Comprehensive Analysis of Methyl-ß-D-ribofuranoside: A Multifaceted Spectroscopic and Theoretical Approach.

This study presents a comprehensive analysis of the vibrational spectra of methyl-ß-D-ribofuranoside. Employing a combination of inelastic neutron scattering, Raman, and infrared spectroscopy allows for the observation of all modes regardless of the selection rules. The experimental techniques were complemented by density functional theory computational methods using both gas-phase (Gaussian) and solid-state (CRYSTAL, CASTEP) approaches to provide an unambiguous assignment of the defining vibrational features. Two distinct structures of the molecule were identified in the unit cell, differentiated mainly by the orientation of the furanose ring O-H bonds. The low-energy region of the spectrum (<400 cm-1) is dominated by lattice vibrations and functional group rotation, while the midenergy region is dominated by out-of-plane bending motions of the furanose ring (400-900 cm-1) and by C-H bending in the methyl and methylene groups (1400-1600 cm-1). The high-energy region (>2800 cm-1) encompasses the C-H and O-H stretching modes and offers convincing evidence of at least one H-bonding interaction between the two structures of methyl-ß-D-ribofuranoside.

Theoretical Study on the Optoelectronic Properties of Merocyanine-Dyes.

Merocyanines, as prototypes of highly polar π-conjugated molecules, have been intensively investigated for their self-assembly and optoelectronic properties, both experimentally and theoretically. However, an accurate description of their structural and electronic properties remains challenging for quantum-chemical methods. We assessed several theoretical approaches, TD-DFT, GW-BSE, STEOM-DLPNO-CCSD, and CASSCF/NEVPT2-FIC for their reliability in reproducing optoelectronic properties of a series of donor/acceptor (D/A) merocyanines, focusing on the first excitation energy. Additionally, we tested an all-electron perturbative method based on time-dependent coupled-perturbed density functional theory, denoted as TDCP-DFT. Particular focus was set on direct and indirect solvent effects, which affect excited-state energies by electrostatic interaction and molecular geometry. The molecular configuration space was sampled at the semiempirical tight-binding level. Our results corroborate previous investigations, showing that the S0 - S1 excitation energy strongly depends on the merocyanine molecular structure and the dielectric constant of the solvent. We found significant effects of the polar solution environment on the geometry of the merocyanines, which strongly affect the calculated excitation energies. Taking these effects into account, the best agreement between calculated and measured excitation energies was obtained with TDCP-DFT and GW-BSE. We also calculated excitation energies of molecular crystals at the TDCP-DFT level and compared the results to the corresponding monomers.

Machine Learning Electron Density Prediction Using Weighted Smooth Overlap of Atomic Positions.

Having access to accurate electron densities in chemical systems, especially for dynamical systems involving chemical reactions, ion transport, and other charge transfer processes, is crucial for numerous applications in materials chemistry. Traditional methods for computationally predicting electron density data for such systems include quantum mechanical (QM) techniques, such as density functional theory. However, poor scaling of these QM methods restricts their use to relatively small system sizes and short dynamic time scales. To overcome this limitation, we have developed a deep neural network machine learning formalism, which we call deep charge density prediction (DeepCDP), for predicting charge densities by only using atomic positions for molecules and condensed phase (periodic) systems. Our method uses the weighted smooth overlap of atomic positions to fingerprint environments on a grid-point basis and map it to electron density data generated from QM simulations. We trained models for bulk systems of copper, LiF, and silicon; for a molecular system, water; and for two-dimensional charged and uncharged systems, hydroxyl-functionalized graphane, with and without an added proton. We showed that DeepCDP achieves prediction R2 values greater than 0.99 and mean squared error values on the order of 10-5e2 Å-6 for most systems. DeepCDP scales linearly with system size, is highly parallelizable, and is capable of accurately predicting the excess charge in protonated hydroxyl-functionalized graphane. We demonstrate how DeepCDP can be used to accurately track the location of charges (protons) by computing electron densities at a few selected grid points in the materials, thus significantly reducing the computational cost. We also show that our models can be transferable, allowing prediction of electron densities for systems on which it has not been trained but that contain a subset of atomic species on which it has been trained. Our approach can be used to develop models that span different chemical systems and train them for the study of large-scale charge transport and chemical reactions.

In Silico Demonstration of Fast Anhydrous Proton Conduction on Graphanol.

Development of new materials capable of conducting protons in the absence of water is crucial for improving the performance, reducing the cost, and extending the operating conditions for proton exchange membrane fuel cells. We present detailed atomistic simulations showing that graphanol (hydroxylated graphane) will conduct protons anhydrously with very low diffusion barriers. We developed a deep learning potential (DP) for graphanol that has near-density functional theory accuracy but requires a very small fraction of the computational cost. We used our DP to calculate proton self-diffusion coefficients as a function of temperature, to estimate the overall barrier to proton diffusion, and to characterize the impact of thermal fluctuations as a function of system size. We propose and test a detailed mechanism for proton conduction on the surface of graphanol. We show that protons can rapidly hop along Grotthuss chains containing several hydroxyl groups aligned such that hydrogen bonds allow for conduction of protons forward and backward along the chain without hydroxyl group rotation. Long-range proton transport only takes place as new Grotthuss chains are formed by rotation of one or more hydroxyl groups in the chain. Thus, the overall diffusion barrier consists of a convolution of the intrinsic proton hopping barrier and the intrinsic hydroxyl rotation barrier. Our results provide a set of design rules for developing new anhydrous proton conducting membranes with even lower diffusion barriers.

Combined Deep Learning and Classical Potential Approach for Modeling Diffusion in UiO-66.

Modeling of diffusion of adsorbates through porous materials with atomistic molecular dynamics (MD) can be a challenging task if the flexibility of the adsorbent needs to be included. This is because potentials need to be developed that accurately account for the motion of the adsorbent in response to the presence of adsorbate molecules. In this work, we show that it is possible to use accurate machine learning atomistic potentials for metal-organic frameworks in concert with classical potentials for adsorbates to accurately compute diffusivities though a hybrid potential approach. As a proof-of-concept, we have developed an accurate deep learning potential (DP) for UiO-66, a metal-organic framework, and used this DP to perform hybrid potential simulations, modeling diffusion of neon and xenon through the crystal. The adsorbate-adsorbate interactions were modeled with Lennard-Jones (LJ) potentials, the adsorbent-adsorbent interactions were described by the DP, and the adsorbent-adsorbate interactions used LJ cross-interactions. Thus, our hybrid potential allows for adsorbent-adsorbate interactions with classical potentials but models the response of the adsorbent to the presence of the adsorbate through near-DFT accuracy DPs. This hybrid approach does not require refitting the DP for new adsorbates. We calculated self-diffusion coefficients for Ne in UiO-66 from DFT-MD, our hybrid DP/LJ approach, and from two different classical potentials for UiO-66. Our DP/LJ results are in excellent agreement with DFT-MD. We modeled diffusion of Xe in UiO-66 with DP/LJ and a classical potential. Diffusion of Xe in UiO-66 is about a factor of 30 slower than that of Ne, so it is not computationally feasible to compute Xe diffusion with DFT-MD. Our hybrid DP-classical potential approach can be applied to other MOFs and other adsorbates, making it possible to use an accurate DP generated from DFT simulations of an empty adsorbent in concert with existing classical potentials for adsorbates to model adsorption and diffusion within the porous material, including adsorbate-induced changes to the framework.

The binding of atomic hydrogen on graphene from density functional theory and diffusion Monte Carlo calculations.

In this work, density functional theory (DFT) and diffusion Monte Carlo (DMC) methods are used to calculate the binding energy of a H atom chemisorbed on the graphene surface. The DMC value of the binding energy is about 16% smaller in magnitude than the Perdew-Burke-Ernzerhof (PBE) result. The inclusion of exact exchange through the use of the Heyd-Scuseria-Ernzerhof functional brings the DFT value of the binding energy closer in line with the DMC result. It is also found that there are significant differences in the charge distributions determined using PBE and DMC approaches.

Neutron Scattering Techniques for Studying Metal Complexes in Aqueous Solution.

Neutron scattering combined with ab initio calculations provides a powerful tool for studying metal complexes in different solvents and, particularly, in water. The majority of traditional characterization techniques in catalysis provide only limited information on homogeneous catalytic processes. Neutron scattering, on the other hand, thanks to its sensitivity to hydrogen atoms, and therefore water molecules, can be used to build detailed models of reaction paths and to observe, at a molecular level, the influence of solvent molecules on a catalytic process. In this Mini-Review we describe several examples on how neutron scattering combined with ab initio calculations can be used to examine the nature of the interaction of water molecules with catalytically active metal complexes in solution.

Ab Initio Molecular Dynamics Simulations of the SN1/SN2 Mechanistic Continuum in Glycosylation Reactions.

We report a computational approach to evaluate the reaction mechanisms of glycosylation using ab initio molecular dynamics (AIMD) simulations in explicit solvent. The reaction pathways are simulated via free energy calculations based on metadynamics and trajectory simulations using Born-Oppenheimer molecular dynamics. We applied this approach to investigate the mechanisms of the glycosylation of glucosyl α-trichloroacetimidate with three acceptors (EtOH, i-PrOH, and t-BuOH) in three solvents (ACN, DCM, and MTBE). The reactants and the solvents are treated explicitly using density functional theory. We show that the profile of the free energy surface, the synchronicity of the transition state structure, and the time gap between leaving group dissociation and nucleophile association can be used as three complementary indicators to describe the glycosylation mechanism within the SN1/SN2 continuum for a given reaction. This approach provides a reliable means to rationalize and predict reaction mechanisms and to estimate lifetimes of oxocarbenium intermediates and their dependence on the glycosyl donor, acceptor, and solvent environment.

Density-functional theory models of Fe(iv)O reactivity in metal-organic frameworks: self-interaction error, spin delocalisation and the role of hybrid exchange.

We study the reactivity of Fe(iv)O moieties supported by a metal-organic framework (MOF-74) in the oxidation reaction of methane to methanol using all-electron, periodic density-functional theory calculations. We compare results concerning the electronic properties and reactivity obtained using two hybrid (B3LYP and sc-BLYP) and two standard generalised gradient corrected (PBE and BLYP) semi-local density functional approximations. The semi-local functionals are unable to reproduce the expected reaction profiles and yield a qualitatively incorrect representation of the reactivity. Non-local hybrid functionals provide a substantially more reliable description and predict relatively modest (ca. 60 kJ mol-1) reaction energy barriers for the H-atom abstraction reaction from CH4 molecules. We examine the origin of these differences and we highlight potential means to overcome the limitations of standard semi-local functionals in reactivity calculations in solid-state systems.

Solvation of Na? in the Sodide Solution, LiNa?10MeNH2.

Alkalides, the alkali metals in their ?1 oxidation state, represent some of the largest and most polarizable atomic species in condensed phases. This study determines the solvation environment around the sodide anion, Na?, in a system of co-solvated Li+. We present isotopically varied total neutron scattering experiments alongside empirical potential structure refinement and ab initio molecular dynamics simulations for the alkali?alkalide system, LiNa?10MeNH2. Both local coordination modes and the intermediate range liquid structure are determined, which demonstrate that distinct structural correlations between cation and anion in the liquid phase extend beyond 8.6 ?. Indeed, the local solvation around Na? is surprisingly well defined with strong solvent orientational order, in contrast to the classical description of alkalide anions not interacting with their environment. The ion-paired Li(MeNH2)4+?Na? species appears to be the dominant alkali?alkalide environment in these liquids, whereby Li+ and Na? share a MeNH2 molecule through the amine group in their primary solvation spheres.

Electronic structure and reactivity of Fe(iv)oxo species in metal-organic frameworks.

We investigate the potential use of Fe(iv)oxo species supported on a metal-organic framework in the catalytic hydroxylation of methane to produce methanol. We use periodic density-functional theory calculations at the 6-31G**/B3LYP level of theory to study the electronic structure and chemical reactivity in the hydrogen abstraction reaction from methane in the presence of Fe(iv)O(oxo) supported on MOF-74. Our results indicate that the Fe(iv)O moiety in MOF-74 is characterised by a highly reactive (quintet) ground-state, with a distance between Fe(iv) and O(oxo) of 1.601 Å, consistent with other high-spin Fe(iv)O inorganic complexes in the gas phase and in aqueous solution. Similar to the latter systems, the highly electrophilic character (and thus the reactivity) of Fe(iv)O in MOF-74 is determined by the presence of a low-lying anti-bonding virtual orbital (3σ*), which acts as an electron acceptor in the early stages of the hydrogen atom abstraction from methane. We estimate an energy barrier for hydrogen abstraction of 50.77 kJ mol-1, which is comparable to the values estimated in other gas-phase and hydrated Fe(iv)O-based complexes with the ability to oxidise methane. Our findings therefore suggest that metal-organic frameworks can provide suitable supports to develop new solid-state catalysts for organic oxidation reactions.

Influence of charge transfer on the isomerisation of stilbene derivatives for application in cancer therapy.

The photoisomerisation of non-toxic trans-combretastatin CA4 to its cytotoxic cis isomer demonstrates the high potential of this and similar compounds for localised cancer therapy. The introduction of intramolecular charge-transfer character by altering the substituents of combretastatin systems opens up possibilities to tailor these stilbene derivatives to the special demands of anticancer drugs. In this TDDFT study we explore how absorption wavelengths for both the trans and cis isomers can be red shifted to enable deeper light penetration into tissue and how the trans → cis and cis → trans isomerisations are affected by charge transfer effects to different degrees.

Time-Dependent Density-Functional Theory for Modeling Solid-State Fluorescence Emission of Organic Multicomponent Crystals.

We describe the approach for modeling solid-state fluorescence spectra of organic crystalline materials, using the recent implementation of time-dependent density-functional theory within the plane-wave/pseudopotential code CASTEP. The method accuracy is evaluated on a series of organic cocrystals displaying a range of emission wavelengths. In all cases the calculated spectra are in good to excellent agreement with experiment. The ability to precisely model the emission spectra offers novel insight into the role of intermolecular interactions and crystal packing on solid-state luminescence of organic chromophores, allowing the possibility of in silico design of organic luminescent materials.

Chaotic Soliton Dynamics in Photoexcited trans-Polyacetylene.

We study the photogeneration of topological solitons in trans-polyacetylene and their time evolution using ab initio excited-state dynamics. The system is excited to the optically allowed 1(1)Bu state, and the atoms are then propagated classically using quantum mechanical forces computed using hybrid time-dependent density functional theory (TD-DFT). A soliton/antisoliton pair nucleates spontaneously and creates two independent solitons moving at constant velocity, similar to simulations based on uncorrelated lattice models like the Su-Schrieffer-Heeger (SSH) Hamiltonian [Su, W. P.; Schrieffer, J. R.; Heeger, A. J. Phys. Rev. Lett. 1979, 42, 1698]. At T = 0, the solitons coalesce into bound pairs with a two-soliton functional form, whereas chaotic dynamics, in the form of 2-bounce resonances, is observed at soliton/antisoliton collisions at T ≠ 0. This behavior is related to the onset of a strong correlation regime at short intersoliton distance, which is not accounted for by SSH simulations.

Study of the interaction of water with the aqua-soluble dimeric complex [RuCp(PTA)2-µ-CN-1κC:2κ(2)N-RuCp(PTA)2](CF3SO3) (PTA = 1,3,5-triaza-7-phosphaadamantane) by neutron and X-ray diffraction in solution.

The study of an aqueous solution of [RuCp(PTA)2-µ-CN-1κC:2κ(2)N-RuCp(PTA)2](CF3SO3) by neutron and X-ray diffraction revealed surprising details as to how the water molecules interact with the complex and affect its properties. The present communication demonstrates the applicability of sophisticated scattering techniques in combination with theoretical calculations to the study of coordination compounds in aqueous solution.

Linking electronic and molecular structure: insight into aqueous chloride solvation.

Aqueous chloride solutions are ubiquitous and diverse; systems include sea water, atmospheric droplets, geological processes and biological organisms. However, despite considerable effort, a complete microscopic model of the hydration shell, and local electronic structure of the aqueous chloride ion and its dynamics has not been established. In this work we employ ab initio molecular dynamics to study an aqueous chloride solution. In particular, local solvation events and the electronic structure around the chloride ion are interrogated. We employ the Effective Molecular Orbital (EMO) method which partitions the electronic structure into solute and solvent components while maintaining a rigorous quantum mechanical description of both. Movement of the chloride highest occupied molecular orbital (HOMO) energy within the valence band of water is revealed. The chloride ion has little impact on the average water electronic structure, however, locally the electronic effect of the chloride ion is significant. With the Hofmeister series in mind we find that the electronic effect of the chloride ion extends beyond the first solvation shell, but not beyond the edge of the second solvation shell. The chloride ion sits near the centre of the Hofmeister series because of an essential degeneracy between water-water and water-Cl H-bonding and because of a strong similarity in the water and chloride electronic structure. The chloride ion prefers to be symmetrically solvated by six H-bonding water molecules, however, the chloride HOMO energy and the coordination number oscillate in response to local fluctuations driven by the dynamics of the bulk water. A combined structural and electronic analysis has led to a distinction between two types of water molecule within the first solvation shell, those that H-bond to the chloride ion, and those that remain local (i.e. within the first solvation shell) but which H-bond to other water molecules. There are indications that these exhibit different dynamics with respect to residence times and rotational vs. translational motion.

A frontier orbital study with ab initio molecular dynamics of the effects of solvation on chemical reactivity: solvent-induced orbital control in FeO-activated hydroxylation reactions.

Solvation effects on chemical reactivity are often rationalized using electrostatic considerations: the reduced stabilization of the transition state results in higher reaction barriers and lower reactivity in solution. We demonstrate that the effect of solvation on the relative energies of the frontier orbitals is equally important and may even reverse the trend expected from purely electrostatic arguments. We consider the H abstraction reaction from methane by quintet [EDTAH(n)·FeO]((n-2)+), (n = 0-4) complexes in the gas phase and in aqueous solution, which we examine using ab initio thermodynamic integration. The variation of the charge of the complex with the protonation of the EDTA ligand reveals that the free energy barrier in gas phase increases with the negative charge, varying from 16 kJ mol(-1) for [EDTAH4·FeO](2+) to 57 kJ mol(-1) for [EDTAHn·FeO](2-). In aqueous solution, the barrier for the +2 complex (38 kJ mol(-1)) is higher than in gas phase, as predicted by purely electrostatic arguments. For the negative complexes, however, the barrier is lower than in gas phase (e.g., 45 kJ mol(-1) for the -2 complex). We explain this increase in reactivity in terms of a stabilization of the virtual 3σ* orbital of FeO(2+), which acts as the dominant electron acceptor in the H-atom transfer from CH4. This stabilization originates from the dielectric screening caused by the reorientation of the water dipoles in the first solvation shell of the charged solute, which stabilizes the acceptor orbital energy for the -2 complex sufficiently to outweigh the unfavorable electrostatic destabilization of the transition-state relative to the reactants in solution.

Simulating the pyrolysis of polyazides: a mechanistic case study of the [[P(N3)6]- anion.

Pyrolysis of the homoleptic azido complex [P(N(3))(6)](-) was simulated using density functional theory based molecular dynamics and analyzed further using electronic-structure calculations in atom-centered basis sets to calculate the geometries and electronic structures. Simulations at 600 and 1200 K predict a thermally induced and, on the simulation time scale, irreversible dissociation of an azido anion. The ligand loss is accompanied by a barrierless (free-energy) transition of the geometry of the complex coordination sphere from octahedral to trigonal bipyramidal. [P(N(3))(5)] is fluxional and engages in pseudorotation via a Berry mechanism.

An abiotic analogue of the diiron(IV)oxo "diamond core" of soluble methane monooxygenase generated by direct activation of O2 in aqueous Fe(II)/EDTA solutions: thermodynamics and electronic structure.

We study the generation of a dinuclear Fe(IV)oxo species, [EDTAH·FeO·OFe·EDTAH](2-), in aqueous solution at room temperature using Density Functional Theory (DFT) and Ab Initio Molecular Dynamics (AIMD). This species has been postulated as an intermediate in the multi-step mechanism of autoxidation of Fe(II) to Fe(III) in the presence of atmospheric O(2) and EDTA ligand in water. We examine the formation of [EDTAH·FeO·OFe·EDTAH](2-) by direct cleavage of O(2), and the effects of solvation on the spin state and O-O cleavage barrier. We also study the reactivity of the resulting dinuclear Fe(IV)oxo system in CH(4) hydroxylation, and its tendency to decompose to mononuclear Fe(IV)oxo species. The presence of the solvent is shown to play a crucial role, determining important changes in all these processes compared to the gas phase. We show that, in water solution, [EDTAH·FeO·OFe·EDTAH](2-) (as well as its precursor [EDTAH·Fe·O(2)·Fe·EDTAH](2-)) exists as stable species in a S = 4 ground spin state when hydrogen-bonded to a single water molecule. Its structure comprises two facing Fe(IV)oxo groups, in an arrangement similar to the one evinced for the active centre of intermediate Q of soluble Methane Monooxygenase (sMMO). The inclusion of the water molecule in the complex decreases the overall symmetry of the system, and brings about important changes in the energy and spatial distribution of orbitals of the Fe(IV)oxo groups relative to the gas phase. In particular, the virtual 3σ* orbital of one of the Fe(IV)oxo groups experiences much reduced repulsive orbital interactions from ligand orbitals, and its consequent stabilisation dramatically enhances the electrophilic character of the complex, compared to the symmetrical non-hydrated species, and its ability to act as an acceptor of a H atom from the CH(4) substrate. The computed free energy barrier for H abstraction is 28.2 kJ mol(-1) (at the BLYP level of DFT), considerably below the gas phase value for monomeric [FeO·EDTAH](-), and much below the solution value for the prototype hydrated ferryl ion [FeO(H(2)O)(5)](2+).

O2 activation in a dinuclear Fe(II)/EDTA complex: spin surface crossing as a route to highly reactive Fe(IV)oxo species.

We study the cleavage of O2 in gas phase [(EDTAH)Fe(O2)Fe(EDTAH)]2-, a proposed intermediate in the aqueous Fe(II)-to-Fe(III) autoxidation reaction in the presence of atmospheric dioxygen and EDTA ligand. The role of the exchange coupling between the locally high-spin Fe centers in the O-O dissociation is investigated. Using results from broken symmetry (BS) density functional theory (DFT) calculations, we show that the system can be modeled as two high-spin (HS) S = 5/2 Fe(III) d5 centers coupled through a bridging peroxo O2(2-) ligand, consistent with hypotheses advanced in the literature. We show that in this electronic configuration the O-O cleavage reaction is forbidden by (spin) symmetry. Dissociation of the O2(2-) group to the product ground state may only take place if the system is allowed to undergo a transition to a state of lower spin multiplicity (S = 4) as the O-O bond is stretched. We show that the exchange coupling between the two Fe ions in [(EDTAH)Fe(O2)Fe(EDTAH)]2- plays only a minor role in defining the chemistry of O2 activation in this system. The peroxo/oxo interconversion involves a state outside the Heisenberg spin ladder of the initial S = 5 state. In this S = 4 state, the dinuclear complex evolves to two oxo complexes, [EDTAH x Fe(IV)O]-, with an overall energy barrier of only approximately 86 kJ mol(-1). According to recent theoretical work, the latter species are exceptionally strong oxidants, making them ideal candidate catalysts for organic oxidations (including C-H bond hydroxylation). We highlight the (spin) symmetry forbidden nature of the reaction on the S = 5 surface and its symmetry allowed character in the electronic configuration with S = 4.