Journal of Computational Chemistry

doi: 10.1002/jcc.27159pmid: N/A

Purtscher, Felix R. S.; Hofer, Thomas S.

doi: 10.1002/jcc.27428pmid: 38795379

The previously introduced workflow to achieve an energetically and structurally optimized description of frontier bonds in quantum mechanical/molecular mechanics (QM/MM)‐type applications was extended into the regime of computational material sciences at the example of a layered carbon model systems. Optimized QM/MM link bond parameters at HSEsol/6‐311G(d,p) and self‐consistent density functional tight binding (SCC‐DFTB) were derived for graphitic systems, enabling detailed investigation of specific structure motifs occurring in graphene‐derived structures via quantum‐chemical calculations. Exemplary molecular dynamics (MD) simulations in the isochoric‐isothermic (NVT) ensemble were carried out to study the intercalation of lithium and the properties of the Stone–Thrower–Wales defect. The diffusivity of lithium as well as hydrogen and proton adsorption on a defective graphene surface served as additional example. The results of the QM/MM MD simulations provide detailed insight into the applicability of the employed link‐bond strategy when studying intercalation and adsorption properties of graphitic materials.

Sannino, Gennaro Vincenzo; Pecoraro, Adriana; Veneri, Paola Delli; Pavone, Michele; Muñoz‐García, Ana Belén

doi: 10.1002/jcc.27434pmid: 38795374

Several theoretical studies at different levels of theory have attempted to calculate the absolute position of the SnO2 conduction band, whose knowledge is key for its effective application in optoelectronic devices such us, for example, perovskite solar cells. However, the predicted band edges fall outside the experimentally measured range. In this work, we introduce a computational scheme designed to calculate the conduction band minimum values of SnO2, yielding results aligned with experiments. Our analysis points out the fundamental role of encompassing surface oxygen vacancies to properly describe the electronic profile of this material. We explore the impact of both bridge and in‐plane oxygen vacancy defects on the structural and electronic properties of SnO2, explaining from an atomistic perspective the experimental observables. The results underscore the importance of simulating both types of defects to accurately predict SnO2 features and provide new fundamental insights that can guide future studies concerning design and optimization of SnO2‐based materials and functional interfaces.

Sugisaki, Kenji; Nakano, Tatsuya; Mochizuki, Yuji

doi: 10.1002/jcc.27438pmid: 38795375

The fragment molecular orbital (FMO) scheme is one of the popular fragmentation‐based methods and has the potential advantage of making the circuit shallow for quantum chemical calculations on quantum computers. In this study, we used a GPU‐accelerated quantum simulator (cuQuantum) to perform the electron correlation part of the FMO calculation as unitary coupled‐cluster singles and doubles (UCCSD) with the variational quantum eigensolver (VQE) for hydrogen‐bonded (FH) 3 and (FH) 2‐H 2O systems with the STO‐3G basis set. VQE‐UCCSD calculations were performed using both canonical and localized MO sets, and the results were examined from the point of view of size‐consistency and orbital‐invariance affected by the Trotter error. It was found that the use of localized MO leads to better results, especially for (FH) 2‐H 2O. The GPU acceleration was substantial for the simulations with larger numbers of qubits, and was about a factor of 6.7–7.7 for 18 qubit systems.

Crescenzi, Orlando; Graziano, Giuseppe

doi: 10.1002/jcc.27440pmid: 38795315

According to the Hofmeister series, thiocyanate is the strongest “salting in” anion. In fact, it has a strong denaturant activity against the native state of globular proteins. A molecular level rationalization of the Hofmeister series is still missing, and therefore the denaturant activity of thiocyanate also awaits a robust explanation. In the last years, different types of experimental studies have shown that thiocyanate is capable to directly interact with both polar and nonpolar groups of polypeptide chains. This finding has been scrutinized via a careful computational procedure based on density functional theory approaches. The results indicate that thiocyanate is able to make H‐bonds via both the nitrogen and sulfur atom, and to make strong van der Waals interactions with almost all the groups of polypeptide chains, regardless of their polarity.

Nguyen Thi Minh, Nghia; König, Carolin

doi: 10.1002/jcc.27385pmid: 38831461

Oxazine dyes act as reporters of their near environment by the response of their fluorescence spectra. At the same time, their fluorescence spectra exhibit a pronounced vibrational progression. In this work, we computationally investigate the impact of near‐environment models consisting of aggregated water as well as betaine molecules on the vibrational profile of fluorescence spectra of different oxazine derivatives. For aggregated betaine and a water molecule located above the plane of the dyes, we observe a distinct modification of the vibrational profile, which is more pronounced than the effect of a continuum description of a solvent environment. Our analysis shows that this effect cannot be explained by a pure change in the electronic structure, but that also vibrational degrees of freedom of the environment can be decisive for the vibrational profile and should, hence, not generally be neglected.

Petrus, Enric; Buils, Jordi; Garay‐Ruiz, Diego; Segado‐Centellas, Mireia; Bo, Carles

doi: 10.1002/jcc.27389pmid: 38826122

Elucidating the speciation (in terms of concentration versus pH) and understanding the formation mechanisms of polyoxometalates remains a significant challenge, both in experimental and computational domains. POMSimulator is a new methodology that tackles this problem from a purely computational perspective. The methodology uses results from quantum mechanics based methods to automatically set up the chemical reaction network, and to build speciation models. As a result, it becomes possible to predict speciation and phase diagrams, as well as to derive new insights into the formation mechanisms of large molecular clusters. In this work we present the main features of the first open‐source version of the software. Since the first report [Chem. Sci. 2020, 11, 8448‐8456], POMSimulator has undergone several improvements to keep up with the growing challenges that were tackled. After four years of research, we recognize that the source code is sufficiently stable to share a polished and user‐friendly version. The Python code, manual, examples, and install instructions can be found at https://github.com/petrusen/pomsimulator.

Nguyen, Lam H.; Truong, Thanh N.

doi: 10.1002/jcc.27445pmid: 38838302

This study investigates the formation of partial sigma (σ) covalent bonds in experimentally synthesizable biradicals formed from hydrogenated and fluorinated C8, C20, and C60 cage structures, by assessing their stability, geometry, and bonding character in singlet and triplet states using restricted B3LYP‐D3/6–31+G(d,p) theory, natural bond orbital (NBO) analysis, and complete active space self‐consistent field (CASSCF) method. The results show that these partial σCC bonds have Wiberg bond orders of 0.38 to 0.48 and bond lengths ranging from 2.62 Å to 5.93 Å. Cage size influences the characteristics of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), with electrons favoring more antibonding orbitals in smaller cages where electrons reside more on the exterior of the cage and favoring bonding orbitals in larger ones where electrons are more in the interior. Fluorination enhances electron density on bonding orbitals. The analysis further clarified that the differentiation between antibonding and bonding features of HOMOs and LUMOs extends beyond merely electron transfer from s‐ to p‐atomic orbitals, also noting possible interactions of the same symmetry repel. The study also introduces hyperconjugation from α‐position CH bonds as a factor in stabilizing partial σ‐bond formation. The results also caution against the use of broken symmetry methodology in unrestricted SCF wavefunctions for biradicals, such as those in this study as it may cause large spin contamination and thus errors in the calculated electronic properties results.