117 results match your criteria: "Center for Biomolecules and Complex Molecular Systems[Affiliation]"
Chemphyschem
January 2009
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete basis set limit) interaction energies and scaled third-order energy contributions obtained in small or medium size basis sets agree very closely with the estimated CCSD(T)/CBS interaction energies for the 22 H-bonded, dispersion-controlled and mixed non-covalent complexes from the S22 data set. Performance of this so-called MP2.5 (third-order scaling factor of 0.
View Article and Find Full Text PDFJ Phys Chem A
December 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague, Czech Republic.
The structure of dithienobicyclo[4.4.1]undeca-3,8-diene-11-one ethylene glycol ketal (database code RESVAN) was determined using the wave function theory (WFT) as well as density functional theory (DFT) methods combined with various Gaussian AO basis sets.
View Article and Find Full Text PDFJ Chem Theory Comput
November 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
The dynamic nature of the benzene dimer was explored by on-the-fly molecular dynamics simulations based on the DFT-D method covering the dispersion energy. An all-electron DFT was performed at the BLYP/TZVP level. The parameters in the dispersion correction term were fitted to mimic the benchmark CCSD(T)/complete basis set limit potential energy curves for both the parallel-displaced (PD) and T-shaped (TS) structures of the dimer exactly.
View Article and Find Full Text PDFPhys Chem Chem Phys
November 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
Proline-tryptophan complexes derived from experimental structures are investigated by quantum chemical procedures known to properly describe the London dispersion energy. We study two geometrical arrangements: the "L-shaped", stabilized by an H-bond, and the "stacked-like", where the two residues are in parallel orientation without any H-bond. Interestingly, the interaction energies in both cases are comparable and very large ( approximately 7 kcal mol(-1)).
View Article and Find Full Text PDFPhys Chem Chem Phys
October 2008
Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Praha, Czech Republic.
The nature of the electronic interactions of the stacked nucleic-acid bases (adenine, thymine, cytosine, and uracil) in homodimer and -trimer complexes in their electronically excited states was investigated and analysed in terms of orbital-overlap and Coulombic interactions. The mutual orientations of the adjacent bases were selected so as to correspond to the A- and B-DNA conformations. The extent of the electronic interaction is larger for the former conformation.
View Article and Find Full Text PDFPhys Chem Chem Phys
August 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, Prague 6, Czech Republic.
The behavior of hydronium and hydroxide ions at the water/alkane, water/vapor, and water/rigid wall interfaces was investigated by means of molecular dynamics simulations. All these interfaces exhibit a strong affinity for hydronium, which is in agreement with spectroscopic and low pH zeta-potential measurements. Except for the water/rigid wall interface, which strongly structures water and weakly attracts OH(-), none of the other investigated interfaces shows an appreciable accumulation of hydroxide.
View Article and Find Full Text PDFJ Phys Chem B
September 2008
Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic.
The hepatitis delta virus (HDV) ribozyme is an RNA motif embedded in human pathogenic HDV RNA. Previous experimental studies have established that the active-site nucleotide C75 is essential for self-cleavage of the ribozyme, although its exact catalytic role in the process remains debated. Structural data from X-ray crystallography generally indicate that C75 acts as the general base that initiates catalysis by deprotonating the 2'-OH nucleophile at the cleavage site, while a hydrated magnesium ion likely protonates the 5'-oxygen leaving group.
View Article and Find Full Text PDFJ Am Chem Soc
September 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
Employing detailed atomistic modeling we study the mechanisms behind ion binding to proteins and other biomolecules and conclude that (1) small, hard ions bind via direct ion pairing to charged surface groups and (2) large, soft ions bind to nonpolar groups via a solvent assisted attraction. Our predictions are in qualitative agreement with bulk solution data and may provide an important clue for the basic understanding of ion-specific effects in biological systems.
View Article and Find Full Text PDFChemphyschem
August 2008
Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, CZ-16610, Prague, Czech Republic.
The potential energy surfaces of the naphthalene dimer and benzene-naphthalene complexes are investigated using the recently developed DFT/CCSD(T) correction scheme [J. Chem. Phys.
View Article and Find Full Text PDFJ Phys Chem B
July 2008
Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Palacky University, Trida Svobody 26, 771 46, Olomouc, Czech Republic.
Molecular dynamics (MD) simulations at normal and high temperature were used to study the flexibility and malleability of three microsomal cytochromes P450 (CYPs): CYP3A4, CYP2C9, and CYP2A6. Comparison of B-factors (describing the atomic fluctuations) between X-ray and MD data shows that the X-ray B-factors are significantly lower in the regions where the crystal contacts occur than for other regions. Consequently, the conclusions about CYP flexibility based solely on the X-ray data might be misleading.
View Article and Find Full Text PDFJ Mol Model
August 2008
Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Faculty of Science, Palacký University, tr. Svobody 26, 771 46, Olomouc, Czech Republic.
Ankyrin repeat proteins (ARPs) appear to be abundant in organisms from all phyla, and play critical regulatory roles, mediating specific interactions with target biomolecules and thus ordering the sequence of events in diverse cellular processes. ARPs possess a non-globular scaffold consisting of repeating motifs named ankyrin (ANK) repeats, which stack on each other. The modular architecture of ARPs provides a new paradigm for understanding protein stability and folding mechanisms.
View Article and Find Full Text PDFNucleic Acids Res
June 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, CZ-166 10 Prague, Czech Republic.
The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, B- and Z-DNA forms, we have also identified combined A + B backbone-deformed conformers, e.
View Article and Find Full Text PDFPhys Chem Chem Phys
May 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague 6, Czech Republic.
A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces.
View Article and Find Full Text PDFPhys Chem Chem Phys
May 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic.
A parameter-free DFT/CCSD(T) correction scheme is proposed for precise calculations (close to CCSD(T) accuracy) of weakly bound molecular solids. The correction scheme has been tested for solid benzene and graphite. The CCSD(T)/CBS correction to planewave DFT calculations reproduces the experimentally determined lattice constants for solid benzene.
View Article and Find Full Text PDFPhys Chem Chem Phys
May 2008
Institute of Organic Chemistry and Biochemistry, vvi, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague 6, Czech Republic.
This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature.
View Article and Find Full Text PDFJ Phys Chem A
June 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
Adsorption of environmentally important aromatic molecules on a water surface is studied by means of classical and ab initio molecular dynamics simulations and by reflection-absorption infrared spectroscopy. Both techniques show strong activity and orientational preference of these molecules at the surface. Benzene and naphthalene, which bind weakly to water surface with a significant contribution of dispersion interactions, prefer to lie flat on water but retain a large degree of orientational flexibility.
View Article and Find Full Text PDFJ Chem Phys
April 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague 6, Czech Republic.
Ab initio molecular dynamics simulations modeling low-energy collisions of a sodium atom with a cluster with more than 30 water molecules are presented. We follow the dynamics of the atom-cluster interaction and the delocalization of the valence electron of sodium together with the changes in the electron binding energy. This electron tends to be shared by the nascent sodium cation and the water cluster.
View Article and Find Full Text PDFChemistry
August 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic.
The free-energy surface (FES) of glycyl-phenylalanyl-alanine (GFA) tripeptide was explored by molecular dynamics (MD) simulations in combination with high-level correlated ab initio quantum chemical calculations and metadynamics. Both the MD and metadynamics employed the tight-binding DFT-D method instead of the AMBER force field, which yielded inaccurate results. We classified the minima localised in the FESs as follows: a) the backbone-conformational arrangement; and b) the existence of a COOH.
View Article and Find Full Text PDFJ Chem Phys
March 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic.
A novel method, designated as the density functional theory/coupled-cluster with single and double and perturbative triple excitation [DFT/CCSD(T)] correction scheme, was developed for precise calculations of weakly interacting sp(2) hydrocarbon molecules and applied to the benzene dimer. The DFT/CCSD(T) interaction energies are in excellent agreement with the estimated CCSD(T)/complete basis set interaction energies. The tilted T-shaped structure having C(s) symmetry was determined to be a global minimum on the benzene-dimer potential energy surface (PES), approximately 0.
View Article and Find Full Text PDFJ Phys Chem A
May 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nAm. 2, 166 10 Prague 6, Czech Republic.
The origin of the X-Hal bond-length change in the halogen bond of the X-Hal...
View Article and Find Full Text PDFLangmuir
April 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flamingovo nAm. 2, CZ-16610 Prague 6, Czech Republic.
Using molecular dynamics simulations in an explicit aqueous solvent, we examine the binding of fluoride versus iodide to a spherical macromolecule with both hydrophobic and positively charged patches. Rationalizing our observations, we divide the ion association interaction into two mechanisms: (1) poorly solvated iodide ions are attracted to hydrophobic surface patches, while (2) the strongly solvated fluoride and to a minor extent also iodide bind via cation-anion interactions. Quantitatively, the binding affinities vary significantly with the accessibility of the charged groups as well as the surface potential; therefore, we expect the ion-macromolecule association to be modulated by the local surface characteristics of the (bio-)macromolecule.
View Article and Find Full Text PDFJ Phys Chem B
March 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, Prague 6, Czech Republic.
In this work, we investigate the mode of binding of several steroid hormones, namely aldosterone, deoxycorticosterone, and progesterone to the wild-type and S810L mutated mineralocorticoid (MR) receptor using the newly formulated density functional theory with an empirical dispersion term (DFT-D) molecular electronic structure method. It is found that the MR agonists, aldosterone and deoxycorticosterone, form tight hydrogen bonds with residues Thr945 and Asn770, which leads to the formation of hydrogen bond networks near the steroid D-ring, allowing for activation of this transcription factor. Progesterone, an MR antagonist, fails to form the necessary hydrogen bonds near the steroid D-ring.
View Article and Find Full Text PDFJ Chem Theory Comput
February 2008
Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47005 Valladolid, Spain, Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33007 Oviedo, Spain.
A systematic theoretical study on several models of Zn(II) complexes has been carried out employing both ab initio correlated wave function and density functional methods. The performance of five different functionals namely PW91, PBE, B3LYP, MPWLYP1M, and TPSS in the prediction of metal-ligand bond distances, binding energies, and proton affinities has been assessed comparing the results to those obtained with the MP2 and CCSD(T) wave function methodologies. Several basis sets ranging from double-ζ up to quintuple-ζ quality have been used, including the recently developed all-electron correlation consistent basis sets for zinc.
View Article and Find Full Text PDFJ Chem Theory Comput
February 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
In recent years it has been recognized that, because of their unique properties, halogen bonds have tremendous potential in the development of new pharmaceutical compounds and materials. In this study we investigate the phenomenon of halogen bonding by carrying out ab initio calculations on the halomethane-formaldehyde complexes as well as the fluorine substituted FnH3-nCX···OCH2 dimers, where the halogen bonding halogens (X) are chlorine, bromine, and iodine. Coupled cluster (CCSD(T)/aug-cc-pVTZ) calculations indicate that the binding energies for these type of interactions lie in the range between -1.
View Article and Find Full Text PDFProteins
July 2008
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, Prague, Czech Republic.
We are proposing an interresidue interaction energy map (IEM)--a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. We will show that the IEM can serve as a means for identifying key residues responsible for the stability of a protein.
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