Complexation, computational, magnetic, and structural studies of the Maillard reaction product isomaltol including investigation of an uncommon π interaction with copper(II)

The metal complexation properties of the naturally occurring Maillard reaction product isomaltol HL(2) are investigated by measurement of its stability constants with copper(II), zinc(II), and iron(III) using potentiometric pH titrations in water, by structural and magnetic characterization of its crystalline complex, [Cu(L(2))(2)]·8H(2)O, and by density functional theory calculations. Strong complexation is observed to form the bis(isomaltolato)copper(II) complex incorporating copper in a typical (pseudo-)square-planar geometry. In the solid state, extensive intra- and intermolecular hydrogen bonding involving all three oxygen functions per ligand assembles the complexes into ribbons that interact to form two-dimensional arrays; further hydrogen bonds and π interactions between the furan moiety of the anionic ligands and adjacent copper(II) centers connect the complexes in the third dimension, leading to a compact polymeric three-dimensional (3D) arrangement. The latter interactions involving copper(II), which represent an underappreciated aspect of copper(II) chemistry, are compared to similar interactions present in other copper(II) 3D structures showing interactions with benzene molecules; the results indicate that dispersion forces dominate in the π system to chelated copper(II) ion interactions.     

Model chemistry calculations of thiophene dimer interactions: origin of pi-stacking

The intermolecular interaction energies of thiophene dimers have been calculated by using an aromatic intermolecular interaction (AIMI) model (a model chemistry for the evaluation of intermolecular interactions between aromatic molecules). The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium-size basis set. The calculated interaction energies of the parallel and perpendicular thiophene dimers are -1.71 and -3.12 kcal/mol, respectively. The substantial attractive interaction in the thiophene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge transfer but rather long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases the attraction significantly. The dispersion interaction is found to be the major source of attraction in the thiophene dimer. The calculated total interaction energy of the thiophene dimer is highly orientation dependent. Although electrostatic interaction is substantially weaker than dispersion interaction, it is highly orientation dependent, and therefore electrostatic interaction play an important role in the orientation dependence of the total interaction energy. The large attractive interaction in the perpendicular dimer is the cause of the preference for the herringbone structure in the crystals of nonsubstituted oligothiophenes (alpha-terthienyls), and the steric repulsion between the beta-substituents is the cause of the pi-stacked structure in the crystals of some beta-substituted oligothiophenes.     

Dispersion self-free energies and interaction free energies of finite-sized ions in salt solutions

The role for many-body dipolar (dispersion) potentials in ion-solvent and ion-solvent-interface interactions is explored. Such many-body potentials, accessible in principle from measured dielectric data, are necessary in accounting for Hofmeister specific ion effects. Dispersion self-energy is the quantum electrodynamic analogue of the Born electrostatic self-energy of an ion. We here describe calculations of dispersion self-free energies of four different anions (OH-, Cl-, Br-, and I-) that take finite ion size into account. Three different examples of self-free energy calculations are presented. These are the self-free energy of transfer of an ion to bulk solution, which influences solubility; the dispersion potential acting between one ion and an air-water interface (important for surface tension calculations); and the dispersion potential acting between two ions (relevant to activity coefficient calculations). To illustrate the importance of dispersion self-free energies, we compare the Born and dispersion contributions to the free energy of ion transfer from water to air (oil). We have also calculated the change in interfacial tension with added salt for air (oil)-water interfaces. A new model is used that includes dispersion potentials acting on the ions near the interface, image potentials, and ions of finite size that are allowed to spill over the solution-air interface. It is shown that interfacial free energies require a knowledge of solvent profiles at the interface.     

Binding Site Switch by Dispersion Interactions: Rotational Signatures of Fenchone–Phenol and Fenchone–Benzene Complexes

Non-covalent interactions between molecules determine molecular recognition and the outcome of chemical and biological processes. Characterising how non-covalent interactions influence binding preferences is of crucial importance in advancing our understanding of these events. Here, we analyse the interactions involved in smell and specifically the effect of changing the balance between hydrogen-bonding and dispersion interactions by examining the complexes of the common odorant fenchone with phenol and benzene, mimics of tyrosine and phenylalanine residues, respectively. Using rotational spectroscopy and quantum chemistry, two isomers of each complex have been identified. Our results show that the increased weight of dispersion interactions in these complexes changes the preferred binding site in fenchone and sets the basis for a better understanding of the effect of different residues in molecular recognition and binding events.     

Hofmeister effects: interplay of hydration, nonelectrostatic potentials, and ion size

The classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloids, and corresponding theories of electrolytes, are unable to explain ion specific forces between colloidal particles quantitatively. The same is true generally, for surfactant aggregates, lipids, proteins, for zeta and membrane potentials and in adsorption phenomena. Even with fitting parameters the theory is not predictive. The classical theories of interactions begin with continuum solvent electrostatic (double layer) forces. Extensions to include surface hydration are taken care of with concepts like inner and outer Helmholtz planes, and "dressed" ion sizes. The opposing quantum mechanical attractive forces (variously termed van der Waals, Hamaker, Lifshitz, dispersion, nonelectrostatic forces) are treated separately from electrostatic forces. The ansatz that separates electrostatic and quantum forces can be shown to be thermodynamically inconsistent. Hofmeister or specific ion effects usually show up above ≈10(-2) molar salt. Parameters to accommodate these in terms of hydration and ion size had to be invoked, specific to each case. Ionic dispersion forces, between ions and solvent, for ion-ion and ion-surface interactions are not explicit in classical theories that use "effective" potentials. It can be shown that the missing ionic quantum fluctuation forces have a large role to play in specific ion effects, and in hydration. In a consistent predictive theory they have to be included at the same level as the nonlinear electrostatic forces that form the skeletal framework of standard theory. This poses a challenge. The challenges go further than academic theory and have implications for the interpretation and meaning of concepts like pH, buffers and membrane potentials, and for their experimental interpretation. In this article we overview recent quantitative developments in our evolving understanding of the theoretical origins of specific ion, or Hofmeister effects. These are demonstrated through an analysis that incorporates nonelectrostatic ion-surface and ion-ion dispersion interactions. This is based on ab initio ionic polarisabilities, and finite ion sizes quantified through recent ab initio work. We underline the central role of ionic polarisabilities and of ion size in the nonelectrostatic interactions that involve ions, solvent molecules and interfaces. Examples of mechanisms through which they operate are discussed in detail. An ab initio hydration model that accounts for polarisabilities of the tightly held hydration shell of "cosmotropic" ions is introduced. It is shown how Hofmeister effects depend on an interplay between specific surface chemistry, surface charge density, pH, buffer, and counterion with polarisabilities and ion size. We also discuss how the most recent theories on surface hydration combined with hydrated nonelectrostatic potentials may predict experimental zeta potentials and hydration forces.     

Fluctuation-dissipation theorem density-functional theory

Using the fluctuation-dissipation theorem (FDT) in the context of density-functional theory (DFT), one can derive an exact expression for the ground-state correlation energy in terms of the frequency-dependent density response function. When combined with time-dependent density-functional theory, a new class of density functionals results that use approximations to the exchange-correlation kernel fxc as input. This FDT-DFT scheme holds promise to solve two of the most distressing problems of conventional Kohn-Sham DFT: (i) It leads to correlation energy functionals compatible with exact exchange, and (ii) it naturally includes dispersion. The price is a moderately expensive O(N6) scaling of computational cost and a slower basis set convergence. These general features of FDT-DFT have all been recognized previously. In this paper, we present the first benchmark results for a set of molecules using FDT-DFT beyond the random-phase approximation (RPA)-that is, the first such results with fxc not equal to 0. We show that kernels derived from the adiabatic local-density approximation and other semilocal functionals suffer from an "ultraviolet catastrophe," producing a pair density that diverges at small interparticle distance. Nevertheless, dispersion interactions can be treated accurately if hybrid functionals are employed, as is demonstrated for He2 and HeNe. We outline constraints that future approximations to fxc should satisfy and discuss the prospects of FDT-DFT.     

Buckybowls as adsorbents for CO2, CH4, and C2H2: Binding and structural insights from computational study

Noncovalent functionalization of buckybowls sumanene (S), corannulene (R), and coronene (C) with greenhouse gases (GGs) such as CO₂, CH₄ (M), and C₂H₂ (A) has been studied using hybrid density functional theory. The propensity and preferences of these small molecules to interact with the concave and convex surfaces of the buckybowls has been quantitatively estimated. The results indicate that curvature plays a significant role in the adsorption of these small molecules on the π surface and it is observed that buckybowls have higher binding energies (BEs) compared with their planar counterpart coronene. The concave surface of the buckybowl is found to be more feasible for adsorption of small molecules. BEs of small molecules towards π systems is CO₂ > A > M and the BEs of π systems toward small molecules is S > R > C. Obviously, the binding preference is dictated by the way in which various noncovalent interactions, such as π···π, lone pair···π, and CH···π manifest themselves on carbaneous surfaces. To delineate the intricate details of the interactions, we have employed Bader's quantum theory of atoms in molecule and localized molecular orbital energy decomposition analysis (LMO‐EDA). LMO‐EDA, which measures the contribution of various components and traces the physical origin of the interactions, indicates that the complexes are stabilized largely by dispersion interactions. © 2015 Wiley Periodicals, Inc.     

TATB二聚体分子间作用力及其气相几何构型研究

采用对称性匹配微扰理论(SAPT)定量地求得TATB分子间的静电、交换排斥、诱导和色散等分子间作用能项, 从理论上揭示了TATB分子间作用本质; 在此基础上, 阐明了密度泛函在研究TATB二聚体时的适合性问题. 结果表明: (1)在有分子间氢键的TATB二聚体中, 库仑力足以与交换排斥力相抗衡, 起主导作用. (2)含分子间氢键的气相TATB二聚体的合理几何构型为平面型结构, 此结构的产生与色散力无关, 因此不管泛函是否含有近程色散作用, 均应预测到这种强极性的平面型结构. (3)在无分子间氢键的TATB二聚体中, 库仑力难以与交换排斥力相抗衡, 色散作用起到了关键作用; (4)在这种情况下, 未含有近程色散作用的密度泛函不可能给出合理构型. 恰好相反, 含有近程色散作用的密度泛函PBE0却能正确地预测到具有“平行重叠”结构且呈微弱极性的TATB二聚体, 色散力是导致这种构型产生的根本原因. “平行重叠”TATB二聚体是典型的色散体系, 其色散力占绝对主导地位并极有可能起源于两个TATB分子上π电子的相互作用. (5)对于所有TATB二聚体, 色散力或很显著或起主导作用. 由于密度泛函或未含有近程色散, 或只能部分地把近程色散表达出来, 这样使得当前所有密度泛函不可能精确求得这些二聚体的作用能.     

Origin of attraction and directionality of the pi/pi interaction: model chemistry calculations of benzene dimer interaction.

A model chemistry for the evaluation of intermolecular interaction between aromatic molecules (AIMI Model) has been developed. The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium size basis set. The calculated interaction energies of the parallel, T-shaped,and slipped-parallel benzene dimers are -1.48, -2.46, and -2.48 kcal/mol, respectively. The substantial attractive interaction in benzene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge-transfer but long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases attraction significantly. The dispersion interaction is found to be the major source of attraction in the benzene dimer. The orientation dependence of the dimer interaction is mainly controlled by long-range interactions. Although electrostatic interaction is considerably weaker than dispersion interaction, it is highly orientation dependent. Dispersion and electrostatic interactions are both important for the directionality of the benzene dimer interaction.     

The Thermochemistry of London Dispersion-Driven Transition Metal Reactions: Getting the ‘Right Answer for the Right Reason’

Reliable thermochemical measurements and theoretical predictions for reactions involving large transition metal complexes in which long-range intramolecular London dispersion interactions contribute significantly to their stabilization are still a challenge, particularly for reactions in solution. As an illustrative and chemically important example, two reactions are investigated where a large dipalladium complex is quenched by bulky phosphane ligands (triphenylphosphane and tricyclohexylphosphane). Reaction enthalpies and Gibbs free energies were measured by isotherm titration calorimetry (ITC) and theoretically ‘back-corrected’ to yield 0 K gas-phase reaction energies (ΔE). It is shown that the Gibbs free solvation energy calculated with continuum models represents the largest source of error in theoretical thermochemistry protocols. The (‘back-corrected’) experimental reaction energies were used to benchmark (dispersion-corrected) density functional and wave function theory methods. Particularly, we investigated whether the atom-pairwise D3 dispersion correction is also accurate for transition metal chemistry, and how accurately recently developed local coupled-cluster methods describe the important long-range electron correlation contributions. Both, modern dispersion-corrected density functions (e.g., PW6B95-D3(BJ) or B3LYP-NL), as well as the now possible DLPNO-CCSD(T) calculations, are within the ‘experimental’ gas phase reference value. The remaining uncertainties of 2–3 kcal mol⁻¹ can be essentially attributed to the solvation models. Hence, the future for accurate theoretical thermochemistry of large transition metal reactions in solution is very promising.     

Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptide

Correlated ab initio calculations on large systems, such as the popular MP2 (or RI-MP2) method, suffer from the intramolecular basis set superposition error (BSSE). This error is typically manifested in molecules with folded structures, characterized by intramolecular dispersion interactions. It can dramatically affect the energy differences between various conformers as well as intramolecular stabilities, and it can even impair the accuracy of the predictions of the equilibrium molecular structures. In this study, we will present two extreme cases of intramolecular BSSE, the internal stability of [n]helicene molecules and the relative energies of various conformers of phenylalanyl-glycyl-phenylalanine tripeptide (Phe-Gly-Phe), and compare the calculated data with benchmark values (experimental or high-level theoretical data). As a practical and cheap solution to the accurate treatment of the systems with large anticipated value of intramolecular BSSE, the recently developed density functional method augmented with an empirical dispersion term (DFT-D) is proposed and shown to provide very good results in both of the above described representative cases.     

Quantum mechanics based force field for carbon (QMFF-Cx) validated to reproduce the mechanical and thermodynamics properties of graphite

As assemblies of graphene sheets, carbon nanotubes, and fullerenes become components of new nanotechnologies, it is important to be able to predict the structures and properties of these systems. A problem has been that the level of quantum mechanics practical for such systems (density functional theory at the PBE level) cannot describe the London dispersion forces responsible for interaction of the graphene planes (thus graphite falls apart into graphene sheets). To provide a basis for describing these London interactions, we derive the quantum mechanics based force field for carbon (QMFF-Cx) by fitting to results from density functional theory calculations at the M06-2X level, which demonstrates accuracies for a broad class of molecules at short and medium range intermolecular distances. We carried out calculations on the dehydrogenated coronene (C24) dimer, emphasizing two geometries: parallel-displaced X (close to the observed structure in graphite crystal) and PD-Y (the lowest energy transition state for sliding graphene sheets with respect to each other). A third, eclipsed geometry is calculated to be much higher in energy. The QMFF-Cx force field leads to accurate predictions of available experimental mechanical and thermodynamics data of graphite (lattice vibrations, elastic constants, Poisson ratios, lattice modes, phonon dispersion curves, specific heat, and thermal expansion). This validates the use of M06-2X as a practical method for development of new first principles based generations of QMFF force fields.     

A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions

A thorough energy benchmark study of various density functionals (DFs) is carried out with the new GMTKN30 database for general main group thermochemistry, kinetics and noncovalent interactions [Goerigk and Grimme, J. Chem. Theor. Comput., 2010, 6, 107; Goerigk and Grimme, J. Chem. Theor. Comput., 2011, 7, 291]. In total, 47 DFs are investigated: two LDAs, 14 GGAs, three meta-GGAs, 23 hybrids and five double-hybrids. Besides the double-hybrids, also other modern approaches, i.e., the M05 and M06 classes of functionals and range-separated hybrids, are tested. For almost all functionals, the new DFT-D3 correction is applied in order to consistently test the performance also for important noncovalent interactions; the parameters are taken from previous works or determined for the present study. Basis set and quadrature grid issues are also considered. The general aim of the study is to work out which functionals are generally well applicable and robust to describe the energies of molecules. In summary, we recommend on the GGA level the B97-D3 and revPBE-D3 functionals. The best meta-GGA is oTPSS-D3 although meta-GGAs represent in general no clear improvement compared to numerically simpler GGAs. Notably, the widely used B3LYP functional performs worse than the average of all tested hybrids and is also very sensitive to the application of dispersion corrections. We discourage its usage as a standard method without closer inspection of the results, as it still seems to be often done nowadays. Surprisingly, long-range corrected exchange functionals do in general not perform better than the corresponding standard hybrids. However, the ωB97X-D functional seems to be a promising method. The most robust hybrid is Zhao and Truhlar's PW6B95 functional in combination with DFT-D3. If higher accuracy is required, double-hybrids should be applied. The corresponding DSD-BLYP-D3 and PWPB95-D3 variants are the most accurate and robust functionals of the entire study. Additional calculations with MP2 and and its spin-scaled variants SCS-MP2, S2-MP2 and SOS-MP2 revealed that double-hybrids in general outperform those. Only SCS-MP2 can be recommended, particularly for reaction energies. We suggest its usage when a large self-interaction error is expected that prohibits usage of double-hybrids. Perdews' metaphoric picture of Jacob's Ladder for the classification of density functionals' performance could unbiasedly be confirmed with GMTKN30. We also show that there is no statistical correlation between a functional's accuracy for atomization energies and the performance for chemically more relevant reaction energies.     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center of Rps.viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteria Rhodopseudomonas (Rps.) viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises the ELUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease the ELUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacterioc     

Many-body response of benzene at monolayer MoS2: Van der Waals interactions and spectral broadening

Models of surface enhancement of molecular electronic response properties are challenging for two reasons: (a) molecule-surface interactions require a simultaneous solution of the molecular and the surface dynamic response (a daunting task), and (b) when solving for the electronic structure of the combined molecule + surface system, it is not trivial to single out the particular physical effects responsible for enhancement. To tackle this problem, in this work, we apply a formally exact decomposition of the system's response function into subsystem contributions by using subsystem density functional theory (DFT), which grants access to dynamic polarizabilities and optical spectra. In order to access information about the interactions between the subsystems, we extend a previously developed subsystem-based adiabatic connection fluctuation-dissipation theorem of DFT to separate the additive from the nonadditive correlation energy and identify the nonadditive correlation as the van der Waals interactions. As an example, we choose benzene adsorbed on monolayer MoS₂. We isolate the contributions to benzene's dynamic response arising from the interaction with the surface, and for the first time, we evaluate the enhancements to the effectiveness of C₆ coefficients as a function of benzene-MoS₂ distance and adsorption site. We also quantify the spectral broadening of the benzene's electronic excited states due to their interaction with the surface. We find that the broadening has a similar decay law with the molecule-surface distance as the leading van der Waals interactions (ie, R⁻⁶ ) and that the surface enhancement of dispersion interactions between benzene molecules is less than 5% but is still large enough (0.5 kcal/mol) to likely play a role in the prediction of interface morphologies.     

Parametrization of an empirical correction term to density functional theory for an accurate description of pi-stacking interactions in nucleic acids

We present an accurate parametrization of density functional theory augmented with an empirical correction term to describe properly pi-stacking interactions in nucleic acids. The approach is based on the popular Perdew-Burke-Ernzerhof (PBE), Becke-Perdew (BP), and hybrid Becke-Lee-Yang-Parr (B3LYP) density functionals augmented by a classical London C(6)R(-6) dispersion term. The novelty of our implementation lies in the accurate tuning of the empirical parameters, included in the [formula: see text] damping function, to reproduce high-level post Hartree-Fock calculations. In particular, we present sets of parameters and the needed code to correct the PBE, BP, and B3LYP results from the Turbomole and ADF packages in connection with basis sets of double and triple zeta quality. The developed approach is validated by comparison with the JSCH-2005 benchmark and with best quality stacking energies reported in the literature for the stacking of H-bonded nucleic acids base pairs.     

Host-guest complex of nabumetone: β-cyclodextrin: quantum chemical study and QTAIM analysis

The aim of the present work is the investigation of the inclusion complex of nabumetone (NAB) and β-cyclodextrin (β-CD) using PM3, DFT, DFT-D and ONIOM2 methods. The results indicate that the most energetically favorable structure predicts a preference of the methoxy group to enter the cavity of β-CD from its wide rim. Consequently, the butanone moiety is positioned outside the cavity on the side of the secondary hydroxyls, with a total insertion of naphthalene group. The semi-empirical PM3 results are in good agreement with those obtained by the DFT optimization (with and without dispersion correction). The donor–acceptor interactions between drug and the cavity wall of the host, studied on the basis of natural bonding orbital (NBO) analysis, show the presence of weak intermolecular hydrogen bonds in addition to the most important van der Waals interactions. Furthermore, it is revealed that among the DFT and DFT-D techniques selected to quantify these interactions, WB97X-D functional provides the greatest values of stabilization energies E⁽²⁾. Finally, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM), developed by Bader and co-workers, has been accomplished using the WB97X-D and B3LYP methods on the most favorable complexes. A good correlation between the structural parameters and the electronic density is found.