Puckering Distortion Research Articles

New insight into the photoinduced wavelength dependent decay mechanisms of the ferulic acid system on the excited states.

The ferulic acid (FA) is a kind of phenolic acid widely exists in nature plants. Apart from its medicinal values, the FA is also widely applied in cosmetic industry. Recently, it was found to have potential applications in commercial sunscreens for its strong photostability and photoprotection property from harmful UV rays. Such excellent property lies in the ultrafast decay process of the FA system when exposure to the UV light, but the underlying detailed relaxation pathway is still less clear-cut. In the current work, high-level ab initio electronic structure calculations and on-the-fly surface hopping dynamics simulations were employed to explore the photoinduced decay mechanism of the FA system both on the S1 and S3 states in the gas phase. The results provide a reasonable explanation for the wavelength dependent decay patterns of FA system. The S1 state decay pathway is driven by a re-emission process to dissipate excess energy. While for the S3 state deactivation process, the pathway is dominated by a non-adiabatic process driven by the internal conversion process through the conical intersection regions. A S3-S1-S0 two step decay pattern is proposed, and the pathways are mainly driven by a puckering distortion motion of the aromatic ring and a twisting motion around the bridging double bond. The calculation results contribute to a better understanding of detailed dynamics behavior of the FA deactivation process, and provide theoretical guidance for further design of efficient and environmentally friendly sunscreens.

Current Status of Carbohydrates Information in the Protein Data Bank.

Carbohydrates are well known for their physicochemical, biological, functional, and therapeutic characteristics. Unfortunately, their chemical nature imposes severe challenges for the structural elucidation of these phenomena, impairing not only the depth of our understanding of carbohydrates but also the development of new biotechnological and therapeutic applications based on these molecules. In the recent past, the amount of structural information, obtained mainly from X-ray crystallography, has increased progressively, as well as its quality. In this context, the current work presents a global analysis of the carbohydrate information available in the Protein Data Bank (PDB). From high quality structures, it is clear that most of the data are highly concentrated on a few sets of residue types, on their monosaccharidic forms, and connected by a small diversity of glycosidic linkages. The geometries of these linkages can be mostly associated with the types of linkages instead of residues, while the level of puckering distortion was characterized, quantified, and located in a pseudorotational equilibrium landscape, not only to local minima but also to transitional states. These qualitative and quantitative analyses offer a global picture of the carbohydrate structural content in the PDB, potentially supporting the building of new models for carbohydrate-related biological phenomena at the atomistic level, including new developments on force field parameters.

Does the wavelength dependent photoisomerization process of the p‑coumaric acid come out from the electronic state dependent pathways?

Similar to the anion photoactive yellow protein (PYP) chromophore, the neutral form of the PYP chromophore was also found to exhibit a the wavelength-dependent photoisomerization quantum yield. The isomerization quantum yield increases with the increasing excitation energy on the S1 state, while decreases when being excited to the S2 state. Does this wavelength dependent product yield come out from the specific reaction pathways of the S1 and S2 states? This would mean that, the relaxation pathway of the S2 state is distinct from that of the S1 state and does not involve twisting motion. Does it break Kasha's rule by exhibiting a direct transition from the S2 state to the ground state? The underlying mechanism needs further in. In this article, we employed the on-the-fly dynamics simulations and static electronic structure calculations to reveal the deactivation mechanism of the neutral form of the PYP chromophore. Our results indicated that the CC twisting motion dominates the S1 state decay process. In contrast, for the decay process of the S2 state, an ultrafast transition from the S2 to the S1 state through a planar conical intersection is observed, and the excess energy activates a new reaction channel to the ground state characterized by a puckering distortion of the ring. This pathway competes with the photoisomerization channel. No direct transition from S2 to S0 is observed, hence Kasha's rule is valid for this process. Our calcualtions can provide a reasonable explanation of the wavelength-dependent isomerization quantum yield of neutral PYP chromophore, and we hope it can provide theoretical foundations for comparing the effect of protonation state on the dynamcal behaviors of PYP chromophore.

The effect of octahedral distortions on the electronic properties and magnetic interactions in O3 NaTMO2 compounds (TM = Ti-Ni & Zr-Pd).

The interplay between the coordination environment and magnetic properties in O3 layered sodium transition metal oxides (NaTMO2) is a fascinating and complex problem. Through detailed and comprehensive density functional investigations on O3 NaTMO2 compounds, we demonstrate that the TM ions in O3 NaMnO2, NaFeO2 and NaCoO2 adopt a high spin state. Structurally, NaMnO2 and NaPdO2 undergo Jahn–Teller distortions while NaNbO2 undergoes puckering distortion. Furthermore, in addition to Jahn–Teller distortion, NaPdO2 exhibits charge disproportionation as it contains Pd2+, Pd3+ and Pd4+ species. These distortions stabilize the inter-plane ferromagnetism. Additionally, the inter-plane ferromagnetic coupling is stabilized by kinetic p–d exchange mechanism in undistorted NaCoO2, NaNiO2 and NaTcO2. The intra-plane coupling in this family of compounds on the other hand was found to be generally weak. Only NaMnO2, NaNiO2 and NaTcO2 are predicted to show bulk ferromagnetism with estimated Curie temperatures below ∼50 K.

Buckling on stanene: the role played by spin-orbit coupling and pseudo Jahn-Teller effect

ABSTRACTTwo-dimensional group IV layers beyond graphene, as silicene, germanene and the Sn-based stanene, have been recently synthesized by molecular beam epitaxy. Density Functional Theyory (DFT) calculations predict low-buckled structures for these 2D nanosheets, with a hexagonal honeycomb conformation, typical of the graphene-like surfaces. The buckling parameter δ increases from Si to Sn-based layers, with a maximum predicted of 0.92 Å for stanene. High-buckled structures for these materials resulted to be unstable. We have previously shown that for silicene and germanene, the origin of the buckled structure resides on the pseudo Jahn-Teller puckering distortion, resulting from non-adiabatic effects. It has been shown that hexagermabenzene, the single hexagonal unit of germanene, is subject to a strong vibronic coupling whose origin is the pseudo Jahn-Teller effect. This coupling resulted to be around ten times larger than the one obtained for hexasilabenzene. For stanene, an additional effect needs to be considered to understand the origin of buckling: the spin-orbit coupling (SOC). This SOC contributes to open an electronic band gap, enabling the use of these layers as nanoelectronic components. In this work, we present an analysis based on DFT in the Zeroth-Order Regular Approximation (ZORA) for both scalar relativistic and spin-orbit versions that quantify the influence of the spin-orbit coupling in the puckering of Sn6H6. Also, under the linear vibronic coupling model between the ground and the lowest excited states, we present the pseudo Jahn-Teller contribution. The scalar ZORA approximation is used to perform time-dependent DFT calculations to incorporate the low-energy excitations contributions. Our model leads to the determination of the coupling constants and predicts simultaneously the Adiabatic Potential Energy Surface behavior for the ground and excited states around the maximum symmetry point. These values allow us to compare the Jahn-Teller relevance in buckling with the other group IV layers.

Strong Pseudo Jahn—Teller Effect on the Single Hexagonal Unit of Germanene

ABSTRACTGermanene, the 2D graphene-like Ge nanosheet, has been recently the subject of many theoretical studies and experimental attempts to synthesize it on Ag(111), Au(111) and Pt(111) surfaces. The experimental and theoretical evidences of germanene show a 2D continuous honeycomb layer with a buckled conformation. Density functional theory (DFT) calculations have predicted a larger buckling for germanene than silicene whose origin is also associated with a pseudo Jahn–Teller (PJT) effect. In this work we show that despite the fact that both, silicene and germanene possess a buckled conformation with a PJT origin, their vibronic coupling have different origins. The analysis is based on the PJT puckering instability of the hexagermabenzene molecule, the single hexagonal unit of germanene. This is done through the linear vibronic coupling model between the ground and the lowest excited states, which leads to a puckering distortion of the more symmetric cluster. We study both, the multilevel superposition vibronic model and possible mixing of excited states of different irreducible representations, which have been used to show the origin of similar structural transitions in hexagonal silicon and gold ring systems respectively. We show that contrary to other cases with one six-member rings, for the hexagermabenzene molecule a mixture of both the multilevel PJT and a ground state coupling with two quasi-degenerate excited states is necessary for a satisfactory explanation of puckering. Our model allows a determination of the coupling constants and predicts simultaneously the Adiabatic Potential Energy Surface (APES) behavior for the ground and excited states around the maximum symmetry point. The analysis is based on a scalar relativistic DFT and time-dependent DFT (TD-DFT) calculations in the Zero Order Regular Approximation (ZORA) using the B3LYP hybrid functional.

Pseudo Jahn–Teller effect in the decasilanaphthalene molecule: Towards the origin of the buckling in silicene

It has been theoretically predicted that the ground state of free-standing silicene has a periodic buckled structure, whose origin is attributed to the puckering distortion on the individual six-member rings. In this work we present a theoretical analysis of the vibronic instability of the ground state of two hexagonal silicene units (decasilanaphthalene molecule) of D2h planar symmetry to the 3D puckered structure with C2h symmetry. Both, the multilevel superposition vibronic model and possible mixing of excited states of different irreducible representations are studied. We show that contrary to the one six-member ring case, for the decasilanaphthalene molecule, the multilevel PJT does not provide a satisfactory explanation for puckering and a proper description is given by a ground state coupling with two quasi-degenerate excited states. Hence a simple extrapolation of the origin of the puckering distortion in silicene from one to n-hexagonal components is not straightforward.

Nonadiabatic structure instability of planar hexagonal gold cluster cation Au7 and its spectral signature

Determining the structure for gold nanoclusters at which the 2D–3D transition occurs has been a challenging problem for both theoretical and experimental studies. For gold cation clusters, quantum chemistry calculations have produced controversial results concerning the last most stable planar structure, some indicating that corresponds to n = 7, whereas others conclude that at this value, the structure is already 3D. Experimentally, ion mobility spectroscopy measurements, assisted by DFT calculations, have been interpreted as a planar structure for Au7+. Here, we show that the usually assumed 2D non-degenerate ground state cluster structure for Au7+ with D6h symmetry is unstable against a puckering distortion, ending in a 3D stable structure with D3d symmetry. The analysis is based on the pseudo Jahn–Teller effect through vibronic coupling between the ground state and two excited states. This structure presents, in average, the same surface area than the 2D, being therefore compatible with experimental results. We discuss the effects the vibronic coupling would have on Raman, IR and UV-vis spectra. The study is based on a scalar and spin orbit relativistic DFT calculation in the Zero Order Regular Approximation (ZORA).

Electronic and Bonding Properties of BaGaGeH: Hydrogen-induced Metal-insulator Transition from the AlB2-type BaGaGe Precursor

The hydrogenation of AlB2-type BaGaGe exhibits a metal to insulator (MI) transition, inducing a puckering distortion of the original hexagonal [GaGe] layers. We investigate the electronic structure changes associated with the hydrogen-induced MI transition, using extended Huckel tight-binding band calculations. The results indicate that hydrogen incorporation in the precursor BaGaGe is characterized by an antibonding interaction of π on GaGe with hydrogen 1s and the second-order mixing of the singly occupied antibonding π* orbital into it, through Ga-H bond formation. As a result, the fully occupied bonding π band in BaGaGe changes to a weakly dispersive band with Ge pz (lone pair) character in the hydride, which becomes located just below the Fermi level. The Ga-Ge bonds within a layered polyanion are slightly weakened by hydrogen incorporation. A rationale for this is given.

Static relaxations of puckering distortions in intercalated layered solids

Layered solids have been qualitatively characterized according to their transverse layer rigidity with respect to point-like puckering distortions. In this scheme graphite is a ‘floppy’ layer system, layered aluminosilicates contain ‘rigid’ layers and layer dichalcogenides fall between these extremes. The primary signature of layer rigidity is the dependence of the basal spacing, d( x), on composition, x, in a ternary systems A 1− x B x L where L represents the host layers while A and B are distinct guest species with radii r A < r B. Previous attempts to quantify the layer rigidity (i.e. account for d( x)) using models which employed infinitely rigid layers have been singularly unsuccessful. In the present paper a one-parameter finite layer rigidity model, which yields an extremely good fit to the composition dependent basal spacing of a wide variety of layered solids which includes the floppy and rigid extremes, is described. In this model, a healing length is introduced to quantify the static spatial relaxation of a point-like puckering distortion. Both a discrete and continuous version of the model are presented and shown to yield equivalent results. It is found that, as expected, the more rigid the host layer, the larger the healing length, the values of which are deduced for several important layered solids.

Local Density Approximation Total Energy Calculations for Silica and Titania Structure and Defects

Theoretical structural predictions are presented for three polymorphs of silica (α‐quartz, α‐cristobalite, and stishovite) and the rutile structure of titania. Several defects within the silica system (the oxygen vacancy, a puckering distortion in quartz with no oxygen vacancy, and titanium in silica) are also studied. These ab initio studies are conducted using the local density approximation for electronic structure and total energies and are implemented using some very recent advances in improved pseudopotentials and energy minimization algorithms. Results include two metastable conformations of the oxygen vacancy in silica, similar Si—O and Ti—O bond energies, and equilibrium structures of several defects.

Relaxation effects in the vibrations of a lithium fluoride surface

The vibrational frequencies of a 15-layer slab are calculated for a simple shell model of lithium fluoride, and the surface modes occurring are analyzed. The static relaxations of a slab and of a single surface are calculated for the same model, and the effects of the relaxation on the vibrational frequencies are investigated. A puckering distortion of the surface layer is incorporated in the vibrational calculations for the first time and is found in this case to introduce one extra surface mode.