Publications by authors named "Gabor Pohl"

We performed a series of ab initio molecular dynamics simulations to investigate the physical properties of small methanol cluster anions, [(CH3OH)n]-, (n = 8-32). An excess electron was attached to neutral clusters that were prepared to accommodate the electron in interior cavity states or surface bound states. The computed initial binding energies of the electrons to these clusters indicate appealing similarity to the experimentally observed vertical detachment energies.

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We performed a series of comparative quantum chemical calculations on various size negatively charged methanol clusters, CHOH. The clusters are examined in their optimized geometries (n = 2-4), and in geometries taken from mixed quantum-classical molecular dynamics simulations at finite temperature (n = 2-128). These latter structures model potential electron binding sites in methanol clusters and in bulk methanol.

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Zirconium-89 is an effective radionuclide for antibody-based positron emission tomography (PET) imaging because its physical half-life (78.41 h) matches the biological half-life of IgG antibodies. Desferrioxamine (DFO) is currently the preferred chelator for (89)Zr(4+); however, accumulation of (89)Zr in the bones of mice suggests that (89)Zr(4+) is released from DFO in vivo.

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We present ONIOM calculations using density functional theory (DFT) as the high and AM1 as the medium level that explore the abilities of different hexapeptide sequences to terminate the growth of a model for the tau-amyloid implicated in Alzheimer's disease. We delineate and explore several design principles (H-bonding in the side chains, using antiparallel interactions on the growing edge of a parallel sheet, using all-d residues to form rippled interactions at the edge of the sheet, and replacing the H-bond donor N-H's that inhibit further growth) that can be used individually and in combination to design such peptides that will have a greater affinity for binding to the parallel β-sheet of acetyl-VQIVYK-NHCH3 than the natural sequence and will prevent another strand from binding to the sheet, thus providing a cap to the growing sheet that arrests further growth. We found peptides in which the Q is replaced by an acetyllysine (aK) residue to be particularly promising candidates, particularly if the reverse sequence (KYVIaKV) is used to form an antiparallel interaction with the sheet.

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We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel β-sheets containing four strands of Ac-AAAAAA-NH2 capped with either Ac-AAPAAA-NH2 or Ac-AAAPAA-NH2. Because Pro can form H-bonds from only one side of the peptide linkage (that containing the C═O H-bond acceptor), only one of the two Pro-containing strands can favorably add to the sheet on each side. Surprisingly, when the sheet is capped with AAPAAA-NH2 at one edge, the interaction between the cap and sheet is slightly more stabilizing than that of another all Ala strand.

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To determine local chirality driven conformational preferences of small aminocyclobutane-1-carboxylic acid derivatives, X-(ACBA) n -Y, their matrix-isolation IR spectra were recorded and analyzed. For the very first time model systems of this kind were deposited in a frozen (~10 K) noble gas matrix to reduce line width and thus, the recorded sharp vibrational lines were analyzed in details. For cis-(S,R)-1 monomer two "zigzag" conformers composed of either a six or an eight-membered H-bonded pseudo ring was identified.

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We present density functional theory calculations designed to evaluate the importance of π-stacking interactions to the stability of in-register Phe residues within parallel β-sheets, such as amyloids. We have used a model of a parallel H-bonded tetramer of acetylPheNH2 as a model and both functionals that were specifically designed to incorporate dispersion effects (DFs), as well as, several traditional functionals which have not been so designed. None of the functionals finds a global minimum for the π-stacked conformation, although two of the DFs find this to be a local minimum.

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Chirality of the monomeric residues controls and determines the prevalent folding of small oligopeptides (from di- to tetramers) composed of 2-aminocyclobutane-1-carboxylic acid (ACBA) derivatives with the same or different absolute and relative configuration. The cis-form of the monomeric ACBA gives rise to two conformers, namely, Z6 and Z8, while the trans-form manifests uniquely as an H8 structure. By combining these subunits in oligo- and polypeptides, their local structural preference remains, thus allowing the rational design of new short foldamers.

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We present a new classification of β-turns specific to antiparallel β-sheets based upon the topology of H-bond formation. This classification results from ONIOM calculations using B3LYP/D95** density functional theory and AM1 semiempirical calculations as the high and low levels, respectively. We chose acetyl(Ala)(6)NH(2) as a model system as it is the simplest all-alanine system that can form all the H-bonds required for a β-turn in a sheet.

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The initiation and progression of Alzheimer's disease is coupled to the oligo- and polymerization of amyloid peptides in the brain. Amyloid like aggregates of protein domains were found practically independent of their primary sequences. Thus, the driving force of the transformation from the original to a disordered amyloid fold is expected to lie in the protein backbone common to all proteins.

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Due to the two methylene groups in their backbone, β-amino acids can adopt numerous secondary structures, including helices, sheets and nanotubes. Chirality introduced by the additional side chains can significantly influence the folding preference of β-peptides composed of chiral β-amino acids. However, only conceptual suggestions are present in the literature about the effect of chirality on folding preferences.

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This study is on structure and stability of sheetlike conformers of beta-peptides; never seen new foldamers are reported here for the first time. Single- and double-stranded structures are analyzed, and the seeds of large beta-layers and biocompatible nanomaterials are described here. Both the monomeric, HCO-[NH-CH(2)-CH(2)CO](n)-NH(2), and dimeric forms, [HCO-(beta-Ala)(n)-NH(2)](2) n = 3 and 4, of oligo-beta-alanine supramolecular complexes are evaluated by using an adequate level of theory M052X/6-31G(d) for peptides of this size.

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The infrared absorption (IR) spectra of acetyl-N-methyl-glycine and acetyl-N-methyl-alanine have been recorded in dichloromethane and dimethyl sulfoxide-d(6) solution, as well as in Ar and Kr matrices. The spectra were assigned with the help of quantum chemical calculations. Based on the assignments of the matrix-isolation IR spectra, in line with theoretical predictions, two different hydrogen bonded conformers were identified, furthermore a third conformer is likely to be present, which cannot be unambiguously identified.

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Because of their great flexibility and strength resistance, both spider silks and silkworm silks are of increasing scientific and commercial interest. Despite numerous spectroscopic and theoretical studies, several structural properties at the atomic level have yet to be identified. The present theoretical investigation focuses on these issues by studying three silk-like model peptides: (AG)(64), [(AG)(4)EG](16), and [(AG)(4)PEG](16), using a Lego-type approach to construct these polypeptides.

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