Kestutis Aidas

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Kestutis Aidas,1 Celestino Angeli,2 Keld L. Bak,3 Vebjørn Bakken,4 Radovan Bast,5 Linus Boman,6 Ove Christiansen,7 Renzo Cimiraglia,2 Sonia Coriani,8 Pål Dahle,9 Erik K. Dalskov,10 Ulf Ekström,11 Thomas Enevoldsen,12 Janus J. Eriksen,7 Patrick Ettenhuber,7 Berta Fernández,13 Lara Ferrighi,14 Heike Fliegl,11 Luca Frediani,14 Kasper Hald,15 Asger Halkier,16(More)
We present the theory and an implementation of the combined quantum mechanics/molecular mechanics/polarizable dielectric continuum (QM/MM/PCM) method. This is a fully polarizable layered model designed for effective inclusion of a medium in a quantum-mechanical calculation. The short-range part of the solvent electrostatic potential is described by an(More)
The (15)N NMR spectrum of adenine in aqueous solution has been modeled using high-level combined density functional theory/molecular mechanics techniques coupled to a dynamical averaging scheme. The explicit consideration of the three lowest-energy tautomers of adenine-H9, H7 and H3-allows for a well-founded comparison to experimental data. Based on a very(More)
In this work the role of higher molecular aggregation in the proton transfer processes within hydrogen bond (H-bond) is investigated. The H-bonded complex consisting of 4-cyanopyridine (CyPy) with trichloroacetic acid (TCA) has been studied in the solutions of acetonitrile, carbon tetrachloride, chloroform and dichloroethane as solvent by FTIR spectroscopy(More)
In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning(More)
We present the first systematic investigation of shifts in the nuclear magnetic resonance (NMR) shielding constant due to hydrogen bonding using either the series of wave function based methods, Hartree-Fock (HF), second-order Møller-Plesset perturbation theory (MP2), Coupled Cluster Singles and Doubles (CCSD) and CCSD extended with an approximate(More)
Uracil is a commonly occurring pyrimidine derivative found in RNA where it base pairs with adenine. Rationalizing the electronic properties of uracil in both gas phase and aqueous solution is of fundamental importance because of the significant biological role played by this molecule. This paper presents accurate predictions of the solvatochromic shifts of(More)
The combined linear response coupled cluster/molecular mechanics (CC/MM) scheme including mutual polarization effects in the coupling Hamiltonian is applied together with supermolecular CC methods to the study of the gas-to-aqueous solution blue shift of the n --> pi* excitation energy in acetone. The aug-cc-pVDZ basis set is found to be adequate for the(More)
Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical(More)
Motivated by future possibilities to design target molecules for fibrils with diagnostic or therapeutic capability related to amyloidosis diseases, we investigate in this work the dielectric nature of amyloid fibril microenvironments in different binding sites using an optical probe, thioflavin-T (THT), which has been used extensively to stain such fibrils.(More)