Interaction Energy Landscapes of Aromatic Heterocycles through a Reliable yet Affordable Computational Approach

Interaction of tautomers of doxorubicin with guanine-cytosine base pair: a density functional theory study

CONTEXT

Anthracycline anticancer antibiotics from Streptomyces peucetius show high affinity for nucleobases. This study uses quantum mechanical density functional theory (DFT) to investigate interactions between doxorubicin (DOX) tautomers and the guanine-cytosine (GC) base pair. Intermolecular distances and interaction energies reveal structural relationships and stabilization. Interaction energy studies show that DOX-GC has greater binding affinity and greater stability in the aqueous phase as compared to that in gaseous phase. Interestingly, the tautomer which show greater affinity for GC in the gas phase is different from the one in the aqueous phase. Reduced density gradient (RDG) scatter plots and quantum theory of atoms in molecules (QTAIM) confirm the presence of hydrogen bonds and its strength. Natural bond orbital (NBO) analysis elucidates donor-acceptor orbital interactions. These findings provide an understanding of the intermolecular interactions between DOX tautomers and the GC base pair, which is likely to provide insight into the molecular basis for DOX's anticancer activity and therapeutic efficacy.

METHODS

DFT calculations were performed using the B3LYP functional with a 6-31G(d,p) basis set in the Gaussian 09 package, including solvent effects through the integral equation formalism polarizable continuum model (IEF-PCM). Topological analysis and quantum theory of atoms in molecules (QTAIM) studies were conducted using the Multiwfn program, while non-covalent interactions were analysed using visual molecular dynamics (VMD) software.

Evaluating Noncovalent Interactions in Halogenated Molecules with Double-Hybrid Functionals and a Dedicated Small Basis Set

We present here an extension of our recently developed PBE-QIDH/DH-SVPD basis set to halogen atoms, with the aim of obtaining, for weakly interacting halogenated molecules, interaction energies close to those provided by a large basis set (def2-TZVPP) coupled to empirical dispersion potential. The core of our approach is the split-valence basis set, DH-SVPD, that has been developed for F, Cl, Br, and I atoms using a self-consistent formula, containing only energy terms computed for dimers and the corresponding monomers at the same level of theory. The basis set developed considering four systems, one for each halogen atoms, has been then tested on the X40, X4 × 10 benchmarks as well as on other two, less standard, data sets. Finally, a large system (380 atoms) has been also considered as a "crash" test. Our results show that the simple and nonempirical PBE-QIDH/DH-SVPD approach is able to provide accurate results for interaction energies of all the considered systems and can thus be considered as a cheaper alternative to DH functionals paired with empirical dispersion corrections and a large basis set of triple-ζ quality.

From Chemical Drawing to Electronic Properties of Semiconducting Polymers in Bulk: A Tool for Chemical Discovery

A quantum chemistry (QC)/molecular dynamics (MD) scheme is developed to calculate electronic properties of semiconducting polymers in three steps: (i) constructing the polymer force field through a unified workflow, (ii) equilibrating polymer models, and (iii) calculating electronic structure properties (e.g., density of states and localization length) from the equilibrated models by QC approaches. Notably, as the second step of this scheme is generally the most time-consuming one, we introduce an alternative method to compute thermally averaged electronic properties in bulk, based on the simulation of a polymer chain in the solution of its repeat units, which is shown to reproduce the microstructure of polymer chains and their electrostatic effect (successfully tested for five benchmark polymers) 10 times faster than state-of-the-art methods. In fact, this scheme offers a consistent and speedy way of estimating electronic properties of polymers from their chemical drawings, thus ensuring the availability of a homogeneous set of simulations to derive structure-property relationships and material design principles. As an example, we show how the electrostatic effect of the polymer chain environment can disturb the localized electronic states at the band tails and how this effect is more significant in the case of diketopyrrolopyrrole polymers as compared to indacenodithiophene and dithiopheneindenofluorene ones.

The structure of liquid thiophene from total neutron scattering

The structure of pure liquid thiophene is revealed by using a combination of total neutron scattering experiments with isotopic substitution and molecular simulations via the next generation empirical potential refinement software, Dissolve. In the liquid, thiophene presents three principle local structural motifs within the first solvation shell, in plane and out of the plane of the thiophene ring. Firstly, above/below the ring plane thiophenes present a single H towards the π cloud, due to a combination of electrostatic and dispersion interactions. Secondly, around the ring plane, perpendicular thiophene molecules find 5 preferred sites driven by bifurcated C-H⋯S interactions, showing that hydrogen-sulfur bonding prevails over the charge asymmetry created by the heteroatom. Finally, parallel thiophenes sit above and below the ring, excluded from directly above the ring center and above the sulfur.

Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6

Heteroaromatic stacking interactions are important in drug binding, supramolecular chemistry, and materials science, making protein-ligand model systems of these interactions of considerable interest. Here we studied 30 congeneric ligands that each present a distinct heteroarene for stacking between tyrosine residues at the dimer interface of procaspase-6. Complex X-ray crystal structures of 10 analogs showed that stacking geometries were well conserved, while high-accuracy computations showed that heteroarene stacking energy was well correlated with predicted overall ligand binding energies. Empirically determined KD values in this system thus provide a useful measure of heteroarene stacking with tyrosine. Stacking energies are discussed in the context of torsional strain, the number and positioning of heteroatoms, tautomeric state, and coaxial orientation of heteroarene in the stack. Overall, this study provides an extensive data set of empirical and high-level computed binding energies in a versatile new protein-ligand system amenable to studies of other intermolecular interactions.

Exploring alkali metal cation⋯hydrogen interaction in the formation half sandwich complexes with cycloalkanes: a DFT approach

Gas and solvent phase stability of half sandwich complexes between cycloalkanes viz. cyclopropane, cyclobutane, cyclopentane, cyclohexane, bicyclo[2.2.2]octane and adamantane with alkali metal cations (Li+, Na+ and K+) are analysed using density functional theory (DFT). M06-2X/6-31++G(d,p) level is primarily used for the study. The studied half sandwich complexes are stable in gas phase (stabilization energy upto 26.55 kcal mol−1). Presence of solvent phase irrespective of its dielectric, imparts negative impact on the stability of the chosen complexes. The formation of the complexes is exothermic in nature. The process of complexation is both enthalpy (ΔH) and free energy (ΔG) driven. Variation in HOMO (highest occupied molecular orbital) energy also indicates towards the chemical stability of complexes. The interaction is non-covalent with primary contribution from induction component. NBO analysis indicates that C–H bond is the donor and antibonding metal orbital is the acceptor site in the process of complexation. Stability of the complexes depends on the size of the interacting monomers.

Accurate Quantum-Mechanically Derived Force-Fields through a Fragment-Based Approach: Balancing Specificity and Transferability in the Prediction of Self-Assembly in Soft Matter

The wide range of time/length scales covered by self-assembly in soft matter makes molecular dynamics (MD) the ideal candidate for simulating such a supramolecular phenomenon at an atomistic level. However, the reliability of MD outcomes heavily relies on the accuracy of the adopted force-field (FF). The spontaneous re-ordering in liquid crystalline materials stands as a clear example of such collective self-assembling processes, driven by a subtle and delicate balance between supramolecular interactions and single-molecule flexibility. General-purpose transferable FFs often dramatically fail to reproduce such complex phenomena, for example, the error on the transition temperatures being larger than 100 K. Conversely, quantum-mechanically derived force-fields (QMD-FFs), specifically tailored for the target system, were recently shown (J. Phys. Chem. Lett.2022,13, 243) to allow for the required accuracy as they not only well reproduced transition temperatures but also yielded a quantitative agreement with the experiment on a wealth of structural, dynamic, and thermodynamic properties. The main drawback of this strategy stands in the computational burden connected to the numerous quantum mechanical (QM) calculations usually required for a target-specific parameterization, which has undoubtedly hampered the routine application of QMD-FFs. In this work, we propose a fragment-based strategy to extend the applicability of QMD-FFs, in which the amount of QM calculations is significantly reduced, being a single-molecule-optimized geometry and its Hessian matrix the only QM information required. To validate this route, a new FF is assembled for a large mesogen, exploiting the parameters obtained for two smaller liquid crystalline molecules, in this and previous work. Lengthy MD simulations are carried out with the new transferred QMD-FF, observing again a spontaneous re-orientation in the correct range of temperatures, with good agreement with the available experimental measures. The present results strongly suggest that a partial transfer of QMD-FF parameters can be invoked without a significant loss of accuracy, thus paving the way to exploit the method's intrinsic predictive capabilities in the simulation of novel soft materials.

Complexes of Alkaline and Ammonium Cations with Dopamine and Eumelanin Precursors: Dissecting the Role of Noncovalent Cation-π and Cation-Lone Pair (σ-Type) Interactions

Cation-π interactions and their possible competition with other noncovalent interactions (NCI) might play a key role in both dopamine- and eumelanin-based bioinspired materials. In this contribution, to unravel the delicate interplay between cation-π interactions and other possible competing forces, the configurational space of noncovalent complexes formed by dopamine or eumelanin precursors (o-benzoquinone, DHI and a semiquinone dimer) and three different cations (Na⁺, K⁺, and NH₄⁺) is sampled by means of accurate ab initio calculations. To this end, we resort to the mp2^mod method, recently validated by us for benzene-, phenol-, and catechol-cation complexes, whose computational convenience allows for an extensive exploration of the cation-molecule interaction energy surface, by sampling a total of more than 10⁴ arrangements. The mp2^mod interaction energy landscapes reveal that, besides the expected cation-π driven arrangements, for all considered molecule-cation pairs the most stable complexes are found when the cation lies within the plane containing the six-membered ring, thus maximizing the σ-type interaction with the oxygen's lone pairs. Due to the loss of aromaticity, the σ-type/cation-π strength ratio is remarkably large in o-benzoquinone, where cation-π complexes seem unlikely to be formed. The above features are shared among all considered cations but are significantly larger when considering the smaller Na⁺. Besides delivering a deeper insight onto the NCI network established by the considered precursors in the presence of ions, the present results can serve as a reference database to validate or refine lower level methods, as, for instance, the force fields employed in classical simulations.

Formation of sandwich and multidecker complexes between O2 and alkali/alkaline earth metals: A DFT study

Abstract: Feasibility of formation of sandwich and multidecker complexes between O2 molecules and alkali/alkaline earth metal has been analyzed in the light of density functional theory (DFT). High value of...

Automated Parameterization of Quantum Mechanically Derived Force Fields for Soft Materials and Complex Fluids: Development and Validation

The reliability of molecular dynamics (MD) simulations in predicting macroscopic properties of complex fluids and soft materials, such as liquid crystals, colloidal suspensions, or polymers, relies on the accuracy of the adopted force field (FF). We present an automated protocol to derive specific and accurate FFs, fully based on ab initio quantum mechanical (QM) data. The integration of the Joyce and Picky procedures, recently proposed by our group to provide an accurate description of simple liquids, is here extended to larger molecules, capable of exhibiting more complex fluid phases. While the standard Joyce protocol is employed to parameterize the intramolecular FF term, a new automated procedure is here proposed to handle the computational cost of the QM calculations required for the parameterization of the intermolecular FF term. The latter is thus obtained by integrating the old Picky procedure with a fragmentation reconstruction method (FRM) that allows for a reliable, yet computationally feasible sampling of the intermolecular energy surface at the QM level. The whole FF parameterization protocol is tested on a benchmark liquid crystal, and the performances of the resulting quantum mechanically derived (QMD) FF were compared with those delivered by a general-purpose, transferable one, and by the third, "hybrid" FF, where only the bonded terms were refined against QM data. Lengthy atomistic MD simulations are carried out with each FF on extended 5CB systems in both isotropic and nematic phases, eventually validating the proposed protocol by comparing the resulting macroscopic properties with other computational models and with experiments. The QMD-FF yields the best performances, reproducing both phases in the correct range of temperatures and well describing their structure, dynamics, and thermodynamic properties, thus providing a clear protocol that may be explored to predict such properties on other complex fluids or soft materials.

The phenoxyl group-modulated interplay of cation-π and σ-type interactions in the alkali metal series

The interaction potential energy surfaces (IPESs) of four alkaline metal cations (Na+, K+, Rb+ and Cs+) complexed with phenol and catechol were explored by accurate ab initio calculations to investigate the interplay of different noncovalent interactions and their behavior along the alkali metal series and upon -OH substitution. Selected one-dimensional interaction energy curves revealed two different minimum energy configurations for all phenol- and catechol-metal complexes, characterized either by cation-π or σ-type interactions. For each investigated complex several two-dimensional IPES maps were also computed, exploiting the computational advantages of the MP2mod approach. The size of the alkali cation was found to play a similar role in modulating both kinds of complexes, as the interaction strength always decreases along the metal series, from Na+ to Cs+. Conversely, the number of hydroxyl substituents markedly affected cation-π complexes vs. σ-type ones. As a most relevant finding, in catechol-metal complexes the strength of cation-π interactions is around half that of the σ-type ones. It is argued that the combined effect of cation dimensions and hydroxyl substitution in catechol-Na+ complexes makes σ-type configurations remarkably more stable and easily accessible than cation-π ones. Besides shedding new light on the origin of biological phenomena connected with underwater adhesion, the quantum mechanical interaction energy database provided herein may offer a useful reference for tuning accurate force fields, suitable for molecular dynamics simulations, where environmental effects might be also taken into account.

Energy, orbital and structural stacking landscape of a purine homodimer system

The multidimensional study, combining the extensive calculations of potential energy surfaces for the parallel-displaced configurations and methods such as energy decomposition and natural bond orbital analysis, has been carried out. The resulted data give an energy, orbital and structural landscapes of this biologically essential system. The balance of the two energy sources, electrostatic and dispersion, is clearly visible. The obtained results, taken as a whole, provide an insight into the hierarchy of intermolecular interactions in the purine system, together with their sources.

Density Functional Study on the Adsorption of 5-Membered N-Heterocycles on B/N/BN-Doped Graphene: Coronene as a Model System

Adsorption of seven 5-membered N-heterocycles on B/N/BN-doped graphene (with coronene as a model system) has been studied using density functional theory (DFT). The geometry of the complexes validated the involvement of both π···π stacking and N-H···π interaction in the adsorption process. The stability of the complexes is measured in terms of stabilization energy, and the results suggested that the complexes are stable enough (stabilization energies are in the range of 7.61-14.77 kcal mol^-1). Studies confirmed the stability of complexes in the solvent phase too irrespective of the dielectric of the solvent. Dispersive force is the major mode of interaction in stabilizing the complexes. Natural bond orbital analysis indicated a small contribution from electrostatic and covalent interactions. Thermochemical analysis revealed that the complexation is exothermic in nature and favorable at a lower temperature. Adsorption of N-heterocycles exerts a nominal impact on the electronic properties of the undoped/doped graphene. The study presents a simple approach to introduce an arbitrary functionality to undoped/doped graphene by preserving its electronic properties.

Fine-tuning the effect of π-π interactions on the stability of the NTB phase

The synthesis and liquid-crystalline properties are reported for novel bent-shaped dimers in which a naphthyl group has been incorporated into the mesogenic cores. In addition to the nematic and twist-bend nematic phase, a new liquid-crystalline phase was observed. The combined experimental and computational study demonstrated how the interplay between the molecular geometry and π-π interactions affects the thermal stability of the twist-bend nematic and nematic phases. Correlation between mesomorphic properties and molecular geometry revealed that a greater conformational diversity leads to a broader distribution of bend-angles and destabilization of the NTB phase. Qualitative correlation between the thermal behaviour and electronic structure of the molecules of a similar geometry suggested that the transition temperatures of both nematic phases depend on the relative contribution of dispersion and electrostatic energies which determines the strength of the π-π interactions. These results provide an insight into how subtle changes in chemical structure can be exploited to tune the intermolecular interactions and influence the thermal stability of the liquid crystalline phase.

Development and Validation of Quantum Mechanically Derived Force-Fields: Thermodynamic, Structural, and Vibrational Properties of Aromatic Heterocycles

A selection of several aromatic molecules, representative of the important class of heterocyclic compounds, has been considered for testing and validating an automated Force Field (FF) parametrization protocol, based only on Quantum Mechanical data. The parametrization is carried out separately for the intra- and intermolecular contributions, employing respectively the Joyce and Picky software packages, previously implemented and refined in our research group. The whole approach is here automated and integrated with a computationally effective yet accurate method, devised very recently ( J. Chem.

THEORY

Comput., 2018, 14, 543-556) to evaluate a large number of dimer interaction energies. The resulting quantum mechanically derived FFs are then used in extensive molecular dynamics simulations, in order to evaluate a number of thermodynamic, structural, and dynamic properties of the heterocycle's gas and liquid phases. The comparison with the available experimental data is good and furnishes a validation of the presented approach, which can be confidently exploited for the design of novel and more complex materials.

On the formation of sandwich and multidecker complexes via π⋯π interaction: a DFT study

Sandwich and multidecker complexes via organic π–inorganic π interaction.

Noncovalent Interactions in the Catechol Dimer

Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the contribution of dispersion and hydrogen bonds in both stacked and T-shaped catechol dimers, with the aim of delineating the respective role of these classes of interactions in determining the most stable structure. By using second-order Møller⁻Plesset (MP2) calculations with a small basis set, specifically optimized for these species, we have explored a number of significant sections of the interaction potential energy surface and found the most stable structures for the dimer, in good agreement with the highly accurate, but computationally more expensive coupled cluster single and double excitation and the perturbative triples (CCSD(T))/CBS) method.