Personal tools
You are here: Home The Code Publications year-2010


Publications during 2010

Article Reference A combined experimental and theoretical study of benzoxaborole derivatives by Raman and IR spectroscopy, static DFT, and first-principle molecular dynamics
Physicochemical properties of 1,3-dihydro-1-hydroxy-3-morpholin-4-yl-2,1-benzoxaborole (IIa) and 1,3-dihydro-1-hydroxy-2,1-benzoxaborole (IIb) were investigated using a combination of spectroscopic and computational approaches. The compound IIa belongs to the group represented by the prototypical benzoxaborole IIb, which exhibits receptor activity toward sugars in aqueous solution. Additionally, the IIb can serve as a pattern structure for physicochemical description of benzoxaborole derivatives. The infrared and Raman spectroscopy measurements were performed in solvents and in the solid state. Furthermore, experimental findings served as a reference data source for further computational investigations. DFT calculations in vacuo were used to estimate the binding energy of the dimeric forms, indicating the strength of the intermolecular hydrogen bonds. AIM and ELF theories were applied to give an insight into the electronic structure of the studied compounds. The last part of this study contains Car-Parrinello molecular dynamics investigations in the solid state. Computational results indicated that the key intermolecular feature, the pair of hydrogen bonds, is rather harmonic and the extent of the anharmonicity is temperature dependent as shown by the O-H stretching envelope calculations performed for IIa. Inclusion of the quantum effects in the proton motion does not significantly change the qualitative description of the intermolecular H-bond dynamics of the investigated compound. Copyright (C) 2009 John Wiley & Sons, Ltd.
Article Reference A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide
Most current biomolecular simulations are based on potential energy functions that treat the electrostatic energy as a sum of pairwise Coulombic interactions between effective fixed atomic charges. This approximation, in which many-body induced polarization effects are included in an average way, is expected to be satisfactory for a wide range of systems, but less accurate for processes involving the transfer and partition of ions among heterogeneous environments. The limitations of these potential energy functions are perhaps most obvious in studies of ion permeation through membrane channels. In many cases, the pore is so narrow that the permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with protein atoms. Interactions of cations with protein backbone carbonyl oxygens, in particular, play a critical role in several important biological channels. As a first step toward meeting the challenge of developing an accurate explicit accounting for induced polarization effects, the present work combines experiments and computation to characterize the interactions of alkali and halide ions with N-methylacetamide chosen to represent the peptide bond. From solubility measurements, we extract the solvation free energies of KCl and NaCl in liquid N-methylacetamide. Polarizable models based on the Drude oscillator are then developed and compared with available experimental and ab initio data. The good agreement for a range of structural and thermodynamic properties in the gas and condensed phases suggests that the polarizable models provide an accurate representation of ion amide interactions in biological systems.
Article Reference A model proton-transfer system in the condensed phase: NH(4)(+)OOH(-), a crystal with short intermolecular H-bonds
The crystal structure of NH(4)(+)OOH(-) is determined from single-crystal x-ray data obtained at 150 K. The crystal belongs to the space group P2(1)/c and has four molecules in a unit cell. The structure consists of discrete NH(4)(+) and OOH(-) ions. The OOH(-) ions are linked by short hydrogen bonds (2.533 angstrom) to form parallel infinite chains. The ammonium ions form links between these chains (the N center dot center dot center dot O distances vary from 2.714 to 2.855 angstrom) giving a three-dimensional network. The harmonic IR spectrum and H-bond energies are computed at the Perdew-Burke-Ernzerhof (PBE)/6-31G** level with periodic boundary conditions. A detailed analysis of the shared (bridging) protons' dynamics is obtained from the CPMD simulations at different temperatures. PBE functional with plane-wave basis set (110 Ry) is used. At 10 K the shared proton sits near the oxygen atom, only a few proton jumps along the chain are detected at 70 K while at 270 K numerous proton jumps exist in the trajectory. The local-minimum structure of the space group Cc is localized. It appears as a result of proton transfer along a chain. This process is endothermic (similar to 2 kJ/mol) and is described as P2(1)/c <-> 2Cc. The computed IR spectrum at 10 K is close to the harmonic one, the numerous bands appear at 70 K while at 270 K it shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1). The advantages of the NH(4)(+)OOH(-) crystal as a promising model for the experimental and DFT based molecular dynamics simulation studies of proton transfer along the chain are discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3493688]
In order to identify the influences imposed by Fe substitution, density functional theory-based Car-Parrinello molecular dynamics simulations were employed to study both oxidized and reduced Fe-bearing smectites. The following basic properties were investigated: local structures in the clay layer, hydroxyl on and the vibration dynamicos of H and Si. Structural analyses indicated that the average Fe-O bond lengths are similar to 2.08 angstrom and 2.02 angstrom in the reduced and oxidized models, respectively, and the Fe substitutions did not affect the coordination structures of the Al-O and Si-O polyhedra. For hydroxyl orientations, Fe(III) substitution had no obvious in but Fe(II) forces the coordinated hydroxyls to present a wide-angle distribution. Furthermore, the present work has shown that both substitutions can red-shift the hydroxyl in-plane bending mode. The analyses also revealed that Fe(III) substitution has no effect on the Si-O stretching, while Fe reduction causes a blue-shift of the out-of-plane stretching mode. The results provide quantitative constraints and clues for future research.
Article Reference Ab Initio Molecular Dynamics Study of an Aqueous Solution of [Fe(bpy)(3)](Cl)(2) in the Low-Spin and in the High-Spin States
Article Reference Ab Initio Study of Microsolvated Al3+-Aromatic Amino Acid Complexes
Article Reference Acid dissociation mechanisms of Si(OH)(4) and Al(H(2)O)(6)(3+) in aqueous solution
Silicic acid and the hexa-aqua of Al(3+) are fundamental model aqueous species of chemical importance in nature. In order to investigate their hydroxyl dissociation mechanisms, Car-Parrinello molecular dynamics (CPMD) simulations were carried out, which allow treating the solutes and solvents on the same footing. The method of constraint was employed to trigger the reactions by taking coordination number as the reaction coordinate and the thermodynamic integration was used to obtain the free-energy profiles. The approximate transition states were located and the reactant and product states were also characterized. The free-energy changes of dissociation are found about 15.0 kcal/mol and 7.7 kcal/mol for silicic acid and Al-aqua, respectively. From the simulation results, the first pKas were calculated by using two approaches, which are based on the pristine thermodynamic relation and the RDF (radial distribution function)-free energy relation, respectively. Because of more uncertainties involved in the RDF way, it is suggested that the pristine way should be favored, which shows an error margin of 1 pKa unit. This study provides an encouraging basis for applying the present methodology to predict acidity constants of those groups that are difficult to measure experimentally. (c) 2009 Elsevier Ltd. All rights reserved.
Article Reference An Ab Initio Molecular Dynamics Study on the Hydrolysis of the Po(IV) Aquaion in Water
Po(IV) in water has been studied by means of Car-Parrinello molecular dynamics (CPMD) simulations. A new Trouiller Martins pseudopotential for Po(I V) has been developed. This pseudopotential was tested by comparing the structure and energetics of small [Po(H(2)O)(n)(OH)(m)](4-m) clusters optimized quantum-mechanically. CP-MD simulations of 1 Po + 60 H(2)O were carried out starting from three different degrees of hydrolysis of the aquaion (m = 0, 2, and 3), in order to check the stability of the hydrolyzed forms under the simulation conditions. The three simulations converge to a description of the solution where the same hydrolyzed species are present. Dynamics of the octahydrate aquaion in water indicates that dehydration couples to hydrolysis processes, and the total coordination number decreases with the hydrolysis degree. The time evolution of the initial [Po(H(2)O)(8)](4+) aquaion in aqueous solution indicates that hydrolysis precedes to dehydration in the process from aquaion to hydroxoaquaion. Structural and dynamical properties of the ligands in the first coordination shell are analyzed. The power spectra and its contribution from fragments of the first coordination shell are also examined.
Article Reference An ab initio molecular dynamics study of hydronium complexation in Na-montmorillonite
Article Reference Atomistic Simulation of the Interaction of an Electrolyte with Graphite Nanostructures in Perspective Supercapacitors
An electrical double layer at the interface between an aqueous electrolyte solution and a carbon electrode has been investigated. In order to estimate the capacitive properties of such a system and to reveal the main factors affecting its properties, quantum molecular dynamics simulation of the electrical double layer has been performed numerically using the density-functional theory. The capacitive properties have been estimated and the prevailing effect of the electron-hole plasma of the carbon electrode on the capacity of the system has been revealed.
Article Reference Bias-Exchange Metadynamics Applied to the Study of Chemical Reactivity
We show how the combination of Bias Exchange metadynamics (BE) with Car-Parrinello molecular dynamics (CPMD) can lead to vast improvements in the study of chemical reactions. Bias Exchange metadynamics is a recently introduced methodology that combines replica exchange techniques with the metadynamics approach. It allows fast parallel reconstruction of the free energy of a system in a virtually unlimited number of variables. The value of the method was previously demonstrated for the folding of a Triptophane cage miniprotein on the classical potential energy surface. As a test case for the DFT implementation, we investigated the competitive S(N)2 reaction of CH(3)Cl with Cl(-) and Br(-). The results illustrate three important advantages of the method. (1) Fast and complete sampling of configuration space occurs in each replica. (2) A significant speed-up can be observed in the convergence of the free energy profiles, compared with regular metadynamics. (3) The best conformational distributions are successfully transferred from one replica to the others. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2299-2307, 2010
Article Reference Bioinorganic Chemistry of Parkinson's Disease: Structural Determinants for the Copper-Mediated Amyloid Formation of Alpha-Synuclein
The aggregation of alpha-synuclein (AS) is a critical step in the etiology of Parkinson's disease (PD). A central, unresolved question in the pathophysiology of PD relates to the role of AS-metal interactions in amyloid fibril formation and neurodegeneration. Our previous works established a hierarchy in alpha-synuclein-metal ion interactions, where Cu(II) binds specifically to the protein and triggers its aggregation under conditions that might be relevant for the development of PD. Two independent, non-interacting copper-binding sites were identified at the N-terminal region of AS, with significant difference in their affinities for the metal ion. In this work we have solved unknown details related to the structural binding specificity and aggregation enhancement mediated by Cu(II). The high-resolution structural characterization of the highest affinity N-terminus AS-Cu(II) complex is reported here. Through the measurement of AS aggregation kinetics we proved conclusively that the copper-enhanced AS amyloid formation is a direct consequence of the formation of the AS-Cu(II) complex at the highest affinity binding site. The kinetic behavior was not influenced by the His residue at position 50, arguing against an active role for this residue in the structural and biological events involved in the mechanism of copper-mediated AS aggregation. These new findings are central to elucidate the mechanism through which the metal ion participates in the fibrillization of AS and represent relevant progress in the understanding of the bionorganic chemistry of PD.
Article Reference Calculation of NMR parameters in ionic solids by an improved self-consistent embedded cluster method
Article Reference Car-Parrinello Molecular Dynamics Study of the Intramolecular Vibrational Mode-Sensitive Double Proton-Transfer Mechanisms in Porphycene
Article Reference Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate
We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology. (C) 2010 American Institute of Physics. [doi:10.1063/1.3429251]
Article Reference Chiral Transformation in Protonated and Deprotonated Adipic Acids through Multistep Internal Proton Transfer
Protonated and deprotonated adipic acids (PAA: HOOC-(CH(2))(4)-COOH(2)(+) and DAA: HOOC-(CH(2))(4)-COO(-)) have a charged hydrogen bond under the influence of steric constraint due to the molecular skeleton of a circular ring. Despite the similarity between PAA and DAA, it is surprising that the lowest energy structure of PAA is predicted to have (H(2)O center dot center dot center dot H center dot center dot center dot OH(2))(+) Zundel-like symmetric hydrogen bonding, whereas that of DAA has H(3)O(+) Eigen-like asymmetric hydrogen bonding. The energy profiles show that direct proton transfer between mirror image structures is unfavorable. Instead, the chiral transformation is possible by subsequent backbone twistings through stepwise proton transfer along multistep intermediate structures, which are Zundel-like ions for PAA and Eigen-like ions for DAA. This type of chiral transformation by multistep intramolecular proton transfers is unprecedented. Several prominent OH center dot center dot center dot O short hydrogen-bond stretching peaks are predicted in the range of 1000-1700 cm(-1) in the Car-Parrinello molecular dynamics (CPMD) simulations, which show distinctive signatures different from ordinary hydrogen-bond peaks. The O-H-O stretching peaks in the range of 1800-2700 cm(-1) become insignificant above around 150 K and are almost washed out at about 300 K.
Article Reference Combining ab initio quantum mechanics with a dipole-field model to describe acid dissociation reactions in water: First-principles free energy and entropy calculations
Article Reference Comparison of cationic, anionic and neutral hydrogen bonded dimers
Article Reference Compression-induced transformation of aldehydes into polyethers: A first-principles molecular dynamics study
Article Reference Coordination Numbers of K+ and Na+ Ions Inside the Selectivity Filter of the KcsA Potassium Channel: Insights from First Principles Molecular Dynamics
Document Actions
« June 2019 »