Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method.

Recent experimental findings reveal nonconventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed non-aromatic fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states and remains absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remains the primary vibrational mode explaining NAF in these systems. In order to simulate larger model systems taking into account the effects of the surrounding environment, in this work we propose using the density functional tight-binding (DFTB) method in combination with non-adiabatic molecular dynamics (NAMD) and the mixed quantum/molecular mechanics (QM/MM) approach. We investigate the mechanism behind NAF in the crystal structure of l-pyroglutamine-ammonium, comparing it with the related nonfluorescent amino acid l-glutamine. Our results extend our previous findings to more realistic systems, demonstrating the efficiency and robustness of the proposed DFTB method in the context of NAMD in biological systems. Furthermore, due to its inherent low computational cost, this method allows for a better sampling of the nonradiative events at the conical intersection which is crucial for a complete understanding of this phenomenon. Beyond contributing to the ongoing exploration of NAF, this work paves the way for future application of this method in more complex biological systems such as amyloid aggregates, biomaterials, and non-aromatic proteins.

How spin state and oxidation number of transition metal atoms determine molecular adsorption: a first-principles case study for NH3.

Understanding how the electronic state of transition metal atoms can influence molecular adsorption on a substrate is of great importance for many applications. Choosing NH3 as a model molecule, its adsorption behavior on defected SnS2 monolayers is investigated. The number of valence electrons n is controlled by decorating the monolayer with different transition metal atoms, ranging from Sc to Zn. Density-Functional Theory based calculations show that the adsorption energy of NH3 molecules oscillates with n and shows a clear odd-even pattern. There is also a mirror symmetry of the adsorption energies for large and low electron numbers. This unique behavior is mainly governed by the oxidation state of the TM ions. We trace back the observed trends of the adsorption energy to the orbital symmetries and ligand effects which affect the interaction between the 3σ orbitals (NH3) and the 3d orbitals of the transition metals. This result unravels the role which the spin state of TM ions plays in different crystal fields for the adsorption behavior of molecules. This new understanding of the role of the electronic structure on molecular adsorption can be useful for the design of high efficiency nanodevices in areas such as sensing and photocatalysis.

Biaxial compressive strain enhances calcium binding and mobility on two-dimensional Sc2C: a density functional theory investigation.

In this work, we investigated calcium binding and diffusion on pristine and biaxially strained 2D Sc2C via density functional theory calculations, for potential applications in calcium-ion batteries (CIBs). We found that 2D Sc2C is metallic under PBE, HSE06, and DFT+U approximation conditions, and thus can be potentially used as an electrode material for CIBs. Results showed that pristine 2D Sc2C adsorbs calcium modestly, with relatively low binding energy on the most stable site (0.38 eV). Interestingly, this value shoots up to -1.94 eV and -3.23 eV at 5% and 10% biaxial compressive strains, respectively. Furthermore, calcium's diffusion energy barrier, which is already low (80 meV) on pristine 2D Sc2C, goes down further (to 35 meV) upon application of median biaxial compressive strain (5%). As a result of the enhanced binding of calcium on strained 2D Sc2C, the maximum stable calcium concentration was also boosted. Consequently, the calculated theoretical specific energy capacity of 2D Sc2C with biaxial compressive strain is higher compared to that of the pristine case (878.29 mA h g-1vs. 1051.84 mA h g-1). The average open circuit voltages of the two cases are high and quite close at 9.3 V (pristine) and 9.0 V (with 5% biaxial compressive strain). Our results demonstrated that biaxial compressive strain could be tapped to improve the properties of 2D MXenes, such as Sc2C, thereby enhancing the battery performance indicators of these materials, such as theoretical specific energy capacity and open circuit voltage. Such findings are of great importance in the emerging new technology of CIBs.

The Role of Water Molecules on Polaron Behavior at Rutile (110) Surface: A Constrained Density Functional Theory Study.

Understanding the behavior of a polaron in contact with water is of significant importance for many photocatalytic applications. We investigated the influence of water on the localization and transport properties of polarons at the rutile (110) surface by constrained density functional theory. An excess electron at a dry surface favors the formation of a small polaron at the subsurface Ti site, with a preferred transport direction along the [001] axis. As the surface is covered by water, the preferred spatial localization of the polarons is moved from the subsurface to the surface. When the water coverage exceeds half a monolayer, the preferred direction of polaron hopping is changed to the [110] direction toward the surface. This characteristic behavior is related to the Ti3d-orbital occupations and crystal field splitting induced by different distorted structures under water coverage. Our work describes the reduced sites that might eventually play a role in photocatalysis for rutile (110) surfaces in a water environment.

The Oxygen Evolution Reaction at MoS2 Edge Sites: The Role of a Solvent Environment in DFT-Based Molecular Simulations.

Density functional theory (DFT) calculations are employed to study the oxygen evolution reaction (OER) on the edges of stripes of monolayer molybdenum disulfide. Experimentally, this material has been shown to evolve oxygen, albeit with low efficiency. Previous DFT studies have traced this low catalytic performance to the unfavourable adsorption energies of some reaction intermediates on the MoS2 edge sites. In this work, we study the effects of the aqueous liquid surrounding the active sites. A computational approach is used, where the solvent is modeled as a continuous medium providing a dielectric embedding of the catalyst and the reaction intermediates. A description at this level of theory can have a profound impact on the studied reactions: the calculated overpotential for the OER is lowered from 1.15 eV to 0.77 eV. It is shown that such variations in the reaction energetics are linked to the polar nature of the adsorbed intermediates, which leads to changes in the calculated electronic charge density when surrounded by water. These results underline the necessity to computationally account for solvation effects, especially in aqueous environments and when highly polar intermediates are present.

Short hydrogen bonds enhance nonaromatic protein-related fluorescence.

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.

DFT insights into electrocatalytic CO2 reduction to methanol on α-Fe2O3(0001) surfaces.

Electrocatalytic reduction of CO2 to manufacture fuels and other useful chemicals is one of the appealing methods to reuse CO2. Herein, electrocatalytic CO2 reduction on a model α-Fe2O3(0001) surface catalyst has been investigated by means of density functional theory. This systematic study, involving 20 reaction intermediates and 63 distinct elementary reaction steps, has allowed the identification of a novel mechanism for the decomposition of the key intermediate *COOH. Methanol is the preferred product, with an overpotential of 0.8 V, over carbon monoxide (CO), formic acid (HCOOH), and formaldehyde (CH2O). Formaldehyde formed on the surface will be converted into methanol. This work demonstrates the need for a complete investigation of possible pathways to find the most favourable one, beyond chemical intuition. Moreover, it suggests that hematite could be an interesting material for CO2 reduction.

Heterostructures of ε-Fe2O3 and α-Fe2O3: insights from density functional theory.

Many materials used in energy devices or applications suffer from the problem of electron-hole pair recombination. One promising way to overcome this problem is the use of heterostructures in place of a single material. If an electric dipole forms at the interface, such a structure can lead to a more efficient electron-hole pair separation and thus prevent recombination. Here we model and study a heterostructure comprised of two polymorphs of Fe2O3. Each one of the two polymorphs, α-Fe2O3 and ε-Fe2O3, individually shows promise for applications in photoelectrochemical cells. The heterostructure of these two materials is modeled by means of density functional theory. We consider both ferromagnetic as well as anti-ferromagnetic couplings at the interface between the two systems. Both individual oxides are insulating in nature and have an anti-ferromagnetic spin arrangement in their ground state. The same properties are found also in their heterostructure. The highest occupied electronic orbitals of the combined system are localized at the interface between the two iron-oxides. The localization of charges at the interface is characterized by electrons residing close to the oxygen atoms of ε-Fe2O3 and electron-holes localized on the iron atoms of α-Fe2O3, just around the interface. The band alignment at the interface of the two oxides shows a type-III broken band-gap heterostructure. The band edges of α-Fe2O3 are higher in energy than those of ε-Fe2O3. This band alignment favours a spontaneous transfer of excited photo-electrons from the conduction band of α- to the conduction band of ε-Fe2O3. Similarly, photo-generated holes are transferred from the valence band of ε- to the valence band of α-Fe2O3. Thus, the interface favours a spontaneous separation of electrons and holes in space. The conduction band of ε-Fe2O3, lying close to the valence band of α-Fe2O3, can result in band-to-band tunneling of electrons which is a characteristic property of such type-III broken band-gap heterostructures and has potential applications in tunnel field-effect transistors.

Structural and dynamical heterogeneities at glutamine-water interfaces.

The behavior of water at the surfaces of solid amino acid crystals has received little attention despite its importance in nucleation processes. In this work, we take a first step to fill this gap by using molecular dynamics simulations to study the structural and dynamical properties of water near the (100), (010) and (001) surfaces of l-glutamine crystals. These highly hydrophilic surfaces serve as excellent model systems for interrogating the behavior of water. Despite having the same molecular composition, water at each surface displays characteristic structural, orientational and dynamical correlations. This behavior is tuned by how the different chemical groups of amino acids make contact with the liquid phase. All three surfaces yield a glassy layer of interfacial water which is reflected in different ways such as the presence of a rotationally arrested layer of water molecules and substantial slow down of the diffusion of water near the interface. By increasing the concentration of molecules in solution, we show that the binding of glutamine molecules to the crystal surface creates a crowded environment involving pockets of trapped water molecules altering the water dynamics in a highly non-trivial manner suggesting that the solvent dynamics may have important implications on crystal nucleation.

Understanding the electrochemical double layer at the hematite/water interface: A first principles molecular dynamics study.

Using first principles molecular dynamics simulations, we probe the electrochemical double layer formed at the interface between the hematite surface and water. We consider two terminations of the (001) surface, viz., the fully hydroxylated (OH) and the stoichiometric (FeO3Fe) termination. We explicitly incorporate the counterions (Na+ and F-) in the solution, and model both specific and nonspecific adsorption of F- ions. We find that F- ions prefer to bind directly to the Fe ions (specific adsorption), with a substantial energy gain (0.75 eV/ion). We investigate the effect of the interface and the counterions on the dipole of individual water molecules. We find significant deviations of +0.2/-0.15 D for dipoles of the first solvation shell water molecules of F-/Na+ ions, respectively. Additionally, the hydration layers at the interface show an enhancement in the dipole moment resulting from stronger hydrogen bonding interactions between the water molecules and surface charged species. Furthermore, we analyze the electrostatic potential profile at the solid/liquid interface as a function of the kind of counterion present in the double layer and compute the capacitance of the compact (Helmholtz) layer. We find that our results (40.3 ± 3.5 µF/cm2 for the OH termination and 51 ± 5 µF/cm2 for the FeO3Fe termination) compare favorably with values reported by potentiometric titration based experimental studies (10-100 µF/cm2).

Characterization of peroxo reaction intermediates in the water oxidation process on hematite surfaces.

We use density functional theory-based calculations to study structural, electronic, and magnetic properties of two key reaction intermediates on a hematite, [Formula: see text]-Fe2O3, photoanode during the solar-driven water splitting reaction. Both intermediates contain an oxygen atom bonded to a surface iron atom. In one case, the adsorbed oxygen also forms a peroxo bond with a lattice oxygen from hematite; in the second case no such bond is formed. Both configurations are energetically equivalent and are related to the overpotential-determining step in the oxygen evolution reaction. The calculated reaction path for the breaking of the peroxo bond shows a barrier of about 0.86 eV for the transformation between the two intermediates. We explain this high barrier with the drastically different electronic and magnetic structure, which we also analyze using maximally localized Wannier functions. Photo-generated electron holes are shown to localize preferentially close to the reaction center at the surface in both configurations. In the case of the oxo species, this localization favors subsequent electron transfer steps during the oxygen evolution cycle. In the case of the peroxo configuration, this fact together with the high barrier for breaking the oxygen-oxygen bond indicates a possible loss mechanism due to hole trapping. Graphical Abstract Calculated spin density at a hematite surface with peroxo intermediate.

Magnetoelectric ϵ-Fe2O3: DFT study of a potential candidate for electrode material in photoelectrochemical cells.

The metastable iron oxide ϵ-Fe2O3 is rare but known for its magnetoelectric properties. While the more common alpha phase has been recognized for a long time as a suitable material for photoelectrochemical cells, its use is limited because of the electron-hole recombination problem when exposed to light. The indirect bandgap of the epsilon phase with its spontaneous polarization may offer a better potential for the application in photoelectrochemistry. Here, we report a detailed study of the electronic and structural features of the epsilon phase of iron oxide, its stability in thin films, and possible water dissociation reactions. Our studies are performed using density functional theory with a Hubbard-U correction. We observe that the stable ϵ-Fe2O3 surfaces favor the dissociation of water. The average difference in the energies of the states when water is adsorbed and when it is dissociated is roughly found to be -0.40 eV. Our results compare with the available experimental results where the epsilon phase is reported to be more efficient for the release of hydrogen from renewable oxygenates when exposed to sunlight.

A computational study on how structure influences the optical properties in model crystal structures of amyloid fibrils.

Amyloid fibrils have been shown to have peculiar optical properties since they can exhibit fluorescence in the absence of aromatic residues. In a recent study, we have shown that proton transfer (PT) events along hydrogen bonds (HBs) are coupled to absorption in the near UV range. Here, we gain more insights into the different types of hydrogen bonding interactions that occur in our model systems and the molecular factors that control the susceptibility of the protons to undergo PT and how this couples to the optical properties. In the case of the strong N-C termini interactions, a nearby methionine residue stabilizes the non-zwitterionic NH2-COOH pair, while zwitterionic NH3+-COO- is stabilized by the proximity of nearby crystallographic water molecules. Proton motion along the hydrogen bonds in the fibril is intimately coupled to the compression of the heavier atoms, similar to what is observed in bulk water. Small changes in the compression of the hydrogen bonds in the protein can lead to significant changes in both the ground and excited state potential energy surfaces associated with PT. Finally, we also reinforce the importance of nuclear quantum fluctuations of protons in the HBs of the amyloid proteins.

Hydrogen divacancy diffusion: a new perspective on H migration in MgH2 materials for energy storage.

The formation and diffusion of pairs of hydrogen vacancies (divacancies) in magnesium hydride is modeled using density functional theory. Compared to the commonly studied case of single hydrogen vacancies, it is found that divacancies are energetically favored over two isolated vacancies. Also, as a function of the diffusion axis considered, the calculated diffusion barriers of divacancies are either smaller or of comparable magnitude with respect to the diffusion barriers of a single vacancy. These findings shed new light on hydrogen transport in MgH2, which is of crucial importance to understand the kinetics of hydrogen take-up and release in this storage material.

Nuclear quantum effects in a HIV/cancer inhibitor: The case of ellipticine.

Ellipticine is a natural product that is currently being actively investigated for its inhibitory cancer and HIV properties. Here we use path-integral molecular dynamics coupled with excited state calculations to characterize the role of nuclear quantum effects on the structural and electronic properties of ellipticine in water, a common biological solvent. Quantum effects collectively enhance the fluctuations of both light and heavy nuclei of the covalent and hydrogen bonds in ellipticine. In particular, for the ellipticine-water system, where the proton donor and acceptor have different proton affinities, we find that nuclear quantum effects (NQEs) strengthen both the strong and the weak H bonds. This is in contrast to what is observed for the cases where the proton affinity of the donors and acceptors is same. These structural fluctuations cause a significant red-shift in the absorption spectra and an increase in the broadening, bringing it into closer agreement with the experiments. Our work shows that nuclear quantum effects alter both qualitatively and quantitatively the optical properties of this biologically relevant system and highlights the importance of the inclusion of these effects in the microscopic understanding of their optical properties. We propose that isotopic substitution will produce a blue shift and a reduction in the broadening of the absorption peak.

A well-scaling natural orbital theory.

We introduce an energy functional for ground-state electronic structure calculations. Its variables are the natural spin-orbitals of singlet many-body wave functions and their joint occupation probabilities deriving from controlled approximations to the two-particle density matrix that yield algebraic scaling in general, and Hartree-Fock scaling in its seniority-zero version. Results from the latter version for small molecular systems are compared with those of highly accurate quantum-chemical computations. The energies lie above full configuration interaction calculations, close to doubly occupied configuration interaction calculations. Their accuracy is considerably greater than that obtained from current density-functional theory approximations and from current functionals of the one-particle density matrix.

Passivation of surface states of α-Fe2O3(0001) surface by deposition of Ga2O3 overlayers: A density functional theory study.

There is a big debate in the community regarding the role of surface states of hematite in the photoelectrochemical water splitting. Experimental studies on non-catalytic overlayers passivating the hematite surface states claim a favorable reduction in the overpotential for the water splitting reaction. As a first step towards understanding the effect of these overlayers, we have studied the system Ga2O3 overlayers on hematite (0001) surfaces using first principles computations in the PBE+U framework. Our computations suggest that stoichiometric terminations of Ga2O3 overlayers are energetically more favored than the bare surface, at ambient oxygen chemical potentials. Energetics suggest that the overlayers prefer to grow via a layer-plus-island (Stranski-Krastanov) growth mode with a critical layer thickness of 1-2 layers. Thus, a complete wetting of the hematite surface by an overlayer of gallium oxide is thermodynamically favored. We establish that the effect of deposition of the Ga2O3 overlayers on the bare hematite surface is to passivate the surface states for the stoichiometric termination. For the oxygen terminated surface which is the most stable termination under photoelectrochemical conditions, the effect of deposition of the Ga2O3 overlayer is to passivate the hole-trapping surface state.

Proton Transfer and Structure-Specific Fluorescence in Hydrogen Bond-Rich Protein Structures.

Protein structures which form fibrils have recently been shown to absorb light at energies in the near UV range and to exhibit a structure-specific fluorescence in the visible range even in the absence of aromatic amino acids. However, the molecular origin of this phenomenon has so far remained elusive. Here, we combine ab initio molecular dynamics simulations and fluorescence spectroscopy to demonstrate that these intrinsically fluorescent protein fibrils are permissive to proton transfer across hydrogen bonds which can lower electron excitation energies and thereby decrease the likelihood of energy dissipation associated with conventional hydrogen bonds. The importance of proton transfer on the intrinsic fluorescence observed in protein fibrils is signified by large reductions in the fluorescence intensity upon either fully protonating, or deprotonating, the fibrils at pH = 0 or 14, respectively. Thus, our results point to the existence of a structure-specific fluorophore that does not require the presence of aromatic residues or multiple bond conjugation that characterize conventional fluorescent systems. The phenomenon may have a wide range of implications in biological systems and in the design of self-assembled functional materials.

On the electronic, structural, and thermodynamic properties of Au supported on α-Fe2O3 surfaces and their interaction with CO.

Extensive first principles calculations are carried out to investigate Au monomers and dimers supported on α-Fe2O3(0001) surfaces in terms of structure optimizations, electronic structure analyses, and ab initio thermodynamics calculations of surface phase diagrams. All computations rely on density functional theory in the generalized gradient approximation (Perdew-Burke-Ernzerhof (PBE)) and account for on-site Coulomb interactions via inclusion of a Hubbard correction (PBE+U). The relative stability of Au monomers/dimers on the stoichiometric termination of α-Fe2O3(0001) decorated with various vacancies (multiple oxygen vacancies, iron vacancy, and mixed iron-oxygen vacancies) has been computed as a function of the oxygen chemical potential. The charge rearrangement induced by Au at the oxide contact is analyzed in detail and discussed. On one hand, ab initio thermodynamics predicts that under O-rich conditions, structures obtained by replacing a surface Fe atom with a Au atom are thermodynamically stable over a wide range of temperatures. On the other hand, the complex of a CO molecule on a Au atom substituting surface Fe atoms is thermodynamically stable only in a much more narrow range of values of the O chemical potential under O-rich conditions. In the case of a Au dimer, under O-rich conditions, supported Au atoms at an O-Fe di-vacancy are more stable. However, upon CO adsorption, the complex of a CO molecule and 2 Au atoms located at a single Fe vacancy is more favorable.

Nitrogen electrochemically reduced to ammonia with hematite: density-functional insights.

Licht et al. (Science, 2014, 345, 637) recently proposed a procedure to synthesize NH3 from N2 and by steam electrolysis in molten hydroxide suspensions of nano-Fe2O3. This highly exciting investigation undoubtedly boosts the hope of the CO2-free and low-cost ammonia industry. To provide insights at the atomistic level into the reduction process of N2, we have carried out a density-functional study on the electrochemical formation of NH3 molecules on hematite(0001) surfaces. By considering associative and dissociative mechanisms, we have identified a reaction path that requires an applied bias of -1.1 V to allow the proton transfer processes to occur downhill. The most energy-demanding step is the addition of the first proton to the adsorbed molecular nitrogen. The computed bias is in good agreement with experimental electrolysis potentials that activate the electric current.