the molecular structure and dynamics of water in its supercooled state. In this work, we use density functional theory, which relies on a functional to describe electronic exchange and correlations, to evaluate which functional best describes the temperature evolution of bulk water transport coefficients. We also assess the validity of the Stokes-Einstein relation for all the functionals in the temperature range studied, and explore the link between structure and dynamics. Based on these results, we show how transport coefficients can be computed from structural descriptors, which require shorter simulation times to converge, and we point toward strategies to develop better functionals.

In situ spectroelectrochemical probing of CO redox landscape on copper single-crystal surfaces.

Electrochemical reduction of CO(2) to value-added chemicals and fuels is a promising strategy to sustain pressing renewable energy demands and to address climate change issues. Direct observation of reaction intermediates during the CO(2) reduction reaction will contribute to mechanistic understandings and thus promote the design of catalysts with the desired activity, selectivity, and stability. Herein, we combined in situ electrochemical shell-isolated nanoparticle-enhanced Raman spectroscopy and ab initio molecular dynamics calculations to investigate the CORR process on Cu single-crystal surfaces in various electrolytes. Competing redox pathways and coexistent intermediates of CO adsorption (*COatop and *CObridge), dimerization (protonated dimer *HOCCOH and its dehydrated *CCO), oxidation (*CO2- and *CO32-), and hydrogenation (*CHO), as well as Cu-Oad/Cu-OHad species at Cu-electrolyte interfaces, were simultaneously identified using in situ spectroscopy and further confirmed with isotope-labeling experiments. With AIMD simulations, we report accurate vibrational frequency assignments of these intermediates based on the calculated vibrational density of states and reveal the corresponding species in the electrochemical CO redox landscape on Cu surfaces. Our findings provide direct insights into key intermediates during the CO(2)RR and offer a full-spectroscopic tool (40-4,000 cm-1) for future mechanistic studies.

Electrocatalytic Ammonia Oxidation with a Tailored Molecular Catalyst Heterogenized via Surface Host-Guest Complexation.

Macrocyclic host molecules bound to electrode surfaces enable the complexation of catalytically active guests for molecular heterogeneous catalysis. We present a surface-anchored host-guest complex with the ability to electrochemically oxidize ammonia in both organic and aqueous solutions. With an adamantyl motif as the binding group on the backbone of the molecular catalyst [Ru(bpy-NMe2)(tpada)(Cl)](PF6) (1) (where bpy-NMe2 is 4,4'-bis(dimethylamino)-2,2'-bipyridyl and tpada is 4'-(adamantan-1-yl)-2,2':6',2″-terpyridine), high binding constants with ß-cyclodextrin were observed in solution (in DMSO-d6:D2O (7:3), K11 = 492 ± 21 M-1). The strong binding affinities were also transferred to a mesoporous ITO (mITO) surface functionalized with a phosphonated derivative of ß-cyclodextrin. The newly designed catalyst (1) was compared to the previously reported naphthyl-substituted catalyst [Ru(bpy-NMe2)(tpnp)(Cl)](PF6) (2) (where tpnp is 4'-(naphthalene-2-yl)-2,2':6',2″-terpyridine) for its stability during catalysis. Despite the insulating nature of the adamantyl substituent serving as the binding group, the stronger binding of this unit to the host-functionalized electrode and the resulting shorter distance between the catalytic active center and the surface led to better performance and higher stability. Both guests are able to oxidize ammonia in both organic and aqueous solutions, and the host-anchored electrode can be refunctionalized multiple times (>3) following the loss of the catalytic activity, without a reduction in performance. Guest 1 exhibits significantly higher stability in comparison to guest 2 toward basic conditions, which often constitutes a challenge for anchored molecular systems. Ammonia oxidation in water led to the selective formation of NO3- with Faradaic efficiencies of up to 100%.

X-ray induced ultrafast charge transfer in thiophene-based conjugated polymers controlled by core-hole clock spectroscopy.

We explore ultrafast charge transfer (CT) resonantly induced by hard X-ray radiation in organic thiophene-based polymers at the sulfur K-edge. A combination of core-hole clock spectroscopy with real-time propagation time-dependent density functional theory simulations gives an insight into the electron dynamics underlying the CT process. Our method provides control over CT by a selective excitation of a specific resonance in the sulfur atom with monochromatic X-ray radiation. Our combined experimental and theoretical investigation establishes that the dominant mechanism of CT in polymer powders and films consists of electron delocalisation along the polymer chain occurring on the low-femtosecond time scale.

Low-frequency anharmonic couplings in crystalline bromoform: Theory.

Theoretical calculations of the low-frequency anharmonic couplings of the ß-phase of crystalline bromoform are presented based on density functional theory quantum chemistry calculations. The electrical and mechanical anharmonicities between intra- and intermolecular modes are calculated, revealing that the electrical anharmonicity dominates the cross-peak intensities in the 2D Raman-THz response and crystalline, as well as liquid, bromoform. Furthermore, the experimentally observed difference in relative cross-peak intensities between the two intramolecular modes of bromoform and the intermolecular modes can be explained by the C3v-symmetry of bromoform in combination with orientational averaging. The good agreement with the experimental results provides further evidence for our interpretation that the 2D Raman-THz response of bromoform is, indeed, related to the anharmonic coupling between the intra- and intermolecular modes.

A variational formulation of the Harris functional as a correction to approximate Kohn-Sham density functional theory.

Accurate descriptions of intermolecular interactions are of great importance in simulations of molecular liquids. We present an electronic structure method that combines the accuracy of the Harris functional approach with the computational efficiency of approximately linear-scaling density functional theory (DFT). The non-variational nature of the Harris functional has been addressed by constructing a Lagrangian energy functional, which restores the variational condition by imposing stationarity with respect to the reference density. The associated linear response equations may be treated with linear-scaling efficiency in an atomic orbital based scheme. Key ingredients to describe the structural and dynamical properties of molecular systems are the forces acting on the atoms and the stress tensor. These first-order derivatives of the Harris Lagrangian have been derived and implemented in consistence with the energy correction. The proposed method allows for simulations with accuracies close to the Kohn-Sham DFT reference. Embedded in the CP2K program package, the method is designed to enable ab initio molecular dynamics simulations of molecular solutions for system sizes of several thousand atoms. Available subsystem DFT methods may be used to provide the reference density required for the energy correction at near linear-scaling efficiency. As an example of production applications, we applied the method to molecular dynamics simulations of the binary mixtures cyclohexane-methanol and toluene-methanol, performed within the isobaric-isothermal ensemble, to investigate the hydrogen bonding network in these non-ideal mixtures.

Donors, acceptors, and a bit of aromatics: electronic interactions of molecular adsorbates on hBN and MoS2 monolayers.

The design of low-dimensional organic-inorganic interfaces for the next generation of opto-electronic applications requires in-depth understanding of the microscopic mechanisms ruling electronic interactions in these systems. In this work, we present a first-principles study based on density-functional theory inspecting the structural, energetic, and electronic properties of five molecular donors and acceptors adsorbed on freestanding hexagonal boron nitride (hBN) and molybdenum disulfide (MoS2) monolayers. All considered interfaces are stable, due to the crucial contribution of dispersion interactions, which are maximized by the overall flat arrangement of the physisorbed molecules on both substrates. The level alignment of the hybrid systems depends on the characteristics of the constituents. On hBN, both type-I and type-II interfaces may form, depending on the relative energies of the frontier orbitals with respect to the vacuum level. On the other hand, all MoS2-based hybrid systems exhibit a type-II level alignment, with the molecular frontier orbitals positioned across the energy gap of the semiconductor. The electronic structure of the hybrid materials is further determined by the formation of interfacial dipole moments and by the wave-function hybridization between the organic and inorganic constituents. These results provide important indications for the design of novel low-dimensional hybrid materials with suitable characteristics for opto-electronics.

CO2 adsorption on the pristine and reduced CeO2 (111) surface: Geometries and vibrational spectra by first principles simulations.

First principles simulations of carbon dioxide adsorbed on the ceria (CeO2) (111) surface are discussed in terms of structural features, stability, charge transfer, and vibrational modes. For this purpose, different density functional theory methods, such as Perdew-Burke-Ernzerhof (PBE) PBE and Hubbard correction, hybrid functionals, and different basis sets have been applied and compared. Both the stoichiometric and the reduced (111) surfaces are considered, where the electronic structure of the latter is obtained by introducing oxygen vacancies on the topmost or the subsurface oxygen layer. Both the potential energy surfaces of the reduced ceria surface and the adsorbate-surface complex are characterized by numerous local minima, of which the relative stability depends strongly on the electronic structure method of choice. Bent CO2 configurations in close vicinity to the surface oxygen vacancy that partially re-oxidize the reduced ceria surface have been identified as the most probable stable minima. However, the oxygen vacancy concentration on the surface turns out to have a direct impact on the relative stability of possible adsorption configurations. Finally, the vibrational analyses of selected adsorbed species on both the stoichiometric and reduced surfaces show promising agreement with previous theoretical and experimental results.

Comparison of Penta and Tetra-pyridyl Cobalt-based Catalysts for Water Reduction: H2 Production Cycle, Solvent Response and Reduction Free Energy.

Understanding water reduction towards H2 generation is crucial to overcome today's renewable energy obstacles. Previous studies have shown the superior H2 production performances of Cobalt based penta-pyridyl (CoaPPy) and tetra-pyridyl (CoaTPy) complexes in solution. We investigate H2 production cycles of CoaPPy and CoaTPy complexes immersed in water solution by means of Ab-initio Molecular Dynamics and Density Functional Theory. We monitor dynamic properties of the systems, solvent response and structural changes occurring in the catalysts, by simulating all intermediate steps of the H2 production cycle. Reduction free energies and reorganization energies are calculated. Our results show that, following the first electron injection, H2 production proceeds with the singlet spin state. Following the first electron insertion, we observe a significant rearrangement of the hydrogen bonding network in the first solvation shell. The cobalt center turns out to be more accessible for the surrounding water molecules in the case of CoaTPy at all the intermediate steps, which explains its higher catalytic performance over CoaPPy. Following the first reduction reaction, a larger gain in reduction free energy is estimated for CoaTPy with respect to CoaPPy, with a difference of 0.14 eV, in line with the experiments. For the second reduction, instead, CoaPPy shows more negative reduction potential, by 0.41 eV.

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations.

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

Catalyst Proximity-Induced Functionalization of h-BN with Quat Derivatives.

Inert single-layer boron nitride (h-BN) grown on a catalytic metal may be functionalized with quaternary ammonium compounds (quats) that are widely used as nonreactive electrolytes. We observe that the quat treatment, which facilitates the electrochemical transfer of two-dimensional materials, involves a decomposition of quat ions and leads to covalently bound quat derivatives on top of the 2D layer. Applying tetraoctylammonium and h-BN on rhodium, the reaction product is top-alkylized h-BN as identified with high-resolution X-ray photoelectron spectroscopy. The alkyl chains are homogeneously distributed across the surface, and the properties thereof are well-tunable by the choice of different quats. The functionalization further weakens the 2D material-substrate interaction and promotes easy transfer. Therefore, the functionalization scheme that is presented enables the design of 2D materials with tailored properties and with the freedom to position and orient them as required. The mechanism of this functionalization route is investigated with density functional theory calculations, and we identify the proximity of the catalytic metal substrate to alter the chemical reactivity of otherwise inert h-BN layers.

[CoII(BPyPy2COH)(OH2)2]2+: A Catalytic Pourbaix Diagram and AIMD Simulations on Four Key Intermediates.

Proton reduction by [CoII(BPyPy2COH)(OH2)2]2+ (BPyPy2COH = [2,2'-bipyridin]-6-yl-di[pyridin-2-yl]methanol) proceeds through two distinct, pH-dependent pathways involving proton-coupled electron transfer (PCET), reduction and protonation steps. In this account we give an overview of the key mechanistic aspects in aqueous solution from pH 3 to 10, based on electrochemical data, time-resolved spectroscopy and ab initio molecular dynamics simulations of the key catalytic intermediates. In the acidic pH branch, a PCET to give a CoIII hydride is followed by a reduction and a protonation step, to close the catalytic cycle. At elevated pH, a reduction to CoI is observed, followed by a PCET to a CoII hydride, and the catalytic cycle is closed by a slow protonation step. In our simulation, both CoI and CoII-H feature a strong interaction with the surrounding solvent via hydrogen bonding, which is expected to foster the following catalytic step.

Aqueous Solvation of Ammonia and Ammonium: Probing Hydrogen Bond Motifs with FT-IR and Soft X-ray Spectroscopy.

In a multifaceted investigation combining local soft X-ray and vibrational spectroscopic probes with ab initio molecular dynamics simulations, hydrogen-bonding interactions of two key principal amine compounds in aqueous solution, ammonia (NH3) and ammonium ion (NH4+), are quantitatively assessed in terms of electronic structure, solvation structure, and dynamics. From the X-ray measurements and complementary determination of the IR-active hydrogen stretching and bending modes of NH3 and NH4+ in aqueous solution, the picture emerges of a comparatively strongly hydrogen-bonded NH4+ ion via N-H donating interactions, whereas NH3 has a strongly accepting hydrogen bond with one water molecule at the nitrogen lone pair but only weakly N-H donating hydrogen bonds. In contrast to the case of hydrogen bonding among solvent water molecules, we find that energy mismatch between occupied orbitals of both the solutes NH3 and NH4+ and the surrounding water prevents strong mixing between orbitals upon hydrogen bonding and, thus, inhibits substantial charge transfer between solute and solvent. A close inspection of the calculated unoccupied molecular orbitals, in conjunction with experimentally measured N K-edge absorption spectra, reveals the different nature of the electronic structural effects of these two key principal amine compounds imposed by hydrogen bonding to water, where a pH-dependent excitation energy appears to be an intrinsic property. These results provide a benchmark for hydrogen bonding of other nitrogen-containing acids and bases.

Determining Potentials of Zero Charge of Metal Electrodes versus the Standard Hydrogen Electrode from Density-Functional-Theory-Based Molecular Dynamics.

We develop a computationally efficient scheme to determine the potentials of zero charge (PZC) of metal-water interfaces with respect to the standard hydrogen electrode. We calculate the PZC of Pt(111), Au(111), Pd(111) and Ag(111) at a good accuracy using this scheme. Moreover, we find that the interface dipole potentials are almost entirely caused by charge transfer from water to the surfaces, the magnitude of which depends on the bonding strength between water and the metals, while water orientation hardly contributes at the PZC conditions.

Post-Synthesis Amine Borane Functionalization of a Metal-Organic Framework and Its Unusual Chemical Hydrogen Release Phenomenon.

A novel strategy for post-synthesis amine borane functionalization of MOFs under gas-solid phase transformation, utilizing gaseous diborane, is reported. The covalently confined amine borane derivative decorated on the framework backbone is stable when preserved at low temperature, but spontaneously liberates soft chemical hydrogen at room temperature, leading to the development of an unusual borenium type species (-NH=BH2+ ) ion-paired with a hydroborate anion. Furthermore, the unsaturated amino borane (-NH=BH2 ) and the µ-iminodiborane (-µ-NHB2 H5 ) were detected as final products. A combination of DFT based molecular dynamics simulations and solid state NMR spectroscopy, utilizing isotopically enriched materials, were undertaken to unequivocally elucidate the mechanistic pathways for H2 liberation.

Valence orbitals and local bond dynamics around N atoms of histidine under X-ray irradiation.

The valence orbitals of aqueous histidine under basic, neutral and acidic conditions and their X-ray induced transformations have been monitored through N 1s resonant inelastic X-ray scattering. Using density functional ab initio molecular dynamics simulations in the core-hole state within the Z + 1 approximation, core-excitation-induced molecular transformations are quantified. Spectroscopic evidence for a highly directional X-ray-induced local N-H dissociation within the scattering duration is presented for acidic histidine. Our report demonstrates a protonation-state and chemical-environment dependent propensity for a molecular dissociation, which is induced by the absorption of high energy photons. This case study indicates that structural deformations in biomolecules under exposure to ionizing radiation, yielding possible alteration or loss of function, is highly dependent on the physiological state of the molecule upon irradiation.

Fast evaluation of solid harmonic Gaussian integrals for local resolution-of-the-identity methods and range-separated hybrid functionals.

An integral scheme for the efficient evaluation of two-center integrals over contracted solid harmonic Gaussian functions is presented. Integral expressions are derived for local operators that depend on the position vector of one of the two Gaussian centers. These expressions are then used to derive the formula for three-index overlap integrals where two of the three Gaussians are located at the same center. The efficient evaluation of the latter is essential for local resolution-of-the-identity techniques that employ an overlap metric. We compare the performance of our integral scheme to the widely used Cartesian Gaussian-based method of Obara and Saika (OS). Non-local interaction potentials such as standard Coulomb, modified Coulomb, and Gaussian-type operators, which occur in range-separated hybrid functionals, are also included in the performance tests. The speed-up with respect to the OS scheme is up to three orders of magnitude for both integrals and their derivatives. In particular, our method is increasingly efficient for large angular momenta and highly contracted basis sets.

S-Trifluoromethylation of Thiols by Hypervalent Iodine Reagents: A Joint Experimental and Computational Study.

The radical trifluoromethylation of thiophenol in condensed phase applying reagent 1 (3,3-dimethyl-1-(trifluoromethyl)-1λ(3),2-benziodoxol) has been examined by both theoretical and experimental methodologies. On the basis of ab initio molecular dynamics and metadynamics we show that radical reaction mechanisms favourably compete with polar ones involving the S-centred nucleophile thiophenol, their free energies of activation, ΔF(≠), lying between 9 and 15 kcal mol(-1). We further show that the origin of the proton activating the reagent is important. Hammett plot analysis reveals intramolecular protonation of 1, thus generating negative charge on the sulfur atom in the rate-determining step. The formation of a CF3 radical can be thermally induced by internal dissociative electron transfer, its activation energy, ΔF(≠), amounting to as little as 10.8 and 2.8 kcal mol(-1) for reagent 1 and its protonated form 2, respectively. The reduction of the iodine atom by thiophenol occurs either subsequently or in a concerted fashion.

A Rhodium-Pentane Sigma-Alkane Complex: Characterization in the Solid State by Experimental and Computational Techniques.

The pentane σ-complex [Rh{Cy2 P(CH2 CH2 )PCy2 }(η(2) :η(2) -C5 H12 )][BAr(F) 4 ] is synthesized by a solid/gas single-crystal to single-crystal transformation by addition of H2 to a precursor 1,3-pentadiene complex. Characterization by low temperature single-crystal X-ray diffraction (150 K) and SSNMR spectroscopy (158 K) reveals coordination through two Rh⋅⋅⋅H-C interactions in the 2,4-positions of the linear alkane. Periodic DFT calculations and molecular dynamics on the structure in the solid state provide insight into the experimentally observed Rh⋅⋅⋅H-C interaction, the extended environment in the crystal lattice and a temperature-dependent pentane rearrangement implicated by the SSNMR data.

Dividing a complex reaction involving a hypervalent iodine reagent into three limiting mechanisms by ab initio molecular dynamics.

The electrophilic N-trifluoromethylation of MeCN with a hypervalent iodine reagent to form a nitrilium ion, that is rapidly trapped by an azole nucleophile, is thought to occur via reductive elimination (RE). A recent study showed that, depending on the solvent representation, the S(N)2 is favoured to a different extent over the RE. However, there is a discriminative solvent effect present, which calls for a statistical mechanics approach to fully account for the entropic contributions. In this study, we perform metadynamic simulations for two trifluoromethylation reactions (with N- and S-nucleophiles), showing that the RE mechanism is always favoured in MeCN solution. These computations also indicate that a radical mechanism (single electron transfer) may play an important role. The computational protocol based on accelerated molecular dynamics for the exploration of the free energy surface is transferable and will be applied to similar reactions to investigate other electrophiles on the reagent. Based on the activation parameters determined, this approach also gives insight into the mechanistic details of the trifluoromethylation and shows that these commonly known mechanisms mark the limits within which the reaction proceeds.