The G3-RAD, G3X-RAD, G3͑MP2͒-RAD, and G3X͑MP2͒-RAD, procedures, designed particularly for the prediction of reliable thermochemistry for free radicals, are formulated and their performance assessed using the G2/97 test set. The principal features of the RAD procedures include ͑a͒ the use of B3-LYP geometries and vibrational frequencies ͑in place of UHF and UMP2͒, including the scaling of vibrational frequencies so as to reproduce ZPVEs, ͑b͒ the use of URCCSD͑T͒ ͓in place of UQCISD͑T͔͒ as the highest-level correlation procedure, and ͑c͒ the use of RMP ͑in place of UMP͒ to approximate basis-set-extension effects. G3-RAD and G3X-RAD are found to perform well overall with mean absolute deviations ͑MADs͒ from experiment of 3.96 and 3.65 kJ mol Ϫ1 , respectively, compared with 4.26 and 4.02 kJ mol Ϫ1 for standard G3 and G3X. G3-RAD and G3X-RAD successfully predict heats of formation with MADs of 3.68 and 3.11 kJ mol Ϫ1 , respectively ͑compared with 3.93 and 3.60 kJ mol Ϫ1 for standard G3 and G3X͒, and perform particularly well for radicals with MADs of 2.59 and 2.50 kJ mol Ϫ1 , respectively ͑compared with 3.51 and 3.18 kJ mol Ϫ1 for standard G3 and G3X͒. The G3͑MP2͒-RAD and G3X͑MP2͒-RAD procedures give acceptable overall performance with mean absolute deviations from experiment of 5.17 and 4.92 kJ mol Ϫ1 , respectively, compared with 5.44 and 5.23 kJ mol Ϫ1 for standard G3͑MP2͒ and G3X͑MP2͒. G3͑MP2͒-RAD and G3X͑MP2͒-RAD give improved performance over their standard counterparts for heats of formation ͑MADsϭ4.73 and 4.44 kJ mol Ϫ1 , respectively, versus 4.94 and 4.64 kJ mol Ϫ1 ). G3͑MP2͒-RAD shows similar performance to G3͑MP2͒ for radical heats of formation ͑MADϭ5.10 versus 5.15 kJ mol Ϫ1 ) while G3X͑MP2͒-RAD performs significantly better than G3X͑MP2͒ ͑MADϭ4.67 versus 5.19 kJ mol Ϫ1 ).
Many fatal neurodegenerative diseases such as Alzheimer's, Parkinson, the prion-related diseases, and non-neurodegenerative disorders such as type II diabetes are characterized by abnormal amyloid fiber aggregates, suggesting a common mechanism of pathogenesis. We have discovered that a class of systematically designed natural tri-to hexapeptides with a characteristic sequential motif can simulate the process of fiber assembly and further condensation to amyloid fibrils, probably via unexpected dimeric α-helical intermediate structures. The characteristic sequence motif of the novel peptide class consists of an aliphatic amino acid tail of decreasing hydrophobicity capped by a polar head. To our knowledge, the investigated aliphatic tripeptides are the shortest ever reported naturally occurring amino acid sequence that can adopt α-helical structure and promote amyloid formation. We propose the stepwise assembly process to be associated with characteristic conformational changes from random coil to α-helical intermediates terminating in cross-β peptide structures. Circular dichroism and X-ray fiber diffraction analyses confirmed the concentrationdependent conformational changes of the peptides in water. Molecular dynamics simulating peptide behavior in water revealed monomer antiparallel pairing to dimer structures by complementary structural alignment that further aggregated and stably condensed into coiled fibers. The ultrasmall size and the dynamic facile assembly process make this novel peptide class an excellent model system for studying the mechanism of amyloidogenesis, its evolution and pathogenicity. The ability to modify the properties of the assembled structures under defined conditions will shed light on strategies to manipulate the pathogenic amyloid aggregates in order to prevent or control aggregate formation.self-assembly mechanism | ultrasmall peptides | supramolecular peptide scaffolds | fiber diffraction | molecular dynamics simulation
We present a theoretical study on a series of novel organometallic sandwich molecular wires (SMWs), which are constructed with alternating iron atoms and cyclopentadienyl (Cp) rings, using DFT and nonequilibrium Green's function techniques. It is found that that the SMWs are stable, flexible structures having half-metallic (HM) properties with 100% negative spin polarization near the Fermi level in the ground state. Some SMWs of finite size show a nearly perfect spin filter effect (SFE) when coupled between ferromagnetic electrodes. Moreover, their I-V curves exhibit negative differential resistance (NDR), which is essential for certain electronic applications. The SMWs are the first linear molecules with HM, high SFE, and NDR and can be easily synthesized. In addition, we also analyze the underlying mechanisms via the transmission spectra and spin-dependent calculations. These findings strongly suggest that the SMWs are promising materials for application in molecular electronics.
A series of para-substituted N-methyl-N-phenylnitrenium ions (N-(4-biphenylyl)-N-methylnitrenium ion, N-(4-chlorophenyl)-N-methylnitrenium ion, N-(4-methoxyphenyl)-N-methylnitrenium ion, and N-(4-methylphenyl)-N-methylnitrenium ion) were generated through photolysis of the appropriately substituted 1-aminopyridinium salt. Laser flash photolysis using UV−vis detection as well as photoproduct analysis verified that the expected nitrenium ions were formed cleanly and rapidly following photolysis. Laser flash photolysis with time-resolved infrared detection allowed for structural characterization of the nitrenium ions through observation of a symmetrical aromatic CC stretch in the region 1580−1628 cm-1. The specific frequencies reflect the degree of quinoidal character present in each phenylnitrenium ion (i.e., the degree to which the nitrenium ion resembles a 4-iminocyclohexa-2,5-dienyl cation). The 4-methoxy derivative shows the highest frequency CC stretch, indicating that this strongly π-electron-donating substituent imparts more quinoidal character, and the 4-chloro derivative shows the lowest frequency CC stretch, suggesting that it possesses the least quinoidal character. Quantum calculations using density functional theory (BPW91/cc-pVDZ) were carried out on the same nitrenium ions. The theoretically derived IR frequencies showed excellent quantitative agreement with the experiment. The computed structures show significant bond length alternation in the phenyl rings, shortened C−N bond lengths, and substantial positive charge delocalization into the phenyl rings. All of these effects are more pronounced with increasing π-donating character of the ring substituent. Arylnitrenium ions are well described as 4-iminocyclohexa-2,5-dienyl cations.
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