Supermolecular Interaction Energies Research Articles

New insights in chemical reactivity from quantum chemical topology.

Based on the quantum chemical topology of the modified electron localization function ELFx , an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange-correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first-order variation in the coulomb intermolecular energy defined in terms of the response to changes in the number of electrons. Illustrative examples with the formation of the dative bond B-N involved in the BH3 NH3 molecule and the typical formation of the hydrogen bond in the canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking of Edual onto the DFT intermolecular interaction energy surface calculated between the both reactants. An automated reaction-path algorithm aimed to determine the most favorable relative orientations when the two molecules approach each other is also outlined.

Gas Phase Computational Study of Diclofenac Adsorption on Chitosan Materials.

Environmental pollution with non-steroidal anti-inflammatory drugs and their metabolites exposes living organisms on their long-lasting, damaging influence. Hence, the ways of non-steroidal anti-inflammatory drugs (NSAIDs) removal from soils and wastewater is sought for. Among the potential adsorbents, biopolymers are employed for their good availability, biodegradability and low costs. The first available theoretical modeling study of the interactions of diclofenac with models of pristine chitosan and its modified chains is presented here. Supermolecular interaction energy in chitosan:drug complexes is compared with the the mutual attraction of the chitosan dimers. Supermolecular interaction energy for the chitosan-diclofenac complexes is significantly lower than the mutual interaction between two chitosan chains, suggesting that the diclofenac molecule will encounter problems when penetrating into the chitosan material. However, its surface adsorption is feasible due to a large number of hydrogen bond donors and acceptors both in biopolymer and in diclofenac. Modification of chitosan material introducing long-distanced amino groups significantly influences the intramolecular interactions within a single polymer chain, thus blocking the access of diclofenac to the biopolymer backbone. The strongest attraction between two chitosan chains with two long-distanced amino groups can exceed 120 kcal/mol, while the modified chitosan:diclofenac interaction remains of the order of 20 to 40 kcal/mol.

Revealing the physical nature and the strength of charge-inverted hydrogen bonds by SAPT(DFT), MP2, SCS-MP2, MP2C, and CCSD(T) methods

The physical nature of charge-inverted hydrogen bonds in H3 XH ⋯YH3 (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)-based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS-MP2, MP2C, and CCSD(T) methods utilizing dimer-centered aug-cc-pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge-inverted hydrogen bonds are inductive in nature, although dispersion is also important. Computed interaction energies form the following relation: EintSAPT<EintSCS-MP2≤EintMP2C<EintMP2≈EintCCSD(T). It is confirmed that the aug-cc-pCVDZ basis set performs poorly and that very accurate values of interaction and dispersion energies require basis sets of at least quadrupole-ζ quality. Considerably large binding energies suggest potential usefulness of charge-inverted hydrogen bonds as an important structural motif in molecular binding. Terminology applying to σ- and π-hole interactions as well as to triel and tetrel bonds is discussed. According to this new terminology the charge-inverted hydrogen bond would become the first described case of a hydride-triel bond. © 2017 Wiley Periodicals, Inc.

Characterizing N-acetylcysteine (NAC) and N-acetylcysteine amide (NACA) binding for lead poisoning treatment

Using antioxidants is an important means of treating lead poisoning. Prior in vivo studies showed marked differences between various chelator antioxidants in their ability to decrease both blood Pb(II) levels and oxidative stress resulting from lead poisoning. The comparative abilities of NAC and NACA to Pb(II) were studied in vitro, for the first time, to examine the role of the OH/NH2 functional group in antioxidant binding behavior. To assay the antioxidant–divalent metal interaction, the antioxidants were probed as solid surfaces, adsorbing Pb(II) onto them. Surface characterization was carried out using X-ray photoelectron spectroscopy (XPS) analysis to quantify Pb(II) in the resulting adducts. XPS of the Pb 4f orbitals showed that more Pb(II) was chemically bound to NACA than NAC. In addition, the antioxidant surfaces probed via point-of-zero charge (PZC) measurements of NAC and NACA were obtained to gain further insight into the Pb–NAC and Pb–NACA binding, showing that Coulombic interactions played a partial role in facilitating complex formation. The data correlated well with solution analysis of metal–ligand complexation. UV–vis spectroscopy was used to probe complexation behavior. NACA was found to have the higher binding affinity as shown by free Pb(II) available in the solution after complexation from HPLC data. Electrospray ionization mass spectrometry (ESI-MS) was applied to delineate the structures of Pb–antioxidant complexes. Experimental results were further supported by density functional theory (DFT) calculations of supermolecular interaction energies (Einter) showing a greater interaction of Pb(II) with NACA than NAC.

Estimating the Hydrogen Bond Energy

First, different approaches to detect hydrogen bonds and to evaluate their energies are introduced newly or are extended. Supermolecular interaction energies of 256 dimers, each containing one single hydrogen bond, were correlated to various descriptors by a fit function depending both on the donor and acceptor atoms of the hydrogen bond. On the one hand, descriptors were orbital-based parameters as the two-center or three-center shared electron number, products of ionization potentials and shared electron numbers, and the natural bond orbital interaction energy. On the other hand, integral descriptors examined were the acceptor-proton distance, the hydrogen bond angle, and the IR frequency shift of the donor-proton stretching vibration. Whereas an interaction energy dependence on 1/r(3.8) was established, no correlation was found for the angle. Second, the fit functions are applied to hydrogen bonds in polypeptides, amino acid dimers, and water cluster, thus their reliability is demonstrated. Employing the fit functions to assign intramolecular hydrogen bond energies in polypeptides, several side chain CH...O and CH...N hydrogen bonds were detected on the fly. Also, the fit functions describe rather well intermolecular hydrogen bonds in amino acid dimers and the cooperativity of hydrogen bond energies in water clusters.

Derivation of the supermolecular interaction energy from the monomer densities in the density functional theory

The density functional theory (DFT) interaction energy of a dimer is rigorously derived from the monomer densities. To this end, the supermolecular energy bifunctional is formulated in terms of mutually orthogonal sets of orbitals of the constituent monomers. The orthogonality condition is preserved in the solution of the Kohn–Sham equations through the Pauli blockade method. Numerical implementation of the method provides interaction energies which agree with those obtained from standard supermolecular calculations within less than 0.1% error for three example functionals: Slater–Dirac, PBE0 and B3LYP, and for two model van der Waals dimers: Ne 2 and (C 2H 4) 2, and two model H-bond complexes: (HF) 2 and (NH 3) 2.

Symmetry-Adapted Perturbation Theory Applied to Endohedral Fullerene Complexes: A Stability Study of H2@C60 and 2H2@C60.

Because of difficulties in a description of host-guest interactions, various theoretical methods predict different numbers of hydrogen molecules which can be inserted into the C60 cavity, ranging from one to more than 20. On the other hand, only one H2 molecule inside the C60 fullerene has been detected experimentally. Moreover, a recently synthesized H2@C70 complex prevails in the mixture formed with 2H2@C70. To get a deeper insight into the stability of the complexes created from C60 and hydrogen molecules, we carried out highly accurate calculations for complexes of one or two hydrogen molecules with fullerene applying symmetry-adapted perturbation theory (SAPT) and a large TZVPP basis set for selected points on the potential energy surfaces of H2@C60 and 2H2@C60. The electron correlation in the host and guests has been treated by density functional theory. Our calculations yield the stability of the recently synthesized H2@C60 complex. In addition, for all tried positions of the H2 dimer inside the C60 cage, the 2H2@C60 complex has been characterized by a positive interaction energy corresponding to the instability of this species. Contrary to the conclusions of several theoretical studies, this finding, as well as model considerations and literature experimental data, indicates that only one hydrogen molecule can reside inside the C60 cage. The calculated energy components have been analyzed to identify the most important contributions to the interaction energy. Supermolecular interaction energies obtained with MP2, SCS-MP2, and DFT+Disp methods are also reported and compared to those of DFT-SAPT. The DFT-SAPT interaction energy has also been calculated for several points on the potential energy surface for a larger 2H2@C70 complex, confirming, in agreement with recent experimental findings, that this species is stable. The DFT-SAPT approach has been used for the first time to obtain interaction energies for van der Waals endohedral complexes, demonstrating that the method is capable of handling such difficult cases.

The experimental and theoretical characterisation of the phenyl-perfluorophenyl π–π and hydrogen bond interactions in the aldimine co-crystal

The experimental and theoretical characterisation of optical (UV–Vis and FTIR) properties of aldimine co-crystal complex (system C) formed from C 6H 5CH NC 6H 5 (subsystem A) and C 6F 5CH NC 6F 5 (subsystem B) molecules is presented. As a result of intermolecular interaction, the non-additive intensive band at 987 cm −1 is observed in the finger-print region of infrared spectrum. In the liquid state, the existence of this complex has been suggested on the basis of electrochemical measurements. These experiments reveal a slight decrease in cathodic and anodic peak potentials for the C complex comparing to the non-interacting molecules A and B. The supermolecular interaction energy calculated at MP2/6-31 + G(d) level with the basis set superposition error correction for the twisted head-to-tail orientation has the value 55 kJ mol −1. Finally, the analysis of the frontier molecular orbitals based on the TDDFT method shows for the experimental geometry that the origin of the lowest excitation energy (404 nm), with very small oscillator strength (0.0001) is composed only of mono-excitations from HOMO (localised on system A) to LUMO (localised on system B) orbitals. However, the TDDFT approach could yield to underestimated energies for long-range CT states as this additional low-lying CT state was not observed in the corresponding experimental UV–Vis spectrum.

Monomer basis-set truncation effects in calculations of interaction energies: A model study.

Supermolecular interaction energies are analyzed in terms of the symmetry-adapted perturbation theory and operators defining the inaccuracy of the monomer wave functions. The basis set truncation effects are shown to be of first order in the monomer inaccuracy operators. On the contrary, the usual counterpoise correction schemes are of second order in these operators. Recognition of this difference is used to suggest an approach to corrections for basis-set truncation effects. Also earlier claims--that dimer-centered basis sets may lead to interaction energies free of basis-set superposition effects--are shown to be misleading. According to the present study the basis-set truncation contributions, evaluated by means of the symmetry-adapted perturbation theory with monomer-centered basis sets, provide physically and mathematically justified corrections to supermolecular results for interaction energies.

Origins and modeling of many-body exchange effects in van der Waals clusters

We analyze the many-body exchange interactions in atomic and molecular clusters as they arise in the supermolecular SCF and MP2 approaches. A rigorous formal setting is provided by the symmetry-adapted perturbation theory. Particular emphasis is put on the decomposition into the single exchange (SE) and triple exchange (TE) terms, at the SCF and correlated levels. We also propose a novel approach, whereby selected SE nonadditive exchange terms are evaluated indirectly, as differences of the two-body SAPT corrections arising between the components of the trimer treated as a complex of a dimer and a monomer (pseudodimer approach). This provides additional insights into the nature of various nonadditive effects, an interpretation of supermolecular interaction energies, and may serve as a viable alternative for the calculation of some SE terms.

Electrostatic Interactions Based upon Floating Basis ab Initio Calculations. The Water Pentamer

Electrostatic interactions derived from floating basis HF/D95** ab initio calculations are presented for a tetrahedral water pentamer. Since floating basis ab initio calculations approximately satisfy the Hellmann−Feynman theorem, indicating that the forces on the nuclei can be calculated classically; and, since the wave function of the pentamer includes all polarization and mutual polarization effects, the intermolecular interactions can be calculated classically by using molecular properties extracted from the wave function of the aggregate. We compare classical interactions based upon floating basis functions, as well as analogous interactions based upon normal (nonfloating) Hartree−Fock calculations with supermolecular interaction energies and pairwise interactions. We also compare classical electrostatic calculations based upon interacting point charges with those based upon interactions of charges one molecule with the electric field of the others. We show that the latter method (which is free of pe...

Basis set superposition problem in interaction energy calculations with explicitly correlated bases: Saturated second- and third-order energies for He2

Explicitly correlated basis set of Gaussian-type geminals has been employed in supermolecular calculations of the interaction energy of two helium atoms using the second- and third-order of the many-body perturbation theory and the Mo/ller–Plesset partitioning of the Hamiltonian. A geminal extension of the counterpoise procedure of Boys and Bernardi has been proposed to correct for the basis set superposition error. Performance of the proposed correction scheme has been analyzed at the second-order level using a sequence of geminal bases varying in the degree of completeness in representing the intra- and intermonomer correlation effects. The nonlinear parameters of these bases were optimized by minimizing the second-order energy of the helium atom and the second-order dispersion energy of the He dimer. The best upper bounds to date have been obtained for both quantities. The numerical results show that the counterpoise procedure should be used at all levels of basis set completeness. By employing the union of the largest of the obtained bases and reoptimizing some of the nonlinear parameters using the complete second-order energy functional for the dimer, the best estimates to date of the second- and third-order supermolecular interaction energies for He2 have been computed. At the minimum interatomic separation these energies are estimated to be accurate to 0.01 K or better. Adding higher-order terms computed using orbital bases, leads to a helium dimer interaction potential with the depth of 11.00 K, somewhat larger than current experimental results.

Symmetry-adapted perturbation theory calculations of uracil—water interaction energy

Interaction energies for the uracil—water system at two configurations close to the van der Waals minimum were computed using many-body symmetry-adapted perturbation theory of intermolecular interactions at the level which includes major electron correlation effects. Supermolecular interaction energies at the second-order many-body perturbation theory level were computed as well. A minimal isotropic plus single polarization basis set was used. The results show that correlation effects are responsible for about 30% of the interaction energy. These effects exhibit a strong dependence on the geometry of the system. Our work demonstrates that it is now feasible to compute intermolecular interaction energies for systems of biochemical interest including a reliable treatment of the electron correlation effects.

On decomposition of second-order Mo/ller–Plesset supermolecular interaction energy and basis set effects

The basis set effects on the total self-consistent field (SCF) and second-order Mo/ller–Plesset (MP2) interaction energies in the HF dimer (in the equilibrium geometry) are investigated in relation to their components: electrostatic, exchange, induction, and dispersion, calculated within the framework of intermolecular Mo/ller–Plesset perturbation theory (IMPPT). The basis set dependence of the SCF interaction energy in the HF dimer is almost exactly determined by the electrostatic contribution. The exchange, induction, and the SCF-deformation terms are found substantially less sensitive. The MP2 correlation contribution reflects primarily the basis set dependence of dispersion. However, an accurate image of the basis set dependence is reproduced only if the electrostatic-correlation term is considered as well. Other correlation contributions: the deformation- correlation and exchange terms are found to be much less sensitive to basis set effects. All these conclusions are valid only under the condition that the supermolecular interaction energies are counterpoise-corrected for the basis set superposition error and IMPPT interaction energies are calculated with the full basis set of the dimer.

Correlation correction to the Hartree-Fock electrostatic energy including orbital relaxation

By using the recently developed density approach to the analytic MBPT (2) gradients we derive the spin-adapted form of the correlation correction to the Hartree-Fock electrostatic energy using the relaxed MBPT (2) density matrix. This correction is shown to be essential for a perturbation theory analysis of the MBPT (2) supermolecular interaction energy at large distances. Applications are presented for various configurations of the H 2 dimer and the results are compared to the full CI electrostatic energy data.

A theoretical study of the water dimer interaction

We have performed a study of the water dimer interaction using larger basis sets and higher levels of theory than have been previously applied to this system. For the minimum geometry we have used spdf basis sets containing up to 212 orbitals. Our most accurate SCF interaction energy for the minimum is −3.73±0.05 kcal/mol. We have shown that this energy can be reproduced to within 0.1 kcal/mol using much smaller basis sets containing proper (diffuse) exponents. Accounting for the basis set superposition error is shown to be essential. We computed the dispersion energy with neglect of the intramolecular correlation using basis sets of various sizes. The best value obtained in a large spdf basis set with exponents which optimize this quantity is −1.93 kcal/mol and it is expected to be accurate to 0.1 kcal/mol or better. Using some of these basis sets we have performed supermolecular many-body perturbation theory (MBPT) and coupled-cluster (CC) calculations including triple excitations. We have shown that if the correlated supermolecular interaction energies are not corrected for the basis set superposition error, the correlated part of the interaction energy varies widely with the basis set. In contrast, the corrected values converge smoothly. On the basis of the dispersion energy and the MBPT/CC results we predict the correlated part of the interaction energy to be −1.0±0.3 kcal/mol, which leads to the total interaction energy of −4.7±0.35 kcal/mol. Thus, our work favors the lower limit of the experimentally predicted interaction energy of −5.4±0.7 kcal/mol.