Exploring the conformational preferences of 20-residue peptides in isolation: Ac-Ala19-Lys + H+vs. Ac-Lys-Ala19 + H+ and the current reach of DFT

Native like helices in a specially designed β peptide in the gas phase

(2015) Franziska Schubert et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Long-range correlation energy calculated from coupled atomic response functions

(2014) Alberto Ambrosetti et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2014) Mariana Rossi et al.   JOURNAL OF PHYSICAL CHEMISTRY A

How Cations Change Peptide Structure

(2013) Carsten Baldauf et al.   CHEMISTRY-A EUROPEAN JOURNAL

Interatomic methods for the dispersion energy derived from the adiabatic connection fluctuation-dissipation theorem

(2013) Alexandre Tkatchenko et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

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

(2013) Mariana Rossi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energies of Binding from Large-Scale First-Principles Quantum Mechanical Calculations: Application to Ligand Hydration Energies

(2013) Stephen J. Fox et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Density Functional Theory Study of β-Hairpins in Antiparallel β-Sheets, a New Classification Based upon H-Bond Topology

(2012) Dipankar Roy et al.   BIOCHEMISTRY

Conformational Preferences of Gas-Phase Helices: Experiment and Theory Struggle to Agree: The Seven-Residue Peptide Ac-Phe-(Ala)5-Lys-H+

(2012) Yaoming Xie et al.   CHEMISTRY-A EUROPEAN JOURNAL

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ab initioMO Theory - An Important Tool in Foldamer Research: Prediction of Helices in Oligomers ofω-Amino Acids

(2012) Carsten Baldauf et al.   HELVETICA CHIMICA ACTA

Water Adsorption at Two Unsolvated Peptides with a Protonated Lysine Residue: From Self-Solvation to Solvation

(2012) Sucismita Chutia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Globule to Helix Transition in Sodiated Polyalanines

(2012) Jonathan K. Martens et al.   Journal of Physical Chemistry Letters

Resolution-of-identity approach to Hartree–Fock, hybrid density functionals, RPA, MP2 andGWwith numeric atom-centered orbital basis functions

(2012) Xinguo Ren et al.   NEW JOURNAL OF PHYSICS

Accurate and Efficient Method for Many-Body van der Waals Interactions

(2012) Alexandre Tkatchenko et al.   PHYSICAL REVIEW LETTERS

Collective many-body van der Waals interactions in molecular systems

(2012) R. A. DiStasio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

\mathcal{O}(N) methods in electronic structure calculations

(2012) D R Bowler et al.   REPORTS ON PROGRESS IN PHYSICS

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Challenges for Density Functional Theory

(2011) Aron J. Cohen et al.   CHEMICAL REVIEWS

Compact Folding of Isolated Four-Residue Neutral Peptide Chains: H-Bonding Patterns and Entropy Effects

(2011) Richard J. Plowright et al.   CHEMPHYSCHEM

Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules

(2011) Stephen J. Fox et al.   JOURNAL OF CHEMICAL PHYSICS

Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals

(2011) Noa Marom et al.   Journal of Chemical Theory and Computation

Number of Solution States of Bradykinin from Ion Mobility and Mass Spectrometry Measurements

(2011) Nicholas A. Pierson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Unraveling the Stability of Polypeptide Helices: Critical Role of van der Waals Interactions

(2011) Alexandre Tkatchenko et al.   PHYSICAL REVIEW LETTERS

Hydrogen Bonds and van der Waals Forces in Ice at Ambient and High Pressures

(2011) Biswajit Santra et al.   PHYSICAL REVIEW LETTERS

Hydrogen Bonding Cooperativity in polyQ β-Sheets from First Principle Calculations

(2010) Giulia Rossetti et al.   Journal of Chemical Theory and Computation

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

(2010) Mariana Rossi et al.   Journal of Physical Chemistry Letters

Challenges in protein-folding simulations

(2010) Peter L. Freddolino et al.   Nature Physics

Effect of the surface on the secondary structure of soft landed peptide ions

(2010) Qichi Hu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase

(2010) Marie-Pierre Gaigeot   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ab initio molecular simulations with numeric atom-centered orbitals

(2009) Volker Blum et al.   COMPUTER PHYSICS COMMUNICATIONS

Spectroscopic studies of cold, gas-phase biomolecular ions

(2009) Thomas R. Rizzo et al.   INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY

Density functional theory study of the conformational space of an infinitely long polypeptide chain

(2009) Joel Ireta et al.   JOURNAL OF CHEMICAL PHYSICS

Vibrational Spectra of Small Protonated Peptides from Finite Temperature MD Simulations and IRMPD Spectroscopy

(2009) A. Cimas et al.   Journal of Chemical Theory and Computation

Efficient integration for all-electron electronic structure calculation using numeric basis functions

(2009) V. Havu et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Accurate Molecular Van Der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data

(2009) Alexandre Tkatchenko et al.   PHYSICAL REVIEW LETTERS

Potential-Energy and Free-Energy Surfaces of Glycyl-Phenylalanyl-Alanine (GFA) Tripeptide: Experiment and Theory

(2008) Haydee Valdes et al.   CHEMISTRY-A EUROPEAN JOURNAL

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Vibrational Spectroscopy and Conformational Structure of Protonated Polyalanine Peptides Isolated in the Gas Phase

(2008) Timothy D. Vaden et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field

(2008) Haydee Valdes et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Spectroscopy and conformational preferences of gas-phase helices

(2008) Jaime A. Stearns et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS