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Krzysztof Szalewicz - One of the best experts on this subject based on the ideXlab platform.
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sapt codes for calculations of Intermolecular Interaction energies
Journal of Chemical Physics, 2020Co-Authors: Javier Garcia, Rafal Podeszwa, Krzysztof SzalewiczAbstract:Symmetry-adapted perturbation theory (SAPT) is a method for calculations of Intermolecular (noncovalent) Interaction energies. The set of SAPT codes that is described here, the current version named SAPT2020, includes virtually all variants of SAPT developed so far, among them two-body SAPT based on perturbative, coupled cluster, and density functional theory descriptions of monomers, three-body SAPT, and two-body SAPT for some classes of open-shell monomers. The properties of systems governed by noncovalent Interactions can be predicted only if potential energy surfaces (force fields) are available. SAPT is the preferred approach for generating such surfaces since it is seamlessly connected to the asymptotic expansion of Interaction energy. SAPT2020 includes codes for automatic development of such surfaces, enabling generation of complete dimer surfaces with a rigid monomer approximation for dimers containing about one hundred atoms. These codes can also be used to obtain surfaces including internal degrees of freedom of monomers.
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communication density functional theory overcomes the failure of predicting Intermolecular Interaction energies
Journal of Chemical Physics, 2012Co-Authors: Rafal Podeszwa, Krzysztof SzalewiczAbstract:Density-functional theory (DFT) revolutionized the ability of computational quantum mechanics to describe properties of matter and is by far the most often used method. However, all the standard variants of DFT fail to predict Intermolecular Interaction energies. In recent years, a number of ways to go around this problem has been proposed. We show that some of these approaches can reproduce Interaction energies with median errors of only about 5% in the complete range of Intermolecular configurations. Such errors are comparable to typical uncertainties of wave-function-based methods in practical applications. Thus, these DFT methods are expected to find broad applications in modelling of condensed phases and of biomolecules.
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on the effectiveness of monomer dimer and bond centered basis functions in calculations of Intermolecular Interaction energies
Journal of Chemical Physics, 1995Co-Authors: Hayes L Williams, Eric M Mas, Krzysztof SzalewiczAbstract:A range of basis sets differing in the location of basis functions has been explored from the point of view of the effectiveness of calculating the electrostatic, induction, dispersion, and exchange components of Intermolecular Interaction energies. Possible location strategies range from monomer‐centered basis sets, through the dimer‐centered ones, to sets with functions centered at the Intermolecular bond. It is shown that the most effective approach is to use the so‐called ‘‘monomer plus’’ basis sets containing, in addition to monomer‐centered functions and bond functions, a small number of functions centered on the interacting partner. Using such basis sets for He2 and (H2O)2 the best values to date have been obtained for several Interaction energy components. The conclusions from this work are relevant also for supermolecular calculations of Interaction energies.
A Gavezzotti - One of the best experts on this subject based on the ideXlab platform.
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supramolecular synthons validation and ranking of Intermolecular Interaction energies
Crystal Growth & Design, 2012Co-Authors: J D Dunitz, A GavezzottiAbstract:Building upon Desiraju’s concept of a supramolecular synthon, we have calculated cohesive energies and thermal stabilities of molecular systems related to the proposed synthons. The method employed is PIXEL, which allows reliable and extensive mapping of Intermolecular surfaces. Comparisons with accurate ab initio calculations are included. Stability is judged in terms of calculated binding energies and stretching vibrational amplitudes around room temperature. The list of systems treated includes carboxylic acids, amides, alcohols, N–H···N hydrogen bonds, as well as benzene stacking and several types of C–H···O Interactions. Cl···Cl synthons are compared with C–H···Cl synthons. The result is a working table of absolute and relative strengths that could serve as a guideline for crystal engineering.
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calculation of Intermolecular Interaction energies by direct numerical integration over electron densities 2 an improved polarization model and the evaluation of dispersion and repulsion energies
Journal of Physical Chemistry B, 2003Co-Authors: A GavezzottiAbstract:A procedure to adapt electron densities of isolated molecules for the evaluation of Intermolecular energies, first introduced in paper 1 (Gavezzotti, A. J. Phys. Chem. B 2002, 106, 4145) is here improved for polarization energy and extended to dispersion and repulsion terms. Dispersion is evaluated from atomic polarizabilities distributed over the electron density, using an average ionization potential taken as the energy of the highest occupied molecular orbital, in a London-type inverse sixth-power formulation. Repulsion is evaluated from the overlap between electron densities. The method, called semiclassical density sums (SCDS), requires only four disposable numerical parameters and allows a complete evaluation of Intermolecular Interaction energies for a rather wide range of molecular systems. Calculations on molecular dimers, in comparison with results obtained by high-level quantum chemical methods, show that SCDS energies are quite reliable, at a fraction of the computational cost. The sublimation...
Kaili Zhou - One of the best experts on this subject based on the ideXlab platform.
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Intermolecular Interaction of fosinopril with bovine serum albumin bsa the multi spectroscopic and computational investigation
Journal of Molecular Recognition, 2018Co-Authors: Kaili ZhouAbstract:: The Intermolecular Interaction of fosinopril, an angiotensin converting enzyme inhibitor with bovine serum albumin (BSA), has been investigated in physiological buffer (pH 7.4) by multi-spectroscopic methods and molecular docking technique. The results obtained from fluorescence and UV absorption spectroscopy revealed that the fluorescence quenching mechanism of BSA induced by fosinopril was mediated by the combined dynamic and static quenching, and the static quenching was dominant in this system. The binding constant, Kb , value was found to lie between 2.69 × 103 and 9.55 × 103 M-1 at experimental temperatures (293, 298, 303, and 308 K), implying the low or intermediate binding affinity between fosinopril and BSA. Competitive binding experiments with site markers (phenylbutazone and diazepam) suggested that fosinopril preferentially bound to the site I in sub-domain IIA on BSA, as evidenced by molecular docking analysis. The negative sign for enthalpy change (ΔH0 ) and entropy change (ΔS0 ) indicated that van der Waals force and hydrogen bonds played important roles in the fosinopril-BSA Interaction, and 8-anilino-1-naphthalenesulfonate binding assay experiments offered evidence of the involvements of hydrophobic Interactions. Moreover, spectroscopic results (synchronous fluorescence, 3-dimensional fluorescence, and Fourier transform infrared spectroscopy) indicated a slight conformational change in BSA upon fosinopril Interaction.
Rafal Podeszwa - One of the best experts on this subject based on the ideXlab platform.
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sapt codes for calculations of Intermolecular Interaction energies
Journal of Chemical Physics, 2020Co-Authors: Javier Garcia, Rafal Podeszwa, Krzysztof SzalewiczAbstract:Symmetry-adapted perturbation theory (SAPT) is a method for calculations of Intermolecular (noncovalent) Interaction energies. The set of SAPT codes that is described here, the current version named SAPT2020, includes virtually all variants of SAPT developed so far, among them two-body SAPT based on perturbative, coupled cluster, and density functional theory descriptions of monomers, three-body SAPT, and two-body SAPT for some classes of open-shell monomers. The properties of systems governed by noncovalent Interactions can be predicted only if potential energy surfaces (force fields) are available. SAPT is the preferred approach for generating such surfaces since it is seamlessly connected to the asymptotic expansion of Interaction energy. SAPT2020 includes codes for automatic development of such surfaces, enabling generation of complete dimer surfaces with a rigid monomer approximation for dimers containing about one hundred atoms. These codes can also be used to obtain surfaces including internal degrees of freedom of monomers.
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communication density functional theory overcomes the failure of predicting Intermolecular Interaction energies
Journal of Chemical Physics, 2012Co-Authors: Rafal Podeszwa, Krzysztof SzalewiczAbstract:Density-functional theory (DFT) revolutionized the ability of computational quantum mechanics to describe properties of matter and is by far the most often used method. However, all the standard variants of DFT fail to predict Intermolecular Interaction energies. In recent years, a number of ways to go around this problem has been proposed. We show that some of these approaches can reproduce Interaction energies with median errors of only about 5% in the complete range of Intermolecular configurations. Such errors are comparable to typical uncertainties of wave-function-based methods in practical applications. Thus, these DFT methods are expected to find broad applications in modelling of condensed phases and of biomolecules.
Hansjoachim Werner - One of the best experts on this subject based on the ideXlab platform.
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accurate calculations of Intermolecular Interaction energies using explicitly correlated coupled cluster wave functions and a dispersion weighted mp2 method
Journal of Physical Chemistry A, 2009Co-Authors: Oliver Marchetti, Hansjoachim WernerAbstract:Explicitly correlated coupled-cluster calculations of Intermolecular Interaction energies for the S22 benchmark set of Jurecka, Sponer, Cerný, and Hobza (Chem. Phys. Phys. Chem. 2006, 8, 1985) are presented. Results obtained with the recently proposed CCSD(T)-F12a method and augmented double-ζ basis sets are found to be in very close agreement with basis set extrapolated conventional CCSD(T) results. Furthermore, we propose a dispersion-weighted MP2 (DW-MP2) approximation that combines the good accuracy of MP2 for complexes with predominately electrostatic bonding and SCS-MP2 for dispersion-dominated ones. The MP2-F12 and SCS-MP2-F12 correlation energies are weighted by a switching function that depends on the relative HF and correlation contributions to the Interaction energy. For the S22 set, this yields a mean absolute deviation of 0.2 kcal/mol from the CCSD(T)-F12a results. The method, which allows obtaining accurate results at low cost, is also tested for a number of dimers that are not in the traini...
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accurate calculations of Intermolecular Interaction energies using explicitly correlated wave functions
Physical Chemistry Chemical Physics, 2008Co-Authors: Oliver Marchetti, Hansjoachim WernerAbstract:Explicitly correlated second-order Moller–Plesset (MP2-F12) calculations of Intermolecular Interaction energies for the S22 benchmark set of Jurecka, Sponer, Cerný, and Hobza (Chem. Phys. Phys. Chem. 2006, 8, 1985) are presented and compared with standard MP2 results. The MP2 complete basis set limits are estimated using basis set extrapolation and augmented quadruple-zeta and quintuple-zeta basis sets. Already with augmented double-zeta basis sets the MP2-F12 Interaction energies are found to be closer to the complete basis set limits than standard MP2 calculations with augmented quintuple-zeta basis sets. Various possible approximations in the MP2-F12 method are systematically tested. Best results are obtained with localized orbitals and the diagonal MP2-F12/C(D) ansatz. Hybrid approximations, in which some contributions of the auxiliary basis set are neglected and which considerably reduce the computational cost, have a negligible effect on the Interaction energies. Also the orbital-invariant fixed-amplitude approximation of Ten-no leads to only slightly less accurate results. Preliminary results for the neon and benzene dimers, obtained with the recently proposed CCSD(T)-F12a approximation, indicate that the CCSD(T) basis set limits can also be very closely approached using augmented triple-zeta basis sets.