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.

Predicting Spontaneous Orientational Self-Assembly: In Silico Design of Materials with Quantum Mechanically Derived Force Fields

De novo design of self-assembled materials hinges upon our ability to relate macroscopic properties to individual building blocks, thus characterizing in such supramolecular architectures a wide range of observables at varied time/length scales. This work demonstrates that quantum mechanical derived force fields (QMD-FFs) do satisfy this requisite and, most importantly, do so in a predictive manner. To this end, a specific FF, built solely based on the knowledge of the target molecular structure, is employed to reproduce the spontaneous transition to an ordered liquid crystal phase. The simulations deliver a multiscale portrait of such self-assembly processes, where conformational changes within the individual building blocks are intertwined with a 200 ns ensemble reorganization. The extensive characterization provided not only is in quantitative agreement with the experiment but also connects the time/length scales at which it was performed. Realizing QMD-FF predictive power and unmatched accuracy stands as an important leap forward for the bottom-up design of advanced supramolecular materials.

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 mechanism of the reaction between MAO and TMA: DFT study of the electronic structure and characterization of transition states for [AlOMe]6, [AlOMe]9 and [AlOMe]16 cages

Methylaluminoxane (MAO) and trimethylaluminium (TMA) are relevant compounds in organometallic catalysis. Despite many published studies, aspects of their interaction persist an unsolved puzzle. Hence, in this work, we used quantum mechanic approaches based on density functional theory to study this topic. Our calculations revealed that interaction between MAO and TMA occurs initially by the formation of an intermediary Lewis adduct. In agreement with the latent acidity concept, the activation energy for the tensioned Al-O bond break is small, and changes with the local environment of the MAO cages. Breakage of bond belonging to two square faces requires between 4.20 and 5.80 kcal/mol, whereas square-hexagonal faces demand 0.61-9.43 kcal/mol. The products of this reaction present a terminal, acidic 3-coordinate aluminum atom, that can be capped by another TMA molecules. However, our computations suggest that entropic effects may prevent this reaction from occurring at all these sites in the MAO models studied. Additionally, we also characterize the inter/intramolecular methane elimination mechanism. These reactions are not feasible at room temperature but may occur at high temperatures.

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.

An automated approach for the parameterization of accurate intermolecular force-fields: pyridine as a case study

An automated protocol is proposed and validated, which integrates accurate quantum mechanical calculations with classical numerical simulations. Intermolecular force fields, (FF) suitable for molecular dynamics (MD) and Monte Carlo simulations, are parameterized through a novel iterative approach, fully based on quantum mechanical data, which has been automated and coded into the PICKY software, here presented. The whole procedure is tested and validated for pyridine, whose bulk phase, described through MD simulations performed with the specifically parameterized FF, is characterized by computing several of its thermodynamic, structural, and transport properties, comparing them with their experimental counterparts.

Convergence of triples energy in CCSD(T) and CC3 calculations with correlation-consistent basis sets

The convergence behavior of connected triples correlation energy in CCSD(T) and CC3 calculations with (aug-)cc-pVXZ basis sets has been accurately described in terms of a power law of the type E(X)=E(infinity)+AX(-4). Calculations ranging from double-Z through septuple-Z attest the validity of this X(-4) convergence model. Extrapolations generated from (X-1,X)-Z calculations yield energies of nearly (X+1)-Z quality. Typically, the fraction of triples correlation energy recovered is 0.92+/-0.05 in (D,T) extrapolations; 0.98+/-0.01 in (T,Q) extrapolations; 1.0002+/-0.0012 in (Q,5) extrapolations; and 0.9995+/-0.0005 in (5,6) extrapolations.

Chemical and photochemical generated carbon-centered radical intermediate and its reaction with desoxyribonucleic acid

The possible action of carbon-centered radicals in promoting damage to DNA is explored by generation of the 2-phenylethyl radical. The radical is generated during oxidation of phenelzine (2-phenylethyl hydrazine) by ferricyanide, as well as optically from phenylpropionic acid. Covalent binding of the 2-phenylethyl radical to DNA is suggested by studies with the plasmid pBR 322 DNA. Other sensitive techniques used to study DNA damage were the interaction with formaldehyde at 60 degrees C and the fluorescence of DNA-Tb(III) and DNA-DAPI complexes. Theoretical MNDO calculations indicated a preferential attack at position 8 of the guanine residues. This study shows that the 2-phenylethyl radical is able to induce primary effects on nucleic acid structure, leading to alkylated products, especially at purine rings.