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Pavel Hobza - One of the best experts on this subject based on the ideXlab platform.
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The World of Non-Covalent Interactions: 2006
Collection of Czechoslovak Chemical Communications, 2020Co-Authors: Pavel Hobza, Rudolf Zahradník, Klaus Müller-dethlefsAbstract:The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, Nucleic Acid Base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and Nucleic Acid Base pairs. A review with 270 references.
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balance of attraction and repulsion in Nucleic Acid Base stacking ccsd t complete basis set limit calculations on uracil dimer and a comparison with the force field description
Journal of Chemical Theory and Computation, 2009Co-Authors: Claudio A Morgado, Pavel Hobza, Petr Jurecka, Daniel Svozil, Jiři SponerAbstract:We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantum-mechanics (QM) methods. Nonparallel stacking geometries often occur in Nucleic Acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the short-range repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been car...
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benchmark ri mp2 dataBase of Nucleic Acid Base trimers performance of different density functional models for prediction of structures and binding energies
Physical Chemistry Chemical Physics, 2007Co-Authors: Martin Kabelac, Christopher J Cramer, Edward C Sherer, Haydee Valdes, Pavel HobzaAbstract:A new dataBase of Nucleic Acid Base trimers has been developed that includes 141 geometries and stabilization energies obtained at the RI-MP2 level of theory with the TZVPP basis set. Compared to previously compiled biologically oriented dataBases, this new construct includes considerably more complicated structures; the various intermolecular interactions in the trimers are quite heterogeneous and in particular include simultaneous hydrogen bonding and stacking interactions, which is similar to the situation in actual biopolymers. Validation against these benchmark data is therefore a more demanding task for approximate models, since correct descriptions of all energy terms are unlikely to be accomplished by fortuitous cancellations of systematic errors. The density functionals TPSS (both with and without an empirical dispersion term), PWB6K, M05-2X, and BHH removal of the dispersion correction leads to significantly degraded performance. The M05-2X and PWB6K functionals performed very well in reproducing the RI-MP2 geometries, but showed a systematic moderate underestimation of the magnitude of Base stacking interactions. The SCC-DFTB-D method predicts geometries in fair agreement with RI-MP2; given its computational efficiency it represents a good option for initial scanning of analogous biopolymeric potential energy surfaces. BH&H gives geometries of comparable quality to the other functionals but significantly overestimates interaction energies other than stacking.
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density functional theory symmetry adapted perturbation treatment energy decomposition of Nucleic Acid Base pairs taken from dna crystal geometry
Journal of Chemical Physics, 2007Co-Authors: Robert Sedlak, Petr Jurecka, Pavel HobzaAbstract:First- and second-order perturbation energies for H-bonded and stacked structures of Nucleic Acid Base pairs in DNA crystal geometries were determined using the density functional theory symmetry adapted perturbation treatment method. Considerably larger stabilization of the former pairs is due to electrostatic and induction energies. Total E(1) energies for both pairs are, however, similar and the same is true for dispersion energy.
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stability of Nucleic Acid Base pairs in organic solvents molecular dynamics molecular dynamics quenching and correlated ab initio study
Journal of Physical Chemistry B, 2007Co-Authors: Lucie Zendlova, Pavel Hobza, Martin KabelacAbstract:The dynamic structure and potential energy surface of adenine···thymine and guanine···cytosine Base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of ...
James Alexis Platts - One of the best experts on this subject based on the ideXlab platform.
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calculating stacking interactions in Nucleic Acid Base pair steps using spin component scaling and local second order moller plesset perturbation theory
Physical Chemistry Chemical Physics, 2008Co-Authors: Grant J Hill, James Alexis PlattsAbstract:Stacking interaction energies for ten B-DNA Base-pair steps are computed with density fitted local second-order Moller–Plesset perturbation theory (DF-LMP2), and with the spin-component scaled (SCS) and spin-component scaled for nucleoBases (SCSN) variants of DF-LMP2. Comparison with existing CBS(T) reference data indicates larger than expected energy differences for both SCS variants. After an analysis of the errors involved, an alternative method of producing reference data is proposed where DF-LMP2/aug-cc-pVTZ and DF-LMP2/aug-cc-pVQZ energies for the whole complex are extrapolated to produce interaction energies that do not require many-body correction and show reduced error in estimation of the basis set limit. A literature correction term from coupled cluster theory with perturbative triples is then added to the DF-LMP2 estimated basis set limit. These new reference data are consistently around 1 kcal mol−1 less than previous literature data. DF-SCSN-LMP2/aug-cc-pVTZ is found to reproduce the new reference interaction energies with a root mean square error (RMSE) of 0.71 kcal mol−1, while SCS consistently underestimates the binding energy.
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spin component scaling methods for weak and stacking interactions
Journal of Chemical Theory and Computation, 2007Co-Authors: John Grant Hill, James Alexis PlattsAbstract:New scaling parameters are presented for use in the spin-component scaled (SCS) variant of density fitted local second-order Moller−Plesset perturbation theory (DF-LMP2) that have been optimized for use in evaluating the interaction energy between Nucleic Acid Base pairs. The optimal set of parameters completely neglects the contribution from antiparallel-spin electron pairs to the MP2 energy while scaling the parallel contribution by 1.76. These spin-component scaled for nucleoBases (SCSN) parameters are obtained by minimizing, with respect to SCS parameters, the rms interaction energy error relative to the best available literature values, over a set of ten stacked Nucleic Acid Base pairs. The applicability of this scaling to a wide variety of noncovalent interactions is verified through evaluation of a larger set of model complexes, including those dominated by dispersion and electrostatics.
Martin Kabelac - One of the best experts on this subject based on the ideXlab platform.
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benchmark ri mp2 dataBase of Nucleic Acid Base trimers performance of different density functional models for prediction of structures and binding energies
Physical Chemistry Chemical Physics, 2007Co-Authors: Martin Kabelac, Christopher J Cramer, Edward C Sherer, Haydee Valdes, Pavel HobzaAbstract:A new dataBase of Nucleic Acid Base trimers has been developed that includes 141 geometries and stabilization energies obtained at the RI-MP2 level of theory with the TZVPP basis set. Compared to previously compiled biologically oriented dataBases, this new construct includes considerably more complicated structures; the various intermolecular interactions in the trimers are quite heterogeneous and in particular include simultaneous hydrogen bonding and stacking interactions, which is similar to the situation in actual biopolymers. Validation against these benchmark data is therefore a more demanding task for approximate models, since correct descriptions of all energy terms are unlikely to be accomplished by fortuitous cancellations of systematic errors. The density functionals TPSS (both with and without an empirical dispersion term), PWB6K, M05-2X, and BHH removal of the dispersion correction leads to significantly degraded performance. The M05-2X and PWB6K functionals performed very well in reproducing the RI-MP2 geometries, but showed a systematic moderate underestimation of the magnitude of Base stacking interactions. The SCC-DFTB-D method predicts geometries in fair agreement with RI-MP2; given its computational efficiency it represents a good option for initial scanning of analogous biopolymeric potential energy surfaces. BH&H gives geometries of comparable quality to the other functionals but significantly overestimates interaction energies other than stacking.
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stability of Nucleic Acid Base pairs in organic solvents molecular dynamics molecular dynamics quenching and correlated ab initio study
Journal of Physical Chemistry B, 2007Co-Authors: Lucie Zendlova, Pavel Hobza, Martin KabelacAbstract:The dynamic structure and potential energy surface of adenine···thymine and guanine···cytosine Base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of ...
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hydration and stability of Nucleic Acid Bases and Base pairs
Physical Chemistry Chemical Physics, 2007Co-Authors: Martin Kabelac, Pavel HobzaAbstract:Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of Nucleic Acid Bases and structure and properties of Nucleic Acid Base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible Nucleic Acid Base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of Bases and on the spatial arrangement of the Bases in a Base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the Base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the Base pair with a small number of solvent molecules.
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potential energy and free energy surfaces of all ten canonical and methylated Nucleic Acid Base pairs molecular dynamics and quantum chemical ab initio studies
Journal of Physical Chemistry B, 2001Co-Authors: Martin Kabelac, Pavel HobzaAbstract:The potential energy surfaces (PESs) and free energy surfaces (FESs) of all 10 canonical and methylated Nucleic Acid Base pairs were studied by a molecular dynamics/quenching (MD/Q) technique with the Cornell et al. empirical force field and by a correlated ab initio quantum chemical method. More than a dozen energy minima were located on the PES of each Base pair. The global and first local minima of nonmethylated Base pairs have a systematically planar H-bonded structure, while T-shaped and stacked structures are less stable. The MD/Q search sometimes reveals an unexpected structure as the global energy minimum (e.g., the global minimum of the adenine...thymine PES corresponds neither to the Watson−Crick nor the Hoogsteen type of bonding). Entropy does not play an important role and the relative order of individual structures on the PES and FES does not differ too much. Methylation at purine N9 and pyrimidine N1 brings dramatic changes in the PESs and FESs, mainly because the most stable and most popula...
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at nonzero temperatures stacked structures of methylated Nucleic Acid Base pairs and microhydrated nonmethylated Nucleic Acid Base pairs are favored over planar hydrogen bonded structures a molecular dynamics simulations study
Chemistry: A European Journal, 2001Co-Authors: Martin Kabelac, Pavel HobzaAbstract:: The dynamic structure of all ten possible Nucleic Acid (NA) Base pairs and methylated NA Base pairs hydrated by a small number of water molecules (from 1 to 16) was determined by using molecular dynamics simulations in the NVE microcanonical and NVT canonical ensembles with the Cornell force field (W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. E. Caldwell, P. Kollman, J. Am. Chem. Soc. 1995, 117, 5179). The presence of one water molecule does not affect the structure of any hydrogen-bonded (H-bonded) nonmethylated Base pair. An equal population of H-bonded and stacked structures of adenine...adenine, adenine...guanine and adenine... thymine pairs is reached if as few as two water molecules are present, while obtaining equal populations of these structures in the case of adenine...cytosine, cytosine...thymine, guanine... guanine and guanine...thymine required the presence of four water molecules, and in the case of guanine...cytosine, six. A comparable population of planar, H-bonded and stacked structures for cytosine...cytosine and thymine... thymine Base pairs was only obtained if at least eight water molecules hydrated a pair. Methylation of Bases changed the situation dramatically and stacked structures were favoured over H-bonded ones even in the absence of water molecules in most cases. Only in the case of methyl cytosine...methyl cytosine, methyl guanine...methyl guanine and methyl guanine...methyl cytosine pairs were two, two or six water molecules, respectively, needed in order to obtain a comparable population of planar, H-bonded and stacked structures. We believe that these results give clear evidence that the preferred stacked structure of NA Base pairs in the microhydrated environment, and also apparently in a regular solvent, is due to the hydrophilic interaction of a small number of water molecules. In the case of methylated Bases, it is also due to the fact that the hydrogen atoms most suitable for the formation of H-bonds have been replaced by a methyl group. A preferred stacked structure is, thus, not due to a hydrophobic interaction between a large bulk of water molecules and the Base pair, as believed.
Petr Jurecka - One of the best experts on this subject based on the ideXlab platform.
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balance of attraction and repulsion in Nucleic Acid Base stacking ccsd t complete basis set limit calculations on uracil dimer and a comparison with the force field description
Journal of Chemical Theory and Computation, 2009Co-Authors: Claudio A Morgado, Pavel Hobza, Petr Jurecka, Daniel Svozil, Jiři SponerAbstract:We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantum-mechanics (QM) methods. Nonparallel stacking geometries often occur in Nucleic Acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the short-range repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been car...
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density functional theory symmetry adapted perturbation treatment energy decomposition of Nucleic Acid Base pairs taken from dna crystal geometry
Journal of Chemical Physics, 2007Co-Authors: Robert Sedlak, Petr Jurecka, Pavel HobzaAbstract:First- and second-order perturbation energies for H-bonded and stacked structures of Nucleic Acid Base pairs in DNA crystal geometries were determined using the density functional theory symmetry adapted perturbation treatment method. Considerably larger stabilization of the former pairs is due to electrostatic and induction energies. Total E(1) energies for both pairs are, however, similar and the same is true for dispersion energy.
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on geometries of stacked and h bonded Nucleic Acid Base pairs determined at various dft mp2 and ccsd t levels up to the ccsd t complete basis set limit level
Journal of Chemical Physics, 2005Co-Authors: Iwona Dabkowska, Petr Jurecka, Pavel HobzaAbstract:The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adenine⋯thymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller–Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G*) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy ...
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stabilization energies of the hydrogen bonded and stacked structures of Nucleic Acid Base pairs in the crystal geometries of cg at and ac dna steps and in the nmr geometry of the 5 d gcgaagc 3 hairpin complete basis set calculations at the mp2 and cc
Journal of Physical Chemistry A, 2005Co-Authors: Iwona Dabkowska, Petr Jurecka, Haydee Valdes Gonzalez, Pavel HobzaAbstract:Stabilization energies of the H-bonded and stacked structures of a DNA Base pair were studied in the crystal structures of adenine−thymine, cytosine−guanine, and adenine−cytosine steps as well as in the 5‘-d(GCGAAGC)-3‘ hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the ΔECCSD(T) − ΔEMP2 correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of Base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand st...
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accurate interaction energies of hydrogen bonded Nucleic Acid Base pairs
Journal of the American Chemical Society, 2004Co-Authors: Jiri Sponer, Petr Jurecka, Pavel HobzaAbstract:Hydrogen-bonded Nucleic Acids Base pairs substantially contribute to the structure and stability of Nucleic Acids. The study presents reference ab initio structures and interaction energies of selected Base pairs with binding energies ranging from −5 to −47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some Base pairs, Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G** basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of Base pairing energies with a maximum relative error of 2.6 kcal/mol when ap...
Jiři Sponer - One of the best experts on this subject based on the ideXlab platform.
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balance of attraction and repulsion in Nucleic Acid Base stacking ccsd t complete basis set limit calculations on uracil dimer and a comparison with the force field description
Journal of Chemical Theory and Computation, 2009Co-Authors: Claudio A Morgado, Pavel Hobza, Petr Jurecka, Daniel Svozil, Jiři SponerAbstract:We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantum-mechanics (QM) methods. Nonparallel stacking geometries often occur in Nucleic Acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the short-range repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been car...
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c h o contacts in the adenine uracil watson crick and uracil uracil Nucleic Acid Base pairs nonempirical ab initio study with inclusion of electron correlation effects
Journal of Physical Chemistry B, 2000Co-Authors: Pavel Hobza, Jiři Sponer, Elena Cubero, And Modesto Orozco, Javier F LuqueAbstract:Structures and stabilities of H-bonded adenine···uracil Watson−Crick (AU WC) and two uracil···uracil Nucleic Acid Base pairs possessing C−H···O contacts (UU7, UU−C) were determined using gradient optimization with inclusion of electron correlation via the second-order Moller−Plesset (MP2) perturbational method with a 6-31G** basis set of atomic orbitals. In the AU WC pair, closest contacts occur between the N6(A) and O4(U), N1(A) and N3(U), and C2(A) and O2(U) atoms: 2.969, 2.836, and 3.568 A, respectively. For the UU7 pair the closest contact corresponds to O4···N1 and C5···O2 pairs with distances of 2.860 and 3.257 A, respectively, while in UU−C pair the closest contact was found for O4···N3 and C5···O4 heteroatoms with distances of 2.913 and 3.236 A, respectively. The nature of all intermolecular contacts in the sense of a conventional H-bonding or improper, blue-shifting H-bonding was determined on the basis of harmonic vibrational analysis, atom-in-molecules (AIM) Bader analysis of electron density,...
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nature of Nucleic Acid Base stacking nonempirical ab initio and empirical potential characterization of 10 stacked Base dimers comparison of stacked and h bonded Base pairs
The Journal of Physical Chemistry, 1996Co-Authors: Jiři Sponer, And Jerzy Leszczynski, Pavel HobzaAbstract:Ab initio (MP2/6-31G*(0.25)) interaction energies were calculated for almost 240 geometries of 10 stacked Nucleic Acid−Base pairs: A···A, C···C, G···G, U···U, A···C, G···A, A···U, G···C, C···U, and G···U; in some cases uracil was replaced by thymine. The most stable stacked pair is the G···G dimer (−11.3 kcal/mol), and the least stable is the uracil dimer (−6.5 kcal/mol). The interaction energies of H-bonded Base pairs range from −25.8 kcal/mol (G···C) to −10.6 kcal/mol (T···T). The stability of stacked pairs originates in the electron correlation, while all the H-bonded pairs are dominated by the HF energy. The mutual orientation of the stacked Bases is, however, primarily determined by the HF interaction energy. The ab initio Base stacking energies are well reproduced by the empirical potential calculations, provided the atomic charges are derived by the same method as used in the ab initio calculations. Some contributions previously postulated to significantly influence Base stacking (induction interac...
