Journal of Computational Chemistry

Wang, Kai; Zhang, Ying; Wang, Chaoyong; Zhao, Jun; Liu, Le; Chen, Jiaye; Wang, Yarui

doi: 10.1002/jcc.27250pmid: 37942818

Herein, the structural evolution, electronic and magnetic properties of silicon clusters with two different dopants, CrMnSin (n = 4–20) clusters were investigated at density functional theory (DFT) level. Small‐sized CrMnSin (n = 4–9) clusters tend to adopt bipyramid‐based geometries, while clusters with sizes n = 10 and 11 prefer to opening cage‐like structures. For sizes n = 12 to 14, the half‐encapsulated structures gradually transform into closed‐cage Cr@Sin structures, with the Mn atom exposed outside. Starting from size 15, both the Cr and Mn atoms are completely encapsulated by silicon atoms. Meanwhile, the Cr and Mn atoms in smaller‐sized CrMnSin (n = 4–7) clusters tend to be separated, while they prefer to stay together for larger sizes. Cr atom always acts as electron donor, but not for Mn atom. From the average binding energies, one can conclude that it is easier to form larger size clusters. Smaller and larger sized CrMnSin (n = 4–9 and 19–20) clusters prefer to exhibit ferromagnetic Cr–Mn coupling, while sizes n = 10–18 always exhibit ferrimagnetic state. To our knowledge, the CrMnSin clusters is the first kind of neutral transition‐metal doped semiconductor clusters that show ferrimagnetic state within a wide size range.

Liu, Xunshan; Liang, Zhen; Jin, Zhetong; Zhang, Xu; Shen, Chengshuo

doi: 10.1002/jcc.27252pmid: 37945374

In this work, DFT theoretical calculations were employed to investigate the enantiomerization of helicenes embedded with five‐membered heterocycles. The original benzene rings in the helicene backbone were replaced by heterocycles such as furan, thiophene, pyrrole, or phosphole to create [n]helicenes with n ranging from 4 to 7. The impact of the type, position, and number of heterocycles on the enantiomerization barrier was systematically evaluated. Notably, the enantiomerization barrier was found to be significantly dependent on the rotatory angle and the position of the heterocycles, particularly for [4, 5]helicenes. With less rotatory angle of heterocycle, the enantiomerization barrier of helicenes was revealed to be lower, while when the heterocycle was close to the central part of the helicene chain, the barrier was also lower. Furthermore, the number of thiophene rings also had a marked effect on enantiomerization, showing a decrease of the barrier with more thiophene rings placed on the helicenes backbone. We expect this work would deliver new perspective on the relative studies for the helicene conformational conversion.

Krishnapriya, Vilakkathala U.; Suresh, Cherumuttathu H.

doi: 10.1002/jcc.27256pmid: 37950586

A theoretical investigation on the cooperativity of a series of binary, ternary, and quaternary complexes interconnected by pnicogen bonds has been conducted using calculations at the M06‐2X/aug‐cc‐pVTZ level of density functional theory. By measuring changes in the molecular electrostatic potential (MESP) at the nucleus of interacting atoms in all of the complexes, it is possible to quantify the substantial reorganization of the electron density triggered by the formation of pnicogen bonds. The positive change in MESP, indicating a loss of electron density from the donor molecule in a dimer, facilitates the acceptance of electron density from a third molecule, resulting in the formation of a ternary complex with a stronger pnicogen bond compared to the one present in the binary complex. Similarly, the acceptor molecule in a dimer with a negative change in MESP showed an enhanced tendency to donate electron density to an electron‐deficient third molecule. The MESP analysis provided valuable insights into the donor/acceptor characteristics of pnicogen bonds within the quaternary complexes. The proposed MESP hypotheses are consistent with the positive cooperativity observed in the pnicogen‐bonded clusters. To quantify the changes in MESP, both at the donor atom (ΔVdonor) and the acceptor atom (ΔVacceptor), for all pnicogen bonds in the cluster, the total change in MESP (ΔΔVn) was measured as ΔΔVn = ∑(ΔVdonor)−∑(ΔVacceptor). Remarkably, ΔΔVn exhibited a strong linear relationship with the sum of the bond energies of the pnicogen bonds in the cluster. This establishes the MESP analysis as a robust approach for understanding the strength and cooperative behavior of pnicogen‐bonded clusters. Additionally, the MESP features provided clear evidence of pnicogen bond formation, further supporting the reliability of this approach.

Silva, Albert J. F. W. H. de S.; Rodrigues, Gessenildo P.; Ventura, Elizete; Monte, Silmar A.

doi: 10.1002/jcc.27257pmid: 37950575

Although CH2FCl (HCFC‐31) recently became of great atmospheric importance, studies concerning its excited states are almost nonexistent. Several excited singlet states were studied (valence nσ* and Rydberg n3s, n3p, σ3s, and σ3p) through highly correlated multireference configuration interaction with singles and doubles, including extensivity correction. Comparison with the states of CH3Cl indicates a strong influence of the F atom. Potential energy curves suggest formation of an electrostatically bound complex that relaxes to a hydrogen‐bonded contact ion‐pair (HBCIP) which can decay yielding CH2F + Cl or to the ground state minimum of CH2FCl. The HBCIP has a dipole moment of 9.57 D, a CI wavefunction described as 0.65ionic + 0.20biradical and it is strongly bonded by 4.72 eV. Its H bond has characteristics of moderate and strong H bonds. The simulated absorption spectrum confirms the nσ* assignment for the first and suggests the n3s + n3pσ assignment for the second band.

Xu, Wenjun; Zhao, Yanling; Chen, Jialu; Wan, Zhongyu; Yan, Dadong; Zhang, Xinghua; Zhang, Ruiqin

doi: 10.1002/jcc.27259pmid: 37966714

Transition state (TS) on the potential energy surface (PES) plays a key role in determining the kinetics and thermodynamics of chemical reactions. Inspired by the fact that the dynamics of complex systems are always driven by rare but significant transition events, we herein propose a TS search method in accordance with the Q‐learning algorithm. Appropriate reward functions are set for a given PES to optimize the reaction pathway through continuous trial and error, and then the TS can be obtained from the optimized reaction pathway. The validity of this Q‐learning method with reasonable settings of Q‐value table including actions, states, learning rate, greedy rate, discount rate, and so on, is exemplified in 2 two‐dimensional potential functions. In the applications of the Q‐learning method to two chemical reactions, it is demonstrated that the Q‐learning method can predict consistent TS and reaction pathway with those by ab initio calculations. Notably, the PES must be well prepared before using the Q‐learning method, and a coarse‐to‐fine PES scanning scheme is thus introduced to save the computational time while maintaining the accuracy of the Q‐learning prediction. This work offers a simple and reliable Q‐learning method to search for all possible TS and reaction pathway of a chemical reaction, which may be a new option for effectively exploring the PES in an extensive search manner.

Yu, Isseki; Mori, Takaharu; Matsuoka, Daisuke; Surblys, Donatas; Sugita, Yuji

doi: 10.1002/jcc.27260pmid: 37966727

The rapid increase in computational power with the latest supercomputers has enabled atomistic molecular dynamics (MDs) simulations of biomolecules in biological membrane, cytoplasm, and other cellular environments. These environments often contain a million or more atoms to be simulated simultaneously. Therefore, their trajectory analyses involve heavy computations that can become a bottleneck in the computational studies. Spatial decomposition analysis (SPANA) is a set of analysis tools in the Generalized‐Ensemble Simulation System (GENESIS) software package that can carry out MD trajectory analyses of large‐scale biological simulations using multiple CPU cores in parallel. SPANA applies the spatial decomposition of a large biological system to distribute structural and dynamical analyses into individual CPU cores, which reduces the computational time and the memory size, significantly. SPANA opens new possibilities for detailed atomistic analyses of biomacromolecules as well as solvent water molecules, ions, and metabolites in MD simulation trajectories of very large biological systems containing more than millions of atoms in cellular environments.