Capping parallel ß-sheets of acetyl(Ala)6NH2 with an acetyl(Ala)5ProNH2 can arrest the growth of the sheet, suggesting a potential for curtailing amyloid growth. An ONIOM and density functional theory study.

We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel ß-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. Breaking down the interaction enthalpies into H-bonding and distortion energies shows the favorable interaction to be due to lower distortion energies in both the strand and the four-stranded sheet. Because another strand would be inhibited for attachment to the other side of the capping (Pro-containing) strand, we suggest the possible use of Pro residues in peptides designed to arrest the growth of many amyloids.

The interactions of phenylalanines in ß-sheet-like structures from molecular orbital calculations using density functional theory (DFT), MP2, and CCSD(T) methods.

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 ß-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. The stacked phenyls taken from the optimized geometries calculated for each functional have been evaluated using MP2 and CCSD(T) calculations for comparison. The results suggest that π-stacking does not make an important contribution to the stability of this system and (by implication) to amyloid formation.

Density functional theory study of ß-hairpins in antiparallel ß-sheets, a new classification based upon H-bond topology.

We present a new classification of ß-turns specific to antiparallel ß-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 ß-turn in a sheet. Of the 10 different conformations we have found, the most stable structures have C(7) cyclic H-bonds in place of the C(10) interactions specified in the classic definition. Also, the chiralities specified for residues i + 1 and i + 2 in the classic definition disappear when the structures are optimized using our techniques, as the energetic differences among the four diastereomers of each structure are not substantial for 8 of the 10 conformations.

A reinvestigation of the dimer of para-benzoquinone and pyrimidine with MP2, CCSD(T), and DFT using functionals including those designed to describe dispersion.

We reevaluate the interaction of pyridine and p-benzoquinone using functionals designed to treat dispersion. We compare the relative energies of four different structures: stacked, T-shaped (identified for the first time), and two planar H-bonded geometries using these functionals (B97-D, ωB97x-D, M05, M05-2X, M06, M06L, and M06-2X), other functionals (PBE1PBE, B3LYP, X3LYP), MP2, and CCSD(T) using basis sets as large as cc-pVTZ. The functionals designed to treat dispersion behave erratically as the predictions of the most stable structure vary considerably. MP2 predicts the experimentally observed structure (H-bonded) to be the least stable, while single-point CCSD(T) at the MP2 optimized geometry correctly predicts the observed structure to be the most stable. We have confirmed the assignment of the experimental structure using new calculations of the vibrational frequency shifts previously used to identify the structure. The MP2/cc-pVTZ vibrational calculations are in excellent agreement with the observations. All methods used to calculate the energies provide vibrational shifts that agree with the observed structure even though most do not predict this structure to be most stable. The implications for evaluating possible π-stacking in biologically important systems are discussed.

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives.

We compare the energetic and structural properties of fully optimized α-helical and antiparallel ß-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the ß-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).

Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: dispersion, induction, and basis set superposition error.

We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.

The National Spherical Torus Experiment-Upgrade poloidal high-k scattering system pitch angle design modifications.

A 693 GHz, eight-channel, poloidal high-k (k refers to wavenumber) collective scattering system is under development for the National Spherical Torus Experiment-Upgrade device. It will replace the previous 280 GHz, five-channel, tangential scattering system to study high-k electron density fluctuations, thereby providing a measurement of the kθ-spectrum of both electron temperature gradient and ion temperature gradient modes. A tool is under development to calculate the wavenumber that exists in the presence of strong magnetic pitch angles. We use this tool to motivate a new receiver optical design for significantly improved performance, details of which are presented herein.

A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error.

We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP.

The effect of polarization on multiple hydrogen-bond formation in models of self-assembling materials.

We report density functional theory calculations at the B3LYP/D95(d,p) level on several different cyclic H-bonding dimers, where the monomers of each are connected by a pair of N-H···O=C H-bonding interactions, and the H-bonding donors and acceptors on each monomer are separated by polarizable spacers. Depending on the structures, the individual H-bonds vary in strength (enthalpy) by over a factor of four, from 2.41 to 10.99 kcal/mol. We attribute most of the variation in interaction energies to differences in the extent of polarization due to each of the H-bonds, which can either combine constructively or destructively. The dipole-dipole interactions between the pair of H-bonds also contribute somewhat to the relative stabilities. The relevance of these results to the design of self-assembling materials is discussed.

Escape from premature senescence is not sufficient for oncogenic transformation by Ras.

Resistance of primary cells to transformation by oncogenic Ras has been attributed to the induction of replicative growth arrest. This irreversible 'fail-safe mechanism' resembles senescence and requires induction by Ras of p19ARF and p53 (refs 3-5). Mutation of either p19ARF or p53 alleviates Ras-induced senescence and facilitates oncogenic transformation by Ras. Here we report that, whereas Rb and p107 are each dispensable for Ras-induced replicative arrest, simultaneous ablation of both genes disrupts Ras-induced senescence and results in unrestrained proliferation. This occurs despite activation by Ras of the p19ARF /p53 pathway, identifying pRb and p107 as essential mediators of Ras-induced antiproliferative p19ARF/p53 signalling. Unexpectedly, in contrast to p19ARF or p53 deficiency, loss of Rb/p107 function does not result in oncogenic transformation by Ras, as Ras-expressing Rb-/-/p107-/- fibroblasts fail to grow anchorage-independently in vitro and are not tumorigenic in vivo. These results demonstrate that in the absence of both Rb and p107 cells are resistant to p19ARF/p53-dependent protection against Ras-induced proliferation, and uncouple escape from Ras-induced premature senescence from oncogenic transformation.

J-coupling constants for a trialanine peptide as a function of dihedral angles calculated by density functional theory over the full Ramachandran space.

We present 13 (3)J, seven (2)J and four (1)J coupling constants (24 in all) calculated using B3LYP/D95** as a function of the φ and ψ Ramachandran dihedral angles of the acetyl(Ala)(3)NH(2) capped trialanine peptide over the entire Ramachandran space. With the exception of three of these J couplings, all show significant dependence upon both dihedral angles. For each J coupling considered, a two dimensional grid with respect to φ and ψ angles can be used to interpolate the values for any pair of φ and ψ values. Such simple interpolation is shown to be very accurate. Most of these calculated J couplings should prove useful for improving the accuracy of the determination of peptide and protein structures from NMR measurements in solution over that provided by the common procedure of treating the J couplings as functions of a single dihedral angle by means of Karplus-type fittings.

The Effects of Regularly Spaced Glutamine Substitutions on Alpha-Helical Peptide Structures. A DFT/ONIOM Study.

The side-chains of the residues of glutamine (Q) and asparagine (N) contain amide groups. These can H-bond to each other in patterns similar to those of the backbone amides in α-helices. We show that mutating multiple Q's for alanines (A's) in a polyalanine helix stabilizes the helical structure, while similar mutations with multiple N's do not. We suggest that modification of peptides by incorporating Q's in such positions can make more robust helices that can be used to test the effects of secondary structures in biochemical experiments linked to proteins with variable structures such as tau and α-synuclein.

A next generation ultra short pulse reflectometry (USPR) diagnostic.

Ultrashort Pulse Reflectometry (USPR) is a plasma diagnostic technique involving the propagation and reflection of ultrashort duration (∼few ns) chirps. The reflected packets pass through a multichannel filter with time-of-flight measurements performed on each of the filtered packets. A next generation USPR system is under development, spanning 28-75 GHz, for use on compact, short duration, magnetically confined fusion devices. This system presents a dramatic increase in performance compared with an earlier USPR system employed on the LLNL Sustained Spheromak Physics Experiment device more than a decade ago. The new system replaces upconverting mixers with higher power active multiplier chains to generate mm-wave transmitter chirps, with custom time-of-flight electronics reducing the time per measurement by a factor of 3X. Finally, the system is equipped with a field programmable gate array for data acquisition and analysis.

The importance of hydrogen bonding between the glutamine side chains to the formation of amyloid VQIVYK parallel beta-sheets: an ONIOM DFT/AM1 study.

We report DFT calculations indicating that beta-sheet formation involving the capped amino acid sequence VQIVYK is due (at least in part) to cooperative H-bonding between the glutamine side chains. The sequence VQIVYK has been reported to be essential for the aggregation of the tau protein into the amyloids associated with Alzheimer's disease and has been crystallized. Sheets containing only capped Q's form cooperative H-bonds between the side chains that enhance stabilization while keeping the backbones of the individual strands close to the quasi-planarity expected for a beta-sheet. Sheets containing only capped A's cannot form H-bonds between the side chains, do not interact cooperatively, and form helical structures that deviate considerably from the quasi-planarity expected for beta-sheets. Comparisons between the sheets made from capped VQIVYK's, Q's, and A's illustrate the importance of the cooperative H-bonds between the Q's to the stability of tau amyloids.

Ramachandran revisited. DFT energy surfaces of diastereomeric trialanine peptides in the gas phase and aqueous solution.

We report DFT calculations at the B3LYP/D95(d,p) level on the gas phase, aqueous solvation and solvated energies as functions of the central psi and phi dihedral angles (in steps of 5 degrees each) of acetyl-(L)Ala-(L)Ala-(L)Ala-NH(2) (3AL) and its diastereomer, acetyl-(L)Ala-(D)Ala-(L)Ala-NH(2) (3AD). In addition to structures without internal H-bonds (C(5) interactions are neglected), many (95) structures containing internal H-bonds were completely optimized. The only minima for non-H-bonding structures in the gas phase correspond to extended beta-strands for both diastereomers. Some (but not all) structures with internal H-bonds are more stable than those without them. The energy landscapes for the solvated species show multiple minima for the non-H-bonding species and a single minimum for the H-bonding species (3(10)-helix), suggesting that the equilibrium conformational mixture in water be composed of the extended beta-strand, polyproline II, 3(10)-helix, and alpha-helix-like (with no H-bonds) conformations which are all within about 1 kcal/mol of each other. Most H-bonding structures are destabilized relative to the non-H-bonding structures in aqueous solution, but some with large dipole moments are not. The large dipole moment of the alpha-helix-like conformation leads to its increased stability in water (vs the gas phase). Significant qualitative and quantitative differences are reported for the energy landscapes of the two diastereomers when one is compared with the mirror image of the other landscape (particularly in the beta-turn region), suggesting that the differences in the energies of the unfolded peptides need to be considered when considering the stabilities of folded peptides and proteins with single amino acid mutations.

Amide I vibrational frequencies of alpha-helical peptides based upon ONIOM and density functional theory (DFT) studies.

We present ONIOM and pure DFT calculations on infrared spectra of alpha-helical-capped polyalanines. The calculations used two-layer ONIOM (B3LYP/D95**:AM1) calculations of the amide I vibrational frequencies for acetyl(ala)NNH2 (N=8, 10, 12-18) whose structures have been previously completely optimized by the same method. These are the first such calculations based upon structures of alpha-helical peptides that are completely optimized using DFT or molecular orbital methods. As the peptide becomes longer, the amide I band becomes both more intense and more red shifted. However, the individual absorptions that contribute most to the band vary between three patterns: one very intense absorption, two absorptions of similar intensity, and two strong absorptions where one is roughly twice as intense as the other. This pattern appears to be related to the relative number of H bonds in the individual H-bonding chains; however, there is one exception. Using 14C=O's to selectively decouple specific C=O's, we found that the couplings between the C=O's within each of the three individual H-bonding chains within the helices follow the same pattern previously reported for planar H-bonding chains of formamides. The coupling between the H-bonding chains appears to involve through-space coupling between the H-bonding chains. While decoupling individual C=O's always decreases the intensity of the amide I band, it leads to complex changes in the individual amide I absorptions that contribute to the band. Depending upon the position of the 14C=O, the amide I band can either red or blue shift. Moreover, the individual absorptions that contribute to the band can increase or decrease in intensity as well as shift. The patterns of the individual absorptions (mentioned above) also change. Using the C=O stretch of acetamide as a reference, we calculate the red shifts for the most intense absorptions to be much greater than predicted by the transition dipole method.

Attractive strain: the disadvantages of rigid multiple H-bond donors and acceptors. A theoretical analysis of the hydrogen-bonding interactions in complexes of tetraazaanthracenedione with pyridylureas.

We report density functional theory calculations at the B3LYP/D95(d,p) level on the hydrogen-bonding complexes of tetraazaanthracenedione, 1, with N-(pyridin-2-yl)urea, 2H, or N-(6-aminopyridin-2-yl)urea, 2N. The interaction energy of the 1-2H complex exceeds that of 1-2N, despite the fact that 1-2N contains a strong N-H...O interaction in place of a weak C-H...O interaction in 1-2H. We show that the 1-2N interaction is weaker than the sum of the four normal individual H-bonding interactions because the steric constraints of the complex prevent the H-bonding donors and acceptors from optimally approaching each other to form the two central H-bonds. This steric phenomenon, which we call attractive strain, is likely present to some extent in most H-bonding systems that contain more than two H-bonds between rigid monomers. Attractive strain is unusually important in 1-2N. Attractive strain can be conceived of as an enthalpic cost for the entropic benefits of freezing the dihedral angles of the multiple H-bond donors and acceptors by designing rigid systems.

A density functional theory study of vibrational coupling in the amide I band of beta-sheet models.

We report the first molecular orbital/density functional theory (DFT) calculations on the vibrational frequencies involved in the amide I band of completely geometrically optimized models for beta-sheet peptides based upon (up to 16) glycine residues. These calculations use the B3LYP/D95** level of DFT. The primary means of vibrational coupling occurs through H bond, rather than through space, interactions, which is consistent with a previous report on alpha-helical polyalanines and H-bonding chains of both formamides and 4-pyridones. We decoupled the C=O stretching vibrations using selected 14C substitutions to probe the coupling mechanism and to determine "natural" frequencies for individual 14C=Os. The intermolecular H-bonding interactions affect the geometries of the amide groups. Those near the center of H-bonding chains have long C=O bonds. The C=O bond lengths correlate with these "natural" frequencies, The frequencies obtained from the DFT calculations are generally more coupled, and the most intense are more red shifted than those calculated by transition dipole coupling (TDC). TDC inverts the order of the shifted frequencies compared to DFT in several cases.

A new method of out-of-focus millimeter wave imaging in fusion plasma diagnostics using Bessel beams.

Electron cyclotron emission imaging (ECEI) and microwave imaging reflectometry diagnostics have been employed on a number of magnetic fusion plasma confinement devices. The common approach is based on a Gaussian beam assumption, which generates good spatial resolution (centimeter level). However, the radial focal depth is limited by the poloidal resolution, which is comparable with the Rayleigh length (∼150 mm). By contrast, a new Bessel beam approach has been developed and demonstrated to generate much longer focal depth with the property of propagation stability. To test the new approach, the DIII-D tokamak LCP ECEI optics have been re-designed to support a Bessel beam approach based on an axicon lens. The achievable radial coverage can exceed that of the current Gaussian approach by 3×. The imaging result is discussed in this paper based on the simulation analysis and laboratory testing result.

The high-k poloidal scattering system for NSTX-U.

An 8-channel, high-k poloidal far-infrared (FIR) scattering system is under development for the National Spherical Torus eXperiment Upgrade (NSTX-U). The 693 GHz poloidal scattering system replaces a 5-channel, 280 GHz high-k toroidal scattering system to study high-k electron density fluctuations on NSTX-U. The FIR probe beam launched from Bay G is aimed toward Bay L, where large aperture optics collect radiation at 8 simultaneous scattering angles ranging from 2° to 15°. The reduced wavelength in the poloidal system results in less refraction, and coupled with a new poloidal scattering geometry, extends measurement of poloidal wavenumbers from the previous limit of 7 cm-1 up to >40 cm-1. Steerable launch optics coupled with receiver optics that can be remotely translated in 5 axes allow the scattering volume to be placed from r/a = 0.1 out to the pedestal region (r/a ∼ 0.99) and allow for both upward and downward scattering to cover different regions of the 2D fluctuation spectrum.