Impact of Vibrational Entropy on the Stability of Unsolvated Peptide Helices with Increasing Length

Helices are a key folding motif in protein structure. The question of which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van-der-Waals-corrected density functional theory to address a part of this question in a bottom-up approach. We show how intrinsic helical structure is stabilized with length and temperature for a series of experimentally well-studied unsolvated alanine-based polypeptides, Ac-Ala_<i>n</i>-LysH⁺. By exhaustively exploring the conformational space of these molecules, we find that helices emerge as the preferred structure in the length range <i>n</i> = 4–8 not just due to enthalpic factors (hydrogen bonds and their cooperativity, van der Waals dispersion interactions, electrostatics) but importantly also by a vibrational entropic stabilization over competing conformers at room temperature. The stabilization is shown to be due to softer low-frequency vibrational modes in helical conformers than in more compact ones. This observation is corroborated by including anharmonic effects explicitly through <i>ab initio</i> molecular dynamics and generalized by testing different terminations and considering larger helical peptide models

Oxidative Dehydrogenation of Methane by Isolated Vanadium Oxide Clusters Supported on Au (111) and Ag (111) Surfaces

We use density functional theory, with the GGA-PBE functional, to investigate the ability of vanadium oxide clusters, supported on Ag or Au, to break the C–H bond in methane. We perform a thermodynamic analysis to show that the VO₄ cluster is the most likely oxidant and then proceed to calculate the energy of the dissociative adsorption of methane and its activation energy. We explain some peculiar features of the reaction path and propose that they are general for alkane activation on oxides

Oxidative Dehydrogenation of Methane by Isolated Vanadium Oxide Clusters Supported on Au (111) and Ag (111) Surfaces

We use density functional theory, with the GGA-PBE functional, to investigate the ability of vanadium oxide clusters, supported on Ag or Au, to break the C–H bond in methane. We perform a thermodynamic analysis to show that the VO₄ cluster is the most likely oxidant and then proceed to calculate the energy of the dissociative adsorption of methane and its activation energy. We explain some peculiar features of the reaction path and propose that they are general for alkane activation on oxides

Validation Challenge of Density-Functional Theory for PeptidesExample of Ac-Phe-Ala₅‑LysH⁺

We assess the performance of a group of exchange-correlation functionals for predicting the secondary structure of peptide chains, up to a new many-body dispersion corrected hybrid density functional, dubbed PBE0+MBD* by its original authors. For the purpose of validation, we first compare to published, high-level benchmark conformational energy hierarchies (coupled cluster at the singles, doubles, and perturbative triples level, CCSD­(T)) for 73 conformers of small three-residue peptides, establishing that the van der Waals corrected PBE0 functional yields an average error of only ∼20 meV (∼0.5 kcal/mol). This compares to ∼40–50 meV for nondispersion corrected PBE0 and 40–100 meV for different empirical force fields (estimated for the alanine tetrapeptide). For longer peptide chains that form a secondary structure, CCSD­(T) level benchmark data are currently unaffordable. We thus turn to the <i>experimentally</i> well studied Ac-Phe-Ala₅-LysH⁺ peptide, for which four closely competing conformers were established by infrared spectroscopy. For comparison, an exhaustive theoretical conformational space exploration yields at least 11 competing low energy minima. We show that (i) the many-body dispersion correction, (ii) the hybrid functional nature of PBE0+MBD*, and (iii) zero-point corrections are needed to reveal the four experimentally observed structures as the minima that would be populated at low temperature

Integer <i>versus</i> Fractional Charge Transfer at Metal(/Insulator)/Organic Interfaces: Cu(/NaCl)/TCNE

Semilocal and hybrid density functional theory was used to study the charge transfer and the energy-level alignment at a representative interface between an extended metal substrate and an organic adsorbate layer. Upon suppressing electronic coupling between the adsorbate and the substrate by inserting thin, insulating layers of NaCl, the hybrid functional localizes charge. The laterally inhomogeneous charge distribution resulting from this spontaneous breaking of translational symmetry is reflected in observables such as the molecular geometry, the valence and core density of states, and the evolution of the work function with molecular coverage, which we discuss for different growth modes. We found that the amount of charge transfer is determined, to a significant extent, by the ratio of the lateral spacing of the molecules and their distance to the metal. Therefore, charge transfer does not only depend on the electronic structure of the individual components but, just as importantly, on the interface geometry

Secondary Structure of Ac-Ala_<i>n</i>-LysH⁺ Polyalanine Peptides (<i>n</i> = 5,10,15) in Vacuo: Helical or Not?

The polyalanine-based peptide series Ac-Ala_<i>n</i>-LysH⁺ (<i>n</i> = 5−20) is a prime example that a secondary structure motif that is well-known from the solution phase (here: helices) can be formed in vacuo. Here we revisit the series members <i>n</i> = 5,10,15, using density functional theory (van der Waals corrected generalized gradient approximation) for structure predictions, which are then corroborated by room temperature gas-phase infrared vibrational spectroscopy. We employ a <i>quantitative</i> comparison based on Pendry’s reliability factor (popular in surface crystallography). In particular, including <i>anharmonic</i> effects into calculated spectra by way of ab initio molecular dynamics produces remarkably good experiment−theory agreement. We find the longer molecules (<i>n</i> = 10,15) to be firmly α-helical in character. For <i>n</i> = 5, calculated free-energy differences show different H-bond networks to still compete closely. Vibrational spectroscopy indicates a predominance of α-helical motifs at 300 K, but the lowest-energy conformer is not a simple helix

Assessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies

The accurate and reliable prediction of properties of molecules typically requires computationally intensive quantum-chemical calculations. Recently, machine learning techniques applied to <i>ab initio</i> calculations have been proposed as an efficient approach for describing the energies of molecules in their given ground-state structure throughout chemical compound space (Rupp et al. <i>Phys. Rev. Lett.</i> <b>2012</b>, <i>108</i>, 058301). In this paper we outline a number of established machine learning techniques and investigate the influence of the molecular representation on the methods performance. The best methods achieve prediction errors of 3 kcal/mol for the atomization energies of a wide variety of molecules. Rationales for this performance improvement are given together with pitfalls and challenges when applying machine learning approaches to the prediction of quantum-mechanical observables

Toward Low-Temperature Dehydrogenation Catalysis: Isophorone Adsorbed on Pd(111)

Adsorbate geometry and reaction dynamics play essential roles in catalytic processes at surfaces. Here we present a theoretical and experimental study for a model functional organic/metal interface: isophorone (C₉H₁₄O) adsorbed on the Pd(111) surface. Density functional theory calculations with the Perdew–Burke–Ernzerhoff (PBE) functional including van der Waals (vdW) interactions, in combination with infrared spectroscopy and temperature-programmed desorption (TPD) experiments, reveal the reaction pathway between the weakly chemisorbed reactant (C₉H₁₄O) and the strongly chemisorbed product (C₉H₁₀O), which occurs by the cleavage of four C–H bonds below 250 K. Analysis of the TPD spectrum is consistent with the relatively small magnitude of the activation barrier derived from PBE+vdW calculations, demonstrating the feasibility of low-temperature dehydrogenation

Prognostic Impact of [18F]Fluorothymidine and [18F]Fluoro-D-Glucose Baseline Uptakes in Patients with Lung Cancer Treated First-Line with Erlotinib

<div><p>3′-deoxy-3′-[¹⁸F]fluoro-L-thymidine (FLT) and 2′-deoxy-2′-[¹⁸F]fluoro-D-glucose (FDG) are used to visualize proliferative and metabolic activity of tumors. In this study we aimed at evaluating the prognostic value of FLT and FDG uptake measured by positron emission tomography (PET) in patients with metastatic non-small cell lung cancer (NSCLC) prior to systemic therapy with erlotinib. FLT and FDG maximum standardized uptake (SUVmax) values per patient were analyzed in 40 chemotherapy naive patients with advanced NSCLC (stage IV) before treatment with erlotinib. Prior therapy median SUVmax was 6.6 for FDG and 3.0 for FLT, respectively. In univariate analysis, patients with an FDG SUVmax <6.6 had a significantly better overall survival (16.3 months [95% confidence interval [CI] 7.1–25.4 months]) compared to patients with an FDG SUVmax ≥6.6 (3.1 months [95% CI 0.6–5.5 months]) (p<0.001, log rank). Similarly, low FLT uptake (SUVmax <3.0) was associated with significantly longer survival (10.3 months (0–23.3 months, 95% CI) compared to high FLT uptake (3.4 months (0–8.1 months, 95% CI) (p = 0.027). The independent prognostic value of baseline FDG uptake was demonstrated in multivariate analysis (p = 0.05, Cox regression). These data suggest that baseline SUVmax values for both FDG and FLT PET might be further developed as markers for prognostic stratification of patients in advanced NSCLC treated with tyrosine kinase inhibitors (TKI) directed against the epidermal growth factor receptor (EGFR).</p> <h3>Trial Registration</h3><p>Clinicaltrials.gov, Identifier: <a href="http://clinicaltrials.gov/ct2/show/NCT00568841">NCT00568841</a></p> </div

Individual patient characteristics and PET results.

<p>Individual patient characteristics and PET results.</p