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Parkinson's disease is accompanied by the presence of amyloids in the brain that are formed of α-synuclein chains. The correlation between COVID-19 and the onset of Parkinson's disease led to the idea that amyloidogenic segments in SARS-COV-2 proteins can induce aggregation of α-synuclein. Using molecular dynamic simulations, we show that the fragment FKNIDGYFKI of the spike protein, which is unique for SARS-COV-2, preferentially shifts the ensemble of α-synuclein monomer toward rod-like fibril seeding conformations and, at the same time, differentially stabilizes this polymorph over the competing twister-like structure. Our results are compared with earlier work relying on a different protein fragment that is not specific for SARS-COV-2. [ABSTRACT FROM AUTHOR]

The excited-state properties and photoinduced charge-transfer (CT) kinetics in a series of symmetrical and asymmetrical Zn- and Au-ligated meso–meso-connected bacteriochlorin (BChl) complexes are studied computationally. BChl derivatives, which are excellent near-IR absorbing chromophores, are found to play a central role in bacterial photosynthetic reaction centers but are rarely used in artificial solar energy harvesting systems. The optical properties of chemically linked BChl complexes can be tuned by varying the linking group and involving different ligated metal ions. We investigate charge transfer in BChl dyads that are either directly linked or through a phenylene ring (1,4-phenylene) and which are ligating Zn or Au ions. The directly linked dyads with a nearly perpendicular arrangement of the BChl units bear markedly different properties than phenylene linked dyads. In addition, we find that the dielectric dependence of the intramolecular CT rate is very strong in neutral Zn-ligated dyads, whereas cationic Au-ligated dyads show negligible dielectric dependence of the CT rate. Rate constants of the photo induced CT process are calculated at the semiclassical Marcus level and are compared to fully quantum mechanical Fermi's golden rule based values. The rates are calculated using a screened range separated hybrid functional that offers a consistent framework for addressing environment polarization. We study solvated systems in two solvents of a low and a high scalar dielectric constant. [ABSTRACT FROM AUTHOR]

The astrophysically relevant system H+ + CO (vi = 0) → H+ + CO (vf) at ELab = 30 eV is studied with the simplest-level electron nuclear dynamics (SLEND) method. This investigation follows previous successful SLEND studies of H+ + H2 and H+ + N2 at ELab = 30 eV [J. Morales, A. Diz, E. Deumens, and Y. Öhrn, J. Chem. Phys. 103(23), 9968 (1995); C. Stopera, B. Maiti, T. V. Grimes, P. M. McLaurin, and J. A. Morales, J. Chem. Phys. 134(22), 224308 (2011)]. SLEND is a direct, time-dependent, variational, and non-adiabatic method that adopts a classical-mechanics description for the nuclei and a single-determinantal wavefunction for the electrons. A canonical coherent-states (CS) procedure associated with SLEND reconstructs quantum vibrational properties from the SLEND classical dynamics. Present SLEND results include reactivity predictions, snapshots of the electron density evolution, average vibrational energy transfers, rainbow angle predictions, total and vibrationally resolved differential cross sections (DCS), and average vibrational excitation probabilities. SLEND results are compared with available data from experiments and vibrational close-coupling rotational infinite-order sudden (VCC-RIOS) approximation calculations. Present simulations employ four basis sets: STO-3G, 6-31G, 6-31G**, and cc-pVDZ to determine their effect on the results. SLEND simulations predict non-charge-transfer scattering and CO collision-induced dissociation as the main reactions. SLEND/6-31G, /6-31G**, and /cc-pVDZ predict rainbow angles and total DCS in excellent agreement with experiments and more accurate than their VCC-RIOS counterparts. SLEND/6-31G** and /cc-pVDZ predict vibrationally resolved DCS for vf = 0-2 in satisfactory experimental agreement, but less accurate than their comparable H+ + CO VCC-RIOS and H+ + H2 and H+ + N2 SLEND results. SLEND/6-31G** and /cc-pVDZ predict qualitatively correct average vibrational excitation probabilities, which are quantitatively correct for vf = 2, but under(over)estimated for vf = 0(1). Discrepancies in some H+ + CO SLEND vibrational properties, not observed in H+ + H2 and H+ + N2 SLEND results, are attributed to the moderately overestimated SLEND vibrational energy through its effect upon the canonical CS probabilities. Correction of that energy to its experimental values produces a remarkable improvement in the average vibrational excitation probabilities. Ways to obtain more accurate vibrational properties with higher-level versions of electron nuclear dynamics are discussed. [ABSTRACT FROM AUTHOR]

The H+ + N2 system at ELab = 30 eV, relevant in astrophysics, is investigated with the simplest-level electron nuclear dynamics (SLEND) method. SLEND is a time-dependent, direct, variational, non-adiabatic method that employs a classical-mechanics description for the nuclei and a single-determinantal wavefunction for the electrons. A canonical coherent-states procedure, intrinsic to SLEND, is used to reconstruct quantum vibrational properties from the SLEND classical mechanics. Present simulations employ three basis sets: STO-3G, 6-31G, and 6-31G**, to determine their effect on the results, which include reaction visualizations, product predictions, and scattering properties. Present simulations predict non-charge-transfer scattering and N2 collision-induced dissociation as the main reactions. Average vibrational energy transfer, H+ energy-loss spectra, rainbow angle, and elastic vibrational differential cross sections at the SLEND/6-31G** level agree well with available experimental data. SLEND/6-31G** results are comparable to those calculated with the vibrational close-coupling rotational infinite-order sudden approximation and the quasi-classical trajectory method. [ABSTRACT FROM AUTHOR]

Photoinduced cleavage of the bond between the central Si atom in porphyrin macrocycles and the neighboring carbon atom of an axial alkyl ligand is investigated by both experimental and computational tools. Photolysis and electron paramagnetic resonance measurements indicate that the Si-C bond cleavage of Si-phthalocyanine occurs through a homolytic process. The homolytic process follows a low-lying electronic excitation of about 1.8 eV that destabilizes the carbide bond of similar bond dissociation energy. Using electronic structure calculations, we provide insight into the nature of the excited state and the resulting photocleavage mechanism. We explain this process by finding that the electronic excited state is of a charge transfer character from the axial ligand toward the macrocycle in the reverse direction of the ground state polarization. We find that the homolytic process yielding the radical intermediate is energetically the most stable mechanistic route. Furthermore, we demonstrate using our computational approach that changing the phthalocyanine to smaller ring system enhances the homolytic photocleavage of the Si-C bond by reducing the energetic barrier in the relevant excited states. [ABSTRACT FROM AUTHOR]

Abstract: H+ +NO(v i =0)=H+ +NO(v f =0–2) at E Lab =30eV is investigated with the simplest-level electron nuclear dynamics (SLEND) method. In a direct, time-dependent, variational, and non-adiabatic framework, SLEND adopts nuclear classical mechanics and an electronic single-determinantal wavefunction. A coherent-states (CS) procedure recovers quantum vibrational properties from classical mechanics. Besides canonical CS, SU(1,1), SU(2), and Gazeau–Klauder Morse CS are innovatively introduced to treat anharmonicity. SLEND vibrational differential cross, rainbow scattering angles, and H+ energy loss spectra compare well with experimental data and with vibrational close-coupling rotational infinite-order sudden approximation results obtained at a higher computational cost. [Copyright &y& Elsevier]

Glycosylation regulates vital cellular processes and dramatically influences protein folding and stability. In particular, experiments have demonstrated that asparagine (N)-linked disaccharides drive a "conformational switch" in a model peptide. The present work investigates this conformational switch via extensive atomically detailed replica exchange molecular dynamics simulations in explicit solvent. To distinguish the effects of specific and nonspecific interactions upon the peptide conformational ensemble, these simulations considered model peptides that were N-linked to a disaccharide and to a steric crowder of the same shape. The simulations are remarkably consistent with experiment and provide detailed insight into the peptide structure ensemble. They suggest that steric crowding by N-linked disaccharides excludes extended conformations, but does not significantly impact the tetrahedral structure of the surrounding solvent or otherwise alter the peptide free energy surface. However, the combination of steric crowding with specific hydrogen bonds and hydrophobic stacking interactions more dramatically impacts the peptide ensemble and stabilizes new structures. [ABSTRACT FROM AUTHOR]

The H+ + CF4 reaction at collision energies ELab = 20 and 30 eV is investigated with the electron nuclear dynamics (END) theory. The level of END herein employed prescribes a classical-mechanics description for the nuclei and a single-determinantal representation for the electrons. The results include visualizations of the simulated collisions, and calculations of various scattering properties. The present simulations always predict noncharge-transfer scattering (NCTS) for H+ + CF4 and exclude charge-transfer, dissociation, and rearrangement reactions. The predicted rainbow angles and the total NCTS differential cross sections agree satisfactorily with the available experimental results. The present results are compared with those of the previously simulated H+ + CH4. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [ABSTRACT FROM AUTHOR]

Abstract: Results of a complete investigation of the H+ +HF reaction at E Lab =30eV with the electron nuclear dynamics (END) and the coherent-states dynamics (CSD) theories are herein presented. Current END–CSD methodology employs frozen Gaussian wave packet in the semiclassical limit of ℏ →0 for the nuclei, and a single-determinantal Thouless coherent state (CS) for the electrons. The simulated 400 CS trajectories from five independent HF target orientations provide a complete description of the reactive processes in this system, including: non-charge-transfer scattering (NCTS), charge-transfer scattering (CTS), hydrogen fluoride dissociation (H–F D), and hydrogen rearrangement (HR). Several aspects of the reactions dynamics, such as mechanistic details and rainbow angles effects, are discussed. Differential and integral cross sections are evaluated via a novel CS formulation of those properties in conjunction with semiclassical techniques. The calculated total differential cross section shows an excellent agreement with available experimental results. [Copyright &y& Elsevier]

Abstract: Preliminary results of an exhaustive study of H+ +HC:italic>E Lab =30eV within the electron nuclear dynamics (END) and coherent state dynamics (CSD) theories are herein presented. Current END–CSD method employs frozen Gaussian wave packets in the semiclassical limit of ℏ →0 for the nuclei and a single-determinantal Thouless coherent state (CS) for the electrons. The simulated 6800 trajectories from 68 independent HC orientations provide a definite description of all the reactive processes, including H2 formation and charge transfers. Differential and integral cross-sections are evaluated via a novel CS S-matrix formulation in conjunction with semiclassical techniques. Calculated cross-sections show a good agreement with both experimental and previous END results. [Copyright &y& Elsevier]

Ferric and ferrous hemes, such as those present in electron transfer proteins, often have lowlying spin states that are very close in energy. To explore the relationship between spin state, geometry, and cytochrome electron transfer, we investigate, using density functional theory, the relative energies, electronic structure, and optimized geometries for a high- and low-spin ferric and ferrous heme model complex. Our model consists of an iron-porphyrin axially ligated by two imidazotes, which model the interaction of a heme with histidine residues. Using the B3LYP hybrid functional, we found that, in the ferric model heine complex, the doublet is lower in energy than the sextet by 8.4 kcal/mol and the singlet ferrous heme is 6.7 kcal/mol more stable than the quintet. The difference between the high-spin ferric and ferrous model heine energies yields an adiabatic electron affinity (AEA) of 5.24 eV, and the low-spin AEA is 5.17 eV. Both values are large enough to ensure electron trapping, and electronic structure analysis indicates that the iron d[sub π] orbital is involved in the electron transfer between hemes. Mössbauer parameters calculated to verify the B3LYP electronic structure correlate very well with experimental values. Isotropic hyperfine coupling constants for the ligand nitrogen atoms were also evaluated. The optimized geometries of the ferric and ferrous hemes are consistent with structures from X-ray crystallography and reveal that the iron-imidazole distances are significantly longer in the high-spin hemes, which suggests that the protein environment, modeled here by the imidazoles, plays an important role in regulating the spin state, ironimidazole dissociation energies, force constants, and harmonic frequencies were calculated for the ferric and ferrous low-spin and high-spin hemes. In both the ferric and the ferrous cases, a single imidazole ligand is more easily dissociated from the high-spin hemes. [ABSTRACT FROM AUTHOR]

Charge transport in pyridine-ethynyliodophenyl supramolecules that involve intermolecular halogen bonding is studied by a combined experimental and computational approach. Selective fluorination of the molecules determines their crystallization pattern and is found to potentially increase the charge mobilities in the crystal. We report the synthesis of the molecules, full chemical characterization and resolved crystal structures. Computational analysis of the charge transport is provided to understand at the molecular level the structure-function relationships determining the charge mobilities. Combination of selective fluorination, halogen bonding motif and increased π system is highlighted as bearing the potential to achieve both enhanced hole and electron mobilities. Image 1 [ABSTRACT FROM AUTHOR]

A corrective addition to the article "Specific and Nonspecific Effects of Glycosylation" by Christopher R. Ellis, Buddhadev Maiti, and William G. Noid in issue 134 from 2012 is presented.

Excitonically coupled bacteriochlorin (BC) dimers constitute a primary electron donor (special pair) in bacterial photosynthesis and absorbing units in light-harvesting antenna. However, the exact nature of the excited state of these dyads is still not fully understood. Here, we report a detailed spectroscopic and computational investigation of a series of symmetrical bacteriochlorin dimers, where the bacteriochlorins are connected either directly or by a phenylene bridge of variable length. The excited state of these dyads is quenched in high-dielectric solvents, which we attribute to photoinduced charge transfer. The mixing of charge transfer with the excitonic state causes accelerated (within 41 ps) decay of the excited state for the directly linked dyad, which is reduced by orders of magnitude with each additional phenyl ring separating the bacteriochlorins. These results highlight the origins of the excited-state dynamics in symmetric BC dyads and provide a new model for studying the primary processes in photosynthesis and for the development of artificial, biomimetic systems for solar energy conversion. [ABSTRACT FROM AUTHOR]

Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair,APsites must be processed by 5′APendonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5′ AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5 to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 Å resolution APE1-DNA product complex with Mg2+ and a 0.92 Å Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize key APE1 catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg2+. Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases. [ABSTRACT FROM AUTHOR]