Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories

DLPNO-CCSD(T) scaled methods for the accurate treatment of large supramolecular complexes

In this work, we present scaled variants of the DLPNO-CCSD(T) method, dubbed as (LS)DLPNO-CCSD(T) and (NS)DLPNO-CCSD(T), to obtain accurate interaction energies in supramolecular complexes governed by noncovalent interactions. The novel scaled schemes are based on the linear combination of the DLPNO-CCSD(T) correlation energies calculated with the standard (LoosePNO and NormalPNO) and modified (Loose2PNO and Normal2PNO) DLPNO-CCSD(T) accuracy levels. The scaled DLPNO-CCSD(T) variants provide nearly TightPNO accuracy, which is essential for the quantification of weak noncovalent interactions, with a noticeable saving in computational cost. Importantly, the accuracy of the proposed schemes is preserved irrespective of the nature and strength of the supramolecular interaction. The (LS)DLPNO-CCSD(T) and (NS)DLPNO-CCSD(T) protocols have been used to study in depth the role of the CH-π versus π-π interactions in the supramolecular complex formed by the electron-donor truxene-tetrathiafulvalene (truxTTF) and the electron-acceptor hemifullerene (C₃₀ H₁₂ ). (NS)DLPNO-CCSD(T)/CBS calculations clearly reveal the higher stability of staggered (dominated by CH-π interactions) versus bowl-in-bowl (dominated by π-π interactions) arrangements in the truxTTF•C₃₀ H₁₂ heterodimer. Hemifullerene and similar carbon-based buckybowls are therefore expected to self-assemble with donor compounds in a richer way other than the typical concave-convex π-π arrangement found in fullerene-based aggregates. © 2017 Wiley Periodicals, Inc.

Chemical Functionalization of Graphene Family Members

Thanks to their outstanding physicochemical properties, graphene and its derivatives are interesting nanomaterials with a high potential in several fields. Graphene, graphene oxide, and reduced graphene oxide, however, differ partially in their characteristics due to their diverse surface composition. Those differences influence the chemical reactivity of these materials. In the following chapter the reactivity and main functionalization reactions performed on graphene, graphene oxide, and reduced graphene oxide are discussed. A part is also dedicated to the main analytical techniques used for characterization of these materials. Functionalization of graphene and its derivatives is highly important to modulate their characteristics and design graphene-based conjugates with novel properties. Functionalization can be covalent by forming strong and stable bonds with the graphene surface, or non-covalent via π–π, electrostatic, hydrophobic, and/or van der Waals interactions. Both types of functionalization are currently exploited.

Partnering dispersion corrections with modern parameter-free double-hybrid density functionals

The PBE-QIDH and SOS1-PBE-QIDH double-hybrid density functionals are merged with a pair of dispersion corrections, namely the pairwise additive D3(BJ) and the non-local correlation functional VV10, leading to the corresponding dispersion-corrected models.

Structural and energetic study of cation–π–cation interactions in proteins

Statistical and energetic analysis of cation–π–cation motifs in protein structures suggests a potential stabilizing role in the protein fold.

Confinement of hydrogen and hydroxyl radicals in water cages: a density functional theory study

Radicals can be confined in water cages and exhibit similar structures and properties to their corresponding free forms.

Endohedral pnicogen and triel bonds in doped C60 fullerenes

Encapsulation of H_nYF_3−n in C₃₀X₁₅Y₁₅ (X = B, Al and Y = N, P and n = 1, 2) and characterization of the endohedral pnicogen and triel bonds.

Description of Weak Halogen Bonding Using Various Levels of Symmetry-Adapted Perturbation Theory Combined with Effective Core Potentials

The present work starts with providing a description of the halogen bonding (XB) interaction between the halogen atom of MH3X (where M = C–Pb and X = I, At) and the N atom of HCN. This interaction leads to the formation of stable yet very weakly bound MH3X⋯NCH complexes for which the interaction energy (Eint) between MH3X and HCN is calculated using various symmetry-adapted perturbation theory (SAPT) methods combined with the def2-QZVPP basis set and midbond functions. This basis set assigns effective core potentials (ECPs) not only to the I or At atom directly participating in the XB interaction with HCN but also to the M atom when substituted with Sn or Pb. Twelve SAPT methods (or levels) are taken into consideration. According to the SAPT analysis ofEint, the XB interaction in the complexes shows mixed electrostatic-dispersion nature. Next, the accuracy of SAPTEintis evaluated by comparing with CCSD(T) reference data. This comparison reveals that high-order SAPT2+(3)method and the much less computationally demanding SAPT(DFT) method perform very well in describingEintof the complexes. However, the accuracy of these methods decreases dramatically if they are combined with the so-called Hartree-Fock correction.

B–Hb⋯π interaction in borane–graphene complexes: coronene as a case study

N/B/BN doping in graphene enhances adsorption of boranes.

Finding reaction mechanisms, intuitive or otherwise

Mechanism discovery made possible through deterministic, computational reaction pathway searches.

Origin of cooperativity in hydrogen bonding

Hydrogen bond cooperativity results from interactions between effective point dipoles which account for many-body contributions to cooperativity.

Exploring the (Very Flat) Potential Energy Landscape of R-Br⋅⋅⋅π Interactions with Accurate CCSD(T) and SAPT Techniques

Halogen bonds involving an aromatic moiety as an acceptor, otherwise known as R-X⋅⋅⋅π interactions, have increasingly been recognized as being important in materials and in protein-ligand complexes. These types of interactions have been the subject of many recent investigations, but little is known about the ways in which the strengths of R-X⋅⋅⋅π interactions vary as a function of the relative geometries of the interacting pairs. Here we use the accurate CCSD(T) and SAPT2+3δMP2 methods to investigate the potential energy landscapes for systems of HBr, HCCBr, and NCBr complexed with benzene. It is found that only the separation between the complexed molecules have a strong effect on interaction strength while other geometric parameters, such as tilting and shifting R-Br⋅⋅⋅π donor relative to the benzene plane, affect these interactions only mildly. Importantly, it is found that the C_6v (T-shaped) configuration is not the global minimum for any of the dimers investigated.

Self-assembly of acetate adsorbates drives atomic rearrangement on the Au(110) surface

Weak inter-adsorbate interactions are shown to play a crucial role in determining surface structure, with major implications for its catalytic reactivity. This is exemplified here in the case of acetate bound to Au(110), where the small extra energy of the van der Waals interactions among the surface-bound groups drives massive restructuring of the underlying Au. Acetate is a key intermediate in electro-oxidation of CO₂ and a poison in partial oxidation reactions. Metal atom migration originates at surface defects and is likely facilitated by weakened Au–Au interactions due to bonding with the acetate. Even though the acetate is a relatively small molecule, weak intermolecular interaction provides the energy required for molecular self-assembly and reorganization of the metal surface.

The efficiency of a catalyst relies on the stability of intermediates on its surface. Here, the authors find that van der Waals interactions between acetate adsorbates on Au(110) provide a small but necessary energy contribution to stabilize the acetate and drive restructuring of the Au surface.

Enhancement of the physicochemical properties of [Pt(dien)(nucleobase)]2+ for HIVNCp7 targeting

Physicochemical properties of coordination compounds can be exploited for molecular recognition of biomolecules. The inherent π-π stacking properties of [Pt(chelate)(N-donor)]²⁺ ([PtN₄]) complexes were modulated by systematic variation of the chelate (diethylenetriamine and substituted derivatives) and N-donor (nucleobase or nucleoside) in the formally substitution-inert PtN₄ coordination sphere. Approaches to target the HIV nucleocapsid protein HIVNCp7 are summarized building on (i) assessment of stacking interactions with simple tryptophan or tryptophan derivatives to (ii) the tryptophan-containing C-terminal zinc finger and (iii) to the full two-zinc finger peptide and its interactions with RNA and DNA. The xanthosine nucleoside was identified as having significantly enhanced stacking capability over guanosine. Correlation of the LUMO energies of the modified nucleobases with the DFT π-stacking energies shows that frontier orbital energies of the individual monomers can be used as a first estimate of the π-stacking strength to Trp. Cellular accumulation studies showed no significant correlation with lipophilicity of the compounds, but all compounds had very low cytotoxicity suggesting the potential for antiviral selectivity. The conceptual similarities between nucleobase alkylation and platination validates the design of formally substitution-inert coordination complexes as weak Lewis acid electrophiles for selective peptide targeting.

n→π* Interactions Are Competitive with Hydrogen Bonds

Because carbonyl groups can participate in both hydrogen bonds and n→π* interactions, these two interactions likely affect one another. Herein, enhancement of an amidic n→π* interaction is shown to reduce the ability of β-keto amides to tautomerize to the enol, indicating decreased hydrogen-bonding capacity of the amide carbonyl group. Thus, an n→π* interaction can have a significant effect on the strength of a hydrogen bond to the same carbonyl group.

How important is thermal expansion for predicting molecular crystal structures and thermochemistry at finite temperatures?

Molecular crystals expand appreciably upon heating due to both zero-point and thermal vibrational motion, yet this expansion is often neglected in molecular crystal modeling studies. Here, a quasi-harmonic approximation is coupled with fragment-based hybrid many-body interaction calculations to predict thermal expansion and finite-temperature thermochemical properties in crystalline carbon dioxide, ice Ih, acetic acid and imidazole. Fragment-based second-order Möller-Plesset perturbation theory (MP2) and coupled cluster theory with singles, doubles and perturbative triples [CCSD(T)] predict the thermal expansion and the temperature dependence of the enthalpies, entropies and Gibbs free energies of sublimation in good agreement with experiment. The errors introduced by neglecting thermal expansion in the enthalpy and entropy cancel somewhat in the Gibbs free energy. The resulting ∼ 1-2 kJ mol(-1) errors in the free energy near room temperature are comparable to or smaller than the errors expected from the electronic structure treatment, but they may be sufficiently large to affect free-energy rankings among energetically close polymorphs.

The effects of replacing the water model while decoupling water-water and water-solute interactions on computed properties of simple salts

The effects of decoupling the water-water and water-solute interactions are studied with selected mono-valent ions as the solute. Using the ion-water cross terms developed for the BLYPSP-4F water model, we replaced the water potential with WAIL, TIP4P, and TIP3P without changing the ion-water parameters. When the adaptive force matching (AFM) derived BLYPSP-4F model is replaced by the other AFM derived WAIL model, the difference in ion properties, such as hydration free energies, radial distribution functions, relative diffusion constants, is negligible, demonstrating the feasibility for combining AFM parameters from different sources. Interestingly, when the AFM-derived ion-water cross-terms are used with a non-AFM based water model, only small changes in the ion properties are observed. The final combined models with TIP3P or TIP4P water reproduce the salt hydration free energies within 6% of experiments. The feasibility of combining AFM models with other non-AFM models is of significance since such combinations allow more complex systems to be studied without specific parameterization. In addition, the study suggests an interesting prospect of reusing the cross-terms when a part of a general force field is replaced with a different model. The prevailing practice, which is to re-derive all cross-terms with combining rules, may not have been optimal.

Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields

Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.

CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals

A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol(-1) on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems.

A DFT study on the role of long range correlation interaction and solvent effects in homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids

Using B3LYP and B97D functionals of density functional theory (DFT), homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids are studied in gas phase and solvent phase, i. e., Acetonitrile. Both the functionals show that formation of homochiral cyclic tripeptide is thermodynamically and kinetically favorable over its heterochiral counterpart in gas phase. The functional, B97D, decreases the height of reaction barriers significantly compared to those predicted by the functional B3LYP. The reaction pathways explored using PCM implicit solvent model show reduced kinetic favorability for formation of the homochiral cyclic tripeptide over its heterochiral counterpart. The results are substantiated by structural aspects.

Stacking interactions in RNA and DNA: Roll-slide energy hyperspace for ten unique dinucleotide steps

Understanding dinucleotide sequence directed structures of nuleic acids and their variability from experimental observation remained ineffective due to unavailability of statistically meaningful data. We have attempted to understand this from energy scan along twist, roll, and slide degrees of freedom which are mostly dependent on dinucleotide sequence using ab initio density functional theory. We have carried out stacking energy analysis in these dinucleotide parameter phase space for all ten unique dinucleotide steps in DNA and RNA using DFT-D by ωB97X-D/6-31G(2d,2p), which appears to satisfactorily explain conformational preferences for AU/AU step in our recent study. We show that values of roll, slide, and twist of most of the dinucleotide sequences in crystal structures fall in the low energy region. The minimum energy regions with large twist values are associated with the roll and slide values of B-DNA, whereas, smaller twist values correspond to higher stability to RNA and A-DNA like conformations. Incorporation of solvent effect by CPCM method could explain the preference shown by some sequences to occur in B-DNA or A-DNA conformations. Conformational preference of BII sub-state in B-DNA is preferentially displayed mainly by pyrimidine-purine steps and partly by purine-purine steps. The purine-pyrimidine steps show largest effect of 5-methyl group of thymine in stacking energy and the introduction of solvent reduces this effect significantly. These predicted structures and variabilities can explain the effect of sequence on DNA and RNA functionality.

Proline cis-trans isomerization and its implications for the dimerization of analogues of cyclopeptide stylostatin 1: a combined computational and experimental study

Cis and trans proline conformers are often associated with dramatic changes in the biological function of peptides. A slow equilibrium between cis and trans Ile-Pro amide bond conformers occurs in constrained derivatives of the native marine cyclic heptapeptide stylostatin 1 (cyclo-(NSLAIPF)), a potential anticancer agent. In this work, four cyclopeptides, cyclo-(NSTAIPF), cyclo-(KSTAIPF), cyclo-(RSTAIPF) and cyclo-(DSTAIPF), which are structurally related to stylostatin 1, are experimentally and computationally examined in order to assess the effect of residue mutations on the cis-trans conformational ratio and the apparent capacity to form dimeric aggregates. Primarily, cyclo-(KSTAIPF) and cyclo-(RSTAIPF) showed specific trends in circular dichroism, MALDI-TOF and HPLC purification experiments, which suggests the occurrence of peptide dimerization. Meanwhile, the NMR spectrum of cyclo-(KSTAIPF) indicates that this cyclopeptide exists in the two slow-exchange families of conformations mentioned above. Molecular dynamics simulations combined with quantum mechanical calculations have shed light on the factors governing the cis/trans conformational ratio. In particular, we have found that residue mutations affect the internal hydrogen bond pattern which ultimately tunes the cis/trans conformational ratio and that only trans conformers are capable of aggregating due to the shape complementarity of the two subunits.

A machine learning correction for DFT non-covalent interactions based on the S22, S66 and X40 benchmark databases

Background

Non-covalent interactions (NCIs) play critical roles in supramolecular chemistries; however, they are difficult to measure. Currently, reliable computational methods are being pursued to meet this challenge, but the accuracy of calculations based on low levels of theory is not satisfactory and calculations based on high levels of theory are often too costly. Accordingly, to reduce the cost and increase the accuracy of low-level theoretical calculations to describe NCIs, an efficient approach is proposed to correct NCI calculations based on the benchmark databases S22, S66 and X40 (Hobza in Acc Chem Rev 45: 663–672, 2012; Řezáč et al. in J Chem Theory Comput 8:4285, 2012).

Results

A novel type of NCI correction is presented for density functional theory (DFT) methods. In this approach, the general regression neural network machine learning method is used to perform the correction for DFT methods on the basis of DFT calculations. Various DFT methods, including M06-2X, B3LYP, B3LYP-D3, PBE, PBE-D3 and ωB97XD, with two small basis sets (i.e., 6-31G* and 6-31+G*) were investigated. Moreover, the conductor-like polarizable continuum model with two types of solvents (i.e., water and pentylamine, which mimics a protein environment with ε = 4.2) were considered in the DFT calculations. With the correction, the root mean square errors of all DFT calculations were improved by at least 70 %. Relative to CCSD(T)/CBS benchmark values (used as experimental NCI values because of its high accuracy), the mean absolute error of the best result was 0.33 kcal/mol, which is comparable to high-level ab initio methods or DFT methods with fairly large basis sets. Notably, this level of accuracy is achieved within a fraction of the time required by other methods. For all of the correction models based on various DFT approaches, the validation parameters according to OECD principles (i.e., the correlation coefficient R², the predictive squared correlation coefficient q² and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$q_{cv}^{2}$$\end{document}qcv2 from cross-validation) were >0.92, which suggests that the correction model has good stability, robustness and predictive power.

Conclusions

The correction can be added following DFT calculations. With the obtained molecular descriptors, the NCIs produced by DFT methods can be improved to achieve high-level accuracy. Moreover, only one parameter is introduced into the correction model, which makes it easily applicable. Overall, this work demonstrates that the correction model may be an alternative to the traditional means of correcting for NCIs.Graphical abstract

Excited-State Properties of Molecular Solids from First Principles

Molecular solids have attracted attention recently in the context of organic (opto)electronics. These materials exhibit unique charge carrier generation and transport phenomena that are distinct from those of conventional semiconductors. Understanding these phenomena is fundamental to optoelectronics and requires a detailed description of the excited-state properties of molecular solids. Recent advances in many-body perturbation theory (MBPT) and density functional theory (DFT) have made such description possible and have revealed many surprising electronic and optical properties of molecular crystals. Here, we review this progress. We summarize the salient aspects of MBPT and DFT as well as various properties that can be described by these methods. These properties include the fundamental gap and its renormalization, hybridization and band dispersion, singlet and triplet excitations, optical spectra, and excitonic properties. For each, we present concrete examples, a comparison to experiments, and a critical discussion.