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Pavel Hobza - One of the best experts on this subject based on the ideXlab platform.
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accuracy of several wave function and density functional theory methods for description of noncovalent interaction of saturated and unsaturated hydrocarbon dimers
Journal of Chemical Theory and Computation, 2012Co-Authors: Jaroslav Granatier, Michal Pitoňák, Pavel HobzaAbstract:The proper description of noncovalent complexes is a notoriously difficult problem, especially for complexes dominated by the Dispersion Energy. Accurate and reliable results can be obtained using ...
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a reliable docking scoring scheme based on the semiempirical quantum mechanical pm6 dh2 method accurately covering Dispersion and h bonding hiv 1 protease with 22 ligands
Journal of Physical Chemistry B, 2010Co-Authors: Jindrich Fanfrlik, Agnieszka K Bronowska, Jan Rezac, Ondrej Prenosil, Jan Konvalinka, Pavel HobzaAbstract:In this study, we introduce a fast and reliable rescoring scheme for docked complexes based on a semiempirical quantum mechanical PM6-DH2 method. The method utilizes a PM6-based Hamiltonian with corrections for Dispersion Energy and hydrogen bonds. The total score is constructed as the sum of the PM6-DH2 interaction enthalpy, the empirical force field (AMBER) interaction entropy, and the sum of the deformation (PM6-DH2, SMD) and the desolvation (SMD) energies of the ligand. The main advantage of the procedure is the fact that we do not add any empirical parameter for either an individual component of the total score or an individual protein−ligand complex. This rescoring method is applied to a very challenging system, namely, the HIV-1 protease with a set of ligands. As opposed to the conventional DOCK procedure, the PM6-DH2 rescoring based on all of the terms distinguishes between binders and nonbinders and provides a reliable correlation of the theoretical and experimental binding free energies. Such a ...
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On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes
Chemphyschem : a European journal of chemical physics and physical chemistry, 2010Co-Authors: Michal Kolář, Petr Jurecka, Karel Berka, Pavel HobzaAbstract:The reliability of the AMBER force field is tested by comparing the total interaction Energy and Dispersion Energy with the reference data obtained at the density functional theory-symmetry-adapted perturbation treatment (DFT-SAPT)/aug-cc-pVDZ level. The comparison is made for 194 different geometries of noncovalent complexes (H-bonded, stacked, mixed, and Dispersion-bound), at the equilibrium distances as well as at longer distances (up to a relative distance of two). The total interaction energies agree very well with the reference data and only the strength of H-bonded complexes is slightly underestimated. In the case of Dispersion Energy, the overall agreement is even better, with the exception of the stacked aromatic systems, where the empirical Dispersion Energy is overestimated. The use of AMBER interaction Energy and AMBER Dispersion Energy for different types of noncovalent complexes at equilibrium as well as at longer distances is thus justified, except for a few cases, such as the water molecule, where the Dispersion Energy is highly inaccurate.
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double helical ladder structural transition in the b dna is induced by a loss of Dispersion Energy
Journal of the American Chemical Society, 2008Co-Authors: Jiři Cerný, Martin Kabelac, Pavel HobzaAbstract:The role of the Dispersion Energy and electrostatic Energy on the geometry and stability of the B-DNA helix was investigated. Both molecular dynamics simulations with empirical force field and hybrid quantum mechanical/molecular mechanics molecular dynamics simulations, where the Dispersion or electrostatics term is suppressed/increased, on the one hand and an ab initio minimization procedure on the other have shown that the lack of the Dispersion term leads to an increase of the vertical separation of the bases as well as to a loss of helicity, thus resulting in a ladder-like structure. A decrease of the electrostatic term produces a separation of the DNA strands. The biological consequences of both electrostatic and Dispersion forces in DNA are enormous, and without either of them, DNA would become unstable and unable to provide the storage and transfer of genetic information.
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benchmark database on isolated small peptides containing an aromatic side chain comparison between wave function and density functional theory methods and empirical force field
Physical Chemistry Chemical Physics, 2008Co-Authors: Haydee Valdes, Kristýna Pluhackova, Michal Pitonak, Jan řezac, Pavel HobzaAbstract: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. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a ‘-D’ symbol have been augmented by empirical Dispersion Energy while the M06-2X functional was parameterized to cover the London Dispersion Energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the Dispersion Energy. The B3LYP and TPSS functionals—not covering this Energy—fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.
William J Meath - One of the best experts on this subject based on the ideXlab platform.
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dipole oscillator strength distributions properties and Dispersion energies for the dimethyl diethyl and methyl propyl ethers
Molecular Physics, 2008Co-Authors: Ashok Kumar, William J MeathAbstract:Isotropic dipole oscillator strength distributions (DOSDs) have been constructed for the dimethyl, diethyl and methyl–propyl ether molecules through the use of quantum mechanical constraint techniques and experimental dipole oscillator strength data. The constraints are furnished by molar refractivity data and the Thomas–Reiche–Kuhn sum rule. The DOSDs are used to obtain recommended values for a variety of isotropic dipole oscillator strength sums, logarithmic dipole oscillator strength sums, and mean excitation energies for the molecules. Pseudo-DOSDs for the ethers are also constructed and used to obtain reliable results for the isotropic dipole–dipole Dispersion Energy coefficients for all two-body interactions of the ethers with each other and with fifty other species. In addition reliable results are also obtained for the triple–dipole Dispersion Energy coefficients for all three-body interactions involving the ethers. 1Dedicated to Anthony Stone, an excellent scientist and friend, on the occasion of...
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Dipole oscillator strength properties and Dispersion energies for CI2
Molecular Physics, 2002Co-Authors: Mukesh Kumar, Ashok Kumar, William J MeathAbstract:A recommended isotropic dipole oscillator strength distribution (DOSD) has been constructed for the chlorine molecule through the use of quantum mechanical constraint techniques and experimental dipole oscillator strength and molar refractivity data. It has been used to evaluate a variety of dipole oscillator strength sums, logarithmic dipole oscillator strength sums, and mean excitation energies for the molecule. A pseudo-DOSD for C12 is also presented which is used to obtain reliable results for the isotropic dipole-dipole Dispersion Energy coefficients C6, for the interaction of Cl2 with itself and forty-two other species, and the triple-dipole Dispersion Energy coefficient C9 for (Cl2)3.
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reliable anisotropic dipole properties and Dispersion Energy coefficients for o2 evaluated using constrained dipole oscillator strength techniques
Journal of Chemical Physics, 1996Co-Authors: Ashok Kumar, William J Meath, Peter Bundgen, Ajit J ThakkarAbstract:Constrained anisotropic dipole oscillator strength techniques are used to obtain reliable values for a wide range of anisotropic and isotropic dipole properties of O2, including the dipole–dipole Dispersion Energy coefficients for the interaction of O2 with O2, H2, N2, CO, He, Ne, Ar, Kr, and Xe. Some of the anisotropic constraints required for our calculations are obtained via dipole sum rules from ab initio, multireference configuration interaction (CI) wave functions for the ground state of O2. The individual dipole properties of O2 considered include the dipole oscillator strength sums S k , k=2,1,0(−1/2)−2,−3,−4,..., the logarithmic dipole sums L k and mean excitation energiesI k , k=2(−1)−2, and, as a function of wavelength, the dynamic polarizability and its anisotropy, the total depolarization ratio, the Rayleigh scattering cross section, and the Verdet constant. Our constrained dipole oscillator strength results are often the only reliable, and sometimes the only available, ones for many of the properties and Dispersion energies considered.
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reliable isotropic and anisotropic dipole properties and dipolar Dispersion Energy coefficients for co evaluated using constrained dipole oscillator strength techniques
Journal of Chemical Physics, 1994Co-Authors: Ashok Kumar, William J MeathAbstract:Abstract Constrained anisotropic dipole oscillator strength methods are applied to obtain reliable results for a wide selection of anisotropic and isotropic dipole properties of CO and for the dipole-dipole Dispersion Energy coefficients for the interaction of CO with CO, N 2 , H 2 , He, Ne, Ar, Kr and Xe. The properties of CO evaluated include the dipole oscillator strength sums S k , k = 2, 1, 0(− 1 2 ) −2, −3, −4, ⋯, the logarithmic dipole sums L k and mean excitation energies I k , k = 2(−1) −2, and, as a function of wavelength, the dynamic polarizability and its anisotropy, the total depolarization ratio, the Rayleigh scattering cross section, and the Verdet constant. Our constrained dipole oscillator strength results are often the only reliable, and sometimes the only, results available for many of the anisotropic dipole properties and Dispersion energies considered in this paper.
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dipole oscillator strength properties and Dispersion energies for acetylene and benzene
Molecular Physics, 1992Co-Authors: Ashok Kumar, William J MeathAbstract:Dipole oscillator strength distributions (DOSDs), which are globally reliable, have been constructed for the acetylene and benzene molecules, through the use of quantum mechanical constraint techniques and experimental dipole oscillator strength and molar refractivity data. A recommended isotropic DOSD for each molecule is used to evaluate a wide variety of dipole oscillator stength sums, logarithmic dipole sums, and mean excitation energies, for C2H2 and C6H6. Also obtained are reliable results for the isotropic dipole-dipole Dispersion Energy coefficients C 6, for the interaction of acetylene and benzene with themselves and with forty-one other species, and for the triple-dipole Dispersion Energy coefficients C 9, for (C2H2)3 and (C6H6)3. Psuedo-DOSDs for acetylene and benzene are presented which greatly facilitate the evaluation of C 6's and C 9's for a variety of interactions.
Krzysztof Szalewicz - One of the best experts on this subject based on the ideXlab platform.
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intermolecular potentials based on symmetry adapted perturbation theory with Dispersion energies from time dependent density functional calculations
Journal of Chemical Physics, 2005Co-Authors: Alston J Misquitta, Bogumil Jeziorski, Rafal Podeszwa, Krzysztof SzalewiczAbstract:Recently, three of us have proposed a method [Phys. Rev. Lett. 91, 33201 (2003)] for an accurate calculation of the Dispersion Energy utilizing frequency-dependent density susceptibilities of monomers obtained from time-dependent density-functional theory (DFT). In the present paper, we report numerical calculations for the helium, neon, water, and carbon dioxide dimers and show that for a wide range of intermonomer separations, including the van der Waals and short-range repulsion regions, the method provides Dispersion energies with accuracies comparable to those that can be achieved using the current most sophisticated wave-function methods. If the Dispersion Energy is combined with (i) the electrostatic and first-order exchange interaction energies as defined in symmetry-adapted perturbation theory (SAPT) but computed using monomer Kohn-Sham (KS) determinants, and (ii) the induction Energy computed using the coupled KS static response theory, (iii) the exchange-induction and exchange-Dispersion energies computed using KS orbitals and orbital energies, the resulting method, denoted by SAPT(DFT), produces very accurate total interaction potentials. For the helium dimer, the only system with nearly exact benchmark values, SAPT(DFT) reproduces the interaction Energy to within about 2% at the minimum and to a similar accuracy for all other distances ranging from the strongly repulsive to the asymptotic region. For the remaining systems investigated by us, the quality of the SAPT(DFT) interaction energies is so high that these energies may actually be more accurate than the best available results obtained with wave-function techniques. At the same time, SAPT(DFT) is much more computationally efficient than any method previously used for calculating the Dispersion and other interaction Energy components at this level of accuracy.
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Dispersion Energy from density functional theory description of monomers
Physical Review Letters, 2003Co-Authors: Alston J Misquitta, Bogumil Jeziorski, Krzysztof SzalewiczAbstract:A method is proposed for calculations of Dispersion Energy at finite intermonomer separations. It uses a generalized Casimir-Polder formula evaluated with dynamic density susceptibilities provided by time-dependent density-functional theory. The method recovers the Dispersion energies of He, Ne, and H 2 O dimers to within 3% or better. Since the computational effort of the new algorithm scales approximately as the third power of system size, the method is much more efficient than standard wave-function methods capable of predicting the Dispersion Energy at a similarly high level of accuracy.
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Dispersion Energy in the coupled pair approximation with noniterative inclusion of single and triple excitations
Journal of Chemical Physics, 1995Co-Authors: Hayes L Williams, Krzysztof Szalewicz, Robert Moszynski, Bogumil JeziorskiAbstract:The second‐order Dispersion Energy in the coupled‐pair (coupled‐cluster doubles) approximation has been derived. The coupled‐pair amplitudes are subsequently used in a perturbation theory type expression to account for the effects of single and triple excitations. This approach selectively sums to infinite order important classes of intramonomer correlation diagrams resulting in a better theoretical description of the Dispersion interaction compared to a finite‐order perturbation treatment. Numerical results have been obtained for He2, Ar–H2, Ar–HF, (HF)2, (H2O)2, and He–F− in various geometries and basis sets to illustrate the performance of the nonperturbative versus perturbative treatments of the intramonomer correlation contributions to the Energy of the Dispersion interaction.
Ashok Kumar - One of the best experts on this subject based on the ideXlab platform.
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dipole oscillator strength distributions properties and Dispersion energies for the dimethyl diethyl and methyl propyl ethers
Molecular Physics, 2008Co-Authors: Ashok Kumar, William J MeathAbstract:Isotropic dipole oscillator strength distributions (DOSDs) have been constructed for the dimethyl, diethyl and methyl–propyl ether molecules through the use of quantum mechanical constraint techniques and experimental dipole oscillator strength data. The constraints are furnished by molar refractivity data and the Thomas–Reiche–Kuhn sum rule. The DOSDs are used to obtain recommended values for a variety of isotropic dipole oscillator strength sums, logarithmic dipole oscillator strength sums, and mean excitation energies for the molecules. Pseudo-DOSDs for the ethers are also constructed and used to obtain reliable results for the isotropic dipole–dipole Dispersion Energy coefficients for all two-body interactions of the ethers with each other and with fifty other species. In addition reliable results are also obtained for the triple–dipole Dispersion Energy coefficients for all three-body interactions involving the ethers. 1Dedicated to Anthony Stone, an excellent scientist and friend, on the occasion of...
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Dipole oscillator strength properties and Dispersion energies for CI2
Molecular Physics, 2002Co-Authors: Mukesh Kumar, Ashok Kumar, William J MeathAbstract:A recommended isotropic dipole oscillator strength distribution (DOSD) has been constructed for the chlorine molecule through the use of quantum mechanical constraint techniques and experimental dipole oscillator strength and molar refractivity data. It has been used to evaluate a variety of dipole oscillator strength sums, logarithmic dipole oscillator strength sums, and mean excitation energies for the molecule. A pseudo-DOSD for C12 is also presented which is used to obtain reliable results for the isotropic dipole-dipole Dispersion Energy coefficients C6, for the interaction of Cl2 with itself and forty-two other species, and the triple-dipole Dispersion Energy coefficient C9 for (Cl2)3.
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reliable anisotropic dipole properties and Dispersion Energy coefficients for o2 evaluated using constrained dipole oscillator strength techniques
Journal of Chemical Physics, 1996Co-Authors: Ashok Kumar, William J Meath, Peter Bundgen, Ajit J ThakkarAbstract:Constrained anisotropic dipole oscillator strength techniques are used to obtain reliable values for a wide range of anisotropic and isotropic dipole properties of O2, including the dipole–dipole Dispersion Energy coefficients for the interaction of O2 with O2, H2, N2, CO, He, Ne, Ar, Kr, and Xe. Some of the anisotropic constraints required for our calculations are obtained via dipole sum rules from ab initio, multireference configuration interaction (CI) wave functions for the ground state of O2. The individual dipole properties of O2 considered include the dipole oscillator strength sums S k , k=2,1,0(−1/2)−2,−3,−4,..., the logarithmic dipole sums L k and mean excitation energiesI k , k=2(−1)−2, and, as a function of wavelength, the dynamic polarizability and its anisotropy, the total depolarization ratio, the Rayleigh scattering cross section, and the Verdet constant. Our constrained dipole oscillator strength results are often the only reliable, and sometimes the only available, ones for many of the properties and Dispersion energies considered.
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reliable isotropic and anisotropic dipole properties and dipolar Dispersion Energy coefficients for co evaluated using constrained dipole oscillator strength techniques
Journal of Chemical Physics, 1994Co-Authors: Ashok Kumar, William J MeathAbstract:Abstract Constrained anisotropic dipole oscillator strength methods are applied to obtain reliable results for a wide selection of anisotropic and isotropic dipole properties of CO and for the dipole-dipole Dispersion Energy coefficients for the interaction of CO with CO, N 2 , H 2 , He, Ne, Ar, Kr and Xe. The properties of CO evaluated include the dipole oscillator strength sums S k , k = 2, 1, 0(− 1 2 ) −2, −3, −4, ⋯, the logarithmic dipole sums L k and mean excitation energies I k , k = 2(−1) −2, and, as a function of wavelength, the dynamic polarizability and its anisotropy, the total depolarization ratio, the Rayleigh scattering cross section, and the Verdet constant. Our constrained dipole oscillator strength results are often the only reliable, and sometimes the only, results available for many of the anisotropic dipole properties and Dispersion energies considered in this paper.
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dipole oscillator strength properties and Dispersion energies for acetylene and benzene
Molecular Physics, 1992Co-Authors: Ashok Kumar, William J MeathAbstract:Dipole oscillator strength distributions (DOSDs), which are globally reliable, have been constructed for the acetylene and benzene molecules, through the use of quantum mechanical constraint techniques and experimental dipole oscillator strength and molar refractivity data. A recommended isotropic DOSD for each molecule is used to evaluate a wide variety of dipole oscillator stength sums, logarithmic dipole sums, and mean excitation energies, for C2H2 and C6H6. Also obtained are reliable results for the isotropic dipole-dipole Dispersion Energy coefficients C 6, for the interaction of acetylene and benzene with themselves and with forty-one other species, and for the triple-dipole Dispersion Energy coefficients C 9, for (C2H2)3 and (C6H6)3. Psuedo-DOSDs for acetylene and benzene are presented which greatly facilitate the evaluation of C 6's and C 9's for a variety of interactions.
C Sanjeeviraja - One of the best experts on this subject based on the ideXlab platform.
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optical constants and Dispersion Energy parameters of nio thin films prepared by radio frequency magnetron sputtering technique
Journal of Applied Physics, 2013Co-Authors: K S Usha, Raghupathy Sivakumar, C SanjeevirajaAbstract:In this paper, we report on rf power induced change in the structural and optical properties of nickel oxide (NiO) thin films deposited onto glass substrates by rf magnetron sputtering technique. The crystallinity of the film was found to increase with increasing rf power and the deposited film belong to cubic phase. The maximum optical transmittance of 95% was observed for the film deposited at 100 W. The slight shift in transmission threshold towards higher wavelength region with increasing rf power revealed the systematic reduction in optical Energy band gap (3.93 to 3.12 eV) of the films. The Dispersion curve of the refractive index shows an anomalous Dispersion in the absorption region and a normal Dispersion in the transparent region. It was observed that the Dispersion data obeyed the single oscillator of the Wemple-Didomenico model, from which the Dispersion parameters, dielectric constants, relaxation time, and optical non-linear susceptibility were evaluated. We have made an attempt to discuss and correlate these results with the light of possible mechanisms underlying the phenomena.
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optical constants and Dispersion Energy parameters of nio thin films prepared by radio frequency magnetron sputtering technique
Journal of Applied Physics, 2013Co-Authors: K S Usha, Raghupathy Sivakumar, C SanjeevirajaAbstract:In this paper, we report on rf power induced change in the structural and optical properties of nickel oxide (NiO) thin films deposited onto glass substrates by rf magnetron sputtering technique. The crystallinity of the film was found to increase with increasing rf power and the deposited film belong to cubic phase. The maximum optical transmittance of 95% was observed for the film deposited at 100 W. The slight shift in transmission threshold towards higher wavelength region with increasing rf power revealed the systematic reduction in optical Energy band gap (3.93 to 3.12 eV) of the films. The Dispersion curve of the refractive index shows an anomalous Dispersion in the absorption region and a normal Dispersion in the transparent region. It was observed that the Dispersion data obeyed the single oscillator of the Wemple-Didomenico model, from which the Dispersion parameters, dielectric constants, relaxation time, and optical non-linear susceptibility were evaluated. We have made an attempt to discuss a...
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structural and optical properties of indium tin oxide ito thin films with different compositions prepared by electron beam evaporation
Vacuum, 2010Co-Authors: V Senthilkumar, P Vickraman, M Jayachandran, C SanjeevirajaAbstract:Abstract Tin-doped Indium oxide thin films in different compositions (Sn = 0,5,10,15,20 at.wt%) were prepared on glass substrates at the substrate temperature of 250 °C in an oxygen atmosphere by electron beam evaporation. The structural and morphological studies were carried out by X-ray diffraction (XRD) and scanning electron microscopy (SEM). The grain size of the ITO films decreased when increasing the dopant concentration of Sn in the In2O3 lattice. Optical properties of the films were studied in the UV-Visible-NIR region (300–1000 nm). The optical Energy band gap (Eg), as determined by the dependence of the absorption coefficient on the photon Energy at short wavelengths was found to increase from 3.61 to 3.89 eV revealing the ascending loading profile of dopant concentration. Optical Parameters, such as absorption depth, refractive index (n), extinction coefficient (k), packing density, porosity, Dispersion Energy and single effective oscillator Energy were also studied to show the composition dependence of tin-doped indium oxide films.