Journal of Computational Chemistry

doi: 10.1002/jcc.27165pmid: N/A

Lima, Elodie Fernandes; Bredow, Thomas

doi: 10.1002/jcc.27479pmid: 39134305

The development of novel methods in solid‐state quantum chemistry necessitates reliable reference data sets for their assessment. The most fundamental solid‐state property of interest is the crystal structure, quantified by the lattice parameters. In the last decade, several studies were conducted to assess theoretical approaches based on the agreement of calculated lattice parameters with respect to experiment as a measure. However, most of these studies used a limited number of reference systems with high symmetry. The present work offers a more comprehensive reference benchmark denoted as Sol337LC, which consists of 337 inorganic compounds with 553 symmetry‐inequivalent lattice parameters, representing every element of the periodic table for atomic numbers between 1 and 86, except noble gases, the radioactive elements and lanthanoids. The reference values were taken from earlier benchmarks and from measurements at very low temperature or extrapolation to 0 K. The experimental low‐temperature lattice parameters were then corrected for zero‐point energy effects via the quasi‐harmonic approximation for direct comparison with quantum‐chemical optimized structures. A selection of standard density functional approximations was assessed for their deviations from the experimental reference data. The calculations were performed with the crystal orbital program CRYSTAL23, applying optimized atom‐centered basis sets of triple‐zeta plus polarization quality. The SCAN functional family and the global hybrid functional PW1PW, augmented with the D3 dispersion correction, were found to provide closest agreement with the Sol337LC reference data.

Gao, Junyong; Wu, Mincong; Liao, Jun; Meng, Fanjun; Chen, Changjun

doi: 10.1002/jcc.27470pmid: 39143827

Structure clustering is a general but time‐consuming work in the study of life science. Up to now, most published tools do not support the clustering analysis on graphics processing unit (GPU) with root mean square deviation metric. In this work, we specially write codes to do the work. It supports multiple threads on multiple GPUs. To show the performance, we apply the program to a 33‐residue fragment in protein Pin1 WW domain mutant. The dataset contains 1,400,000 snapshots, which are extracted from an enhanced sampling simulation and distribute widely in the conformational space. Various testing results present that our program is quite efficient. Particularly, with two NVIDIA RTX4090 GPUs and single precision data type, the clustering calculation on 1 million snapshots is completed in a few seconds (including the uploading time of data from memory to GPU and neglecting the reading time from hard disk). This is hundreds of times faster than central processing unit. Our program could be a powerful tool for fast extraction of representative states of a molecule among its thousands to millions of candidate structures.

Katsyuba, Sergey A.; Grimme, Stefan

doi: 10.1002/jcc.27472pmid: 39139057

The recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions (S. A. Katsyuba, S. Spicher, T. P. Gerasimova, S. Grimme, J. Phys. Chem. B 2020, 124, 6664) is applied to ionic liquid (IL) 1‐ethyl‐3‐methylimidazolium bromide (EmimBr), its C2‐deuterated analog [Emim‐d]Br and its aqueous solutions. It is shown that the solvation strongly modifies frequencies and IR intensities of the CH/CD stretching vibrations (νCH/νCD) of the imidazolium ring. The main vibrational spectroscopic features of the neat IL are reproduced by the simulations for a cluster (EmimBr)9, in which all three imidazolium CH moieties of the solvated cation form short contacts with three Br− anions, and another two Br− anions are located on top and bottom of imidazolium ring. Cluster models of aqueous solutions reproduce the experimental vibrational frequencies of actual solutions, provided that the Br− anion of solvated contact ion pair (CIP) is situated on top of imidazolium ring, and CH/CD moieties of the latter participate in short contacts with surrounding water molecules. Both structural and spectroscopic analysis allow to interpret the short contacts CH/CD⋯Br− and CH/CD⋯OH2 as hydrogen bonds of approximately equal strength. Enthalpies of bonding of these liquid‐state H‐bonds, estimated with the use of empirical correlations, amount to ca. 1.4 kcal⋅mol−1, while the analogous estimates obtained for the gas‐phase charged species [Emim]2Br+ increase to 5.6 kcal⋅mol−1. It is shown that formation of solvent‐shared ion pair (SIP) in aqueous solution, where the counterions of IL are separated by two water molecules H‐bonded to a Br− anion, produces frequency shifts ΔνCH/CD, strongly different from the case of CIP formation. This difference can be used for IR/Raman spectroscopic differentiation of the type of solvated ion pairs of EmimBr or other related ILs.

Schulz, Timo; Marian, Christel M.

doi: 10.1002/jcc.27475pmid: 39139132

Combined density functional theory and multireference configuration interaction methods have been used to elucidate singlet fission (SF) pathways and mechanisms in three regioisomers of side‐on linked pentacene dimers. In addition to the optically bright singlets (S 1 and S 2) and singly excited triplets (T 1 and T 2), the full spin manifold of multiexcitonic triplet‐pair states ( 1ME,  3ME,  5ME) has been considered. In the ortho‐ and para‐regioisomers, the  1ME and S 1 potentials intersect upon geometry relaxation of the S 1 excitation. In the meta‐regioisomer, the crossing occurs upon delocalization of the optically bright excitation. The energetic accessibility of these conical intersections and the absence of low‐lying charge‐transfer states suggests a direct SF mechanism, assisted by charge‐resonance effects in the  1ME state. While the  5ME state does not appear to play a role in the SF mechanism of the ortho‐ and para‐regioisomers, its participation in the disentanglement of the triplet pair is conceivable in the meta‐regioisomer.

Zamora, Jerimiah A.; Rezende, Armando; Nieman, Reed; Vaz, Neil; Demko, Andrew R.; Pantoya, Michelle L.; Tunega, Daniel; Aquino, Adelia J. A.

doi: 10.1002/jcc.27476pmid: 39142902

In this work, the effects of two TiO2 polymorphs on the decomposition of ammonium perchlorate (NH4ClO4) were studied experimentally and theoretically. The interactions between AP and various surfaces of TiO2 were modeled using density functional theory (DFT) calculations. Specifically, the adsorption of AP on three rutile surfaces (1 1 0), (1 0 0), and (0 0 1), as well as two anatase surfaces (1 0 1), and (0 0 1) were modeled using cluster models, along with the decomposition of adsorbed AP into small molecules. The optimized complexes of the AP molecule on TiO2 surfaces were very stable, indicating strong covalent and hydrogen bonding interactions, leading to highly energetic adsorption reactions. The calculated energy of adsorption (ΔEads) ranged from −120.23 to −301.98 kJ/mol, with highly exergonic calculated Gibbs free energy (ΔGads) of reaction, and highly exothermic enthalpy of reaction (ΔHads). The decomposition of adsorbed AP was also found to have very negative ΔEdec values between −199.08 and −380.73 kJ/mol. The values of ΔGdec and ΔHdec reveal exergonic and exothermic reactions. The adsorption of AP on TiO2 surfaces anticipates the heat release of decomposition, in agreement with experimental results. The most common anatase surface, (1 0 1), was predicted to be more reactive for AP decomposition than the most stable rutile surface, (1 1 0), which was confirmed by experiments. DFT calculations show the mechanism for activation of the two TiO2 polymorphs is entropy driven.

Naskar, Pulak; Talukder, Srijeeta

doi: 10.1002/jcc.27480pmid: 39151062

A system associated with several number of weak interactions supports numerous number of stable structures within a narrow range of energy. Often, a deterministic search method fails to locate the global minimum geometry as well as important local minimum isomers for such systems. Therefore, in this work, the stochastic search technique, namely parallel tempering, has been executed on the quantum chemical surface of the CNO(‐)(H2O)n system for n=1–8 to generate global minimum as well as several number of local minimum isomers. IR spectrum can act as the fingerprint property for such system to be identified. Thus, IR spectroscopic features have also been included in this work. Vertical detachment energy has also been calculated to obtain clear information about number of water molecules in several spheres around the central anion. In addition, in a real experimental scenario, not only the global but also the local minimum isomers play an important role in determining the average value of a particular physically observable property. Therefore, the relative conformational populations have been determined for all the evaluated structures for the temperature range between 20K and 400K. Further to understand the phase change behavior, the configurational heat capacities have also been calculated for different sizes.

Wang, Kai

doi: 10.1002/jcc.27481pmid: 39152778

We have developed a global optimization program named PGA based on particle swarm optimization algorithm coupled with genetic operators for the structures of atomic clusters. The effectiveness and efficiency of the PGA program can be demonstrated by efficiently obtaining the tetrahedral Au20 and double‐ring tubular B20, and identifying the ground state ZrSi17–20− clusters through the comparison between the simulated and the experimental photoelectron spectra (PESs). Then, the PGA was applied to search for the global minimum structures of Mgn− (n = 3–30) clusters, new structures have been found for sizes n = 6, 7, 12, 14, and medium‐sized 21–30 were first determined. The high consistency between the simulated spectra and the experimental ones once again demonstrates the efficiency of the PGA program. Based on the ground‐state structures of these Mgn− (n = 3–30) clusters, their structural evolution and electronic properties were subsequently explored. The performance on Au20, B20, ZrSi17–20−, and Mgn− (n = 3–30) clusters indicates the promising potential of the PGA program for exploring the global minima of other clusters. The code is available for free upon request.

Li, Zilong; Peng, Yue; Ye, Haiyang; Zhang, Yunyi; Zhou, Peng

doi: 10.1002/jcc.27473pmid: 39158951

Orphan nuclear estrogen‐related receptor γ (ERRγ) has been recognized as a potential therapeutic target for cancer, inflammation and metabolic disorder. The ERRγ contains a regulatory AF2 helical tail linked C‐terminally to its ligand‐binding domain (LBD), which is a self‐binding peptide (SBP) and serves as molecular switch to dynamically regulate the receptor alternation between active and inactive states by binding to and unbinding from the AF2‐binding site on ERRγ LBD surface, respectively. Traditional ERRγ modulators are all small‐molecule chemical ligands that can be classified into agonists and inverse agonists in terms of their action mechanism; the agonists stabilize the AF2 in ABS site with an agonist conformation, while the inverse agonists lock the AF2 out of the site to largely abolish ERRγ transcriptional activity. Here, a class of ERRγ peptidic antagonists was described to compete with native AF2 for the ABS site, thus blocking the active state of AF2 binding to ERRγ LBD domain. Self‐inhibitory peptide was derived from the SBP‐covering AF2 region and we expected it can rebind potently to the ABS site by reducing its intrinsic disorder and entropy cost upon the rebinding. Hydrocarbon stapling was employed to do so, which employed an all‐hydrocarbon bridge across the [i, i + 4]‐anchor residue pair in the N‐terminal, middle or C‐terminal region of the self‐inhibitory peptide. As might be expected, it is revealed that the stapled peptides are good binders of ERRγ LBD domain and can effectively compete with the native AF2 helical tail for ERRγ ABS site, which exhibit a basically similar binding mode with AF2 to the site and form diverse noncovalent interactions with the site, thus conferring stability and specificity to the domain–peptide complexes.

Murakami, Tatsuhiro; Hayashi, Daiki; Kikuma, Yuya; Yamaki, Keita; Takayanagi, Toshiyuki

doi: 10.1002/jcc.27484pmid: 39166899

C14H20 (tetradecapentaene) is a simple model system exhibiting post transition‐state behavior, wherein both the (6 + 4) and (4 + 2) cycloaddition products are formed from one ambimocal transition state structure. We studied the bifurcation dynamics starting from the two ambimodal transition state structures, the chair‐form and boat‐form, using the quasi‐classical trajectory, classical molecular dynamics, and ring‐polymer molecular dynamics methods on the parameter‐optimized semiempirical GFN2‐xTB potential energy surface. It was found that the calculated branching fractions differ between the chair‐form and boat‐form due to the different nature in the IRC pathways. We also investigated the effects of temperature on bifurcation dynamics and found that, at higher temperatures, trajectories stay longer in the intermediate region of the potential energy surface.