Journal of Computational Chemistry

doi: 10.1002/jcc.26906pmid: N/A

Bandyopadhyay, Prasanta; Sadhukhan, Mainak

doi: 10.1002/jcc.27073pmid: 36645104

The Quantum Drude Oscillator (QDO) model is a promising candidate for accurately calculating the van der Waals (vdW) interaction. Anisotropic QDO models have recently been used to represent quantum fluctuations of molecular fragments rather than that of single atoms. While this model promises accurate calculation of vdW energy, there is significant room for improvements, such as incorporating a proper fragmentation method, higher‐order dispersion corrections, and so forth. The present work attempts to gauge dipole–dipole interactions' ability without fragmentation. A suitable anisotropic damping function is also introduced to work with anisotropic QDO. This revised model accurately predicts the binding energies of vdW complexes for most of the systems considered. This work indicates the limit of dipole approximation for an anisotropic QDO‐based model.

Ma, Yingjin; Li, ZhiYing; Chen, Xin; Ding, Bowen; Li, Ning; Lu, Teng; Zhang, Baohua; Suo, BingBing; Jin, Zhong

doi: 10.1002/jcc.27075pmid: 36648254

Easy and effective usage of computational resources is crucial for scientific calculations, both from the perspectives of timeliness and economic efficiency. This work proposes a bi‐level optimization framework to optimize the computational sequences. Machine‐learning (ML) assisted static load‐balancing, and different dynamic load‐balancing algorithms can be integrated. Consequently, the computational and scheduling engine of the ParaEngine is developed to invoke optimized quantum chemical (QC) calculations. Illustrated benchmark calculations include high‐throughput drug suit, solvent model, P38 protein, and SARS‐CoV‐2 systems. The results show that the usage rate of given computational resources for high throughput and large‐scale fragmentation QC calculations can primarily profit, and faster accomplishing computational tasks can be expected when employing high‐performance computing (HPC) clusters.

Maltsev, Maxim A.; Aksenova, Svetlana A.; Morozov, Igor V.; Minenkov, Yury; Osina, Evgenia L.

doi: 10.1002/jcc.27078pmid: 36708239

Argon compounds play an important role in the mass spectrometry with inductively coupled plasma and other applications. At the same time, there is a little knowledge of their electronic terms and thermodynamic functions due to the complexity of experimental observations. In this work, the ab initio simulations are performed to obtain the interatomic interaction potentials for the ground and excited states of ArN and ArN+. Using these potentials, the vibrational‐rotational partition functions and thermodynamic properties in the gas phase are calculated for these molecules at the temperature range of 298.15–10,000 K. The errors of the thermodynamic functions associated with the approximation of interatomic interaction potentials are estimated.

Salgado‐Blanco, Daniel; Flores‐Saldaña, Diana S. M.; Jaimes‐Miranda, Fabiola; López‐Urías, Florentino

doi: 10.1002/jcc.27079pmid: 36704941

The TATA box is a promoter sequence able to interact directly with the components of the basal transcription initiation machinery. We investigate the changes in the electronic and magnetic properties of a TATA‐DNA sequence when functionalized with different chemical groups; using the first‐principles density functional theory specifically, the TATA‐DNA sequences were functionalized with methyl groups (CH3, methylation), amino groups (NH2, amination), imine groups (NH, imination), chloroamine groups (NCl2, chloramination), H‐adatom (hydrogenation), and Cl‐adatom (chlorination). The functional groups were anchored at nitrogen atoms from adenine and oxygen atoms from thymine at sites pointed as reactive regions. We demonstrated that chemical functionalization induces significant changes in charge transfer, hydrogen bond distance, and hydrogen bond energy. The hydrogenation and imination increased the hydrogen bond energy. Results also revealed that the chemical functionalization of DNA molecules exhibit a ferromagnetic ground state, reaching magnetization up to 4.665 μB and complex magnetic ordering. We further demonstrated that the functionalization could induce tautomerism (proton migration in the base pair systems). The present study provides a theoretical basis for understanding the functionalization further into DNA molecules and visualizing possible future applications.

Sobhi, Chafia; Merzoud, Lynda; Bouasla, Souad; Nacereddine, Abdelmalek Khorief; Morell, Christophe; Chermette, Henry

doi: 10.1002/jcc.27080pmid: 36708224

The selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction between 2‐(dimethylamino)‐1H‐indene‐1,3(2H)‐dione (AY11) and trans(E)‐3,3,3‐trifluoro‐1‐nitroprop‐1‐ene(FNP10) has been studied, in which the molecular electron density theory using density functional theory methods at the MPWB1K/6‐31G(d) computational level was used. Analysis of the global reactivity indices permits us to characterize FNP10 as a strong electrophile and AY11 as a strong nucleophile. Four reactive pathways associated with the ortho/meta regioselective channels and endo/exo stereoselective approaches modes have been explored and characterized in the gas phase and in the benzene solvent. The analysis of the relative energies associated with the different reaction pathways indicates that the 32CA reactions of the azomethine ylide (AY) with the nitroalkene (FNP) is meta regioselective with high endo stereoselectivity. This result is in good agreement with the experimental observations. electron localization function topological analysis of the most favored reactive pathways allows for characterizing the mechanism of this 32CA reactions as a non‐concerted two‐stage one‐step mechanism. Finally, non‐covalent interactions and quantum theory of atoms in molecule analyses at the meta/endo transition state structure indicate that the presence of different several weak interactions, namely, CF and NH contributed in favoring the formation of a meta‐endo cycloadduct.

Macchiagodena, Marina; Pagliai, Marco; Procacci, Piero

doi: 10.1002/jcc.27077pmid: 36704972

We describe a step‐by‐step protocol and toolkit for the computation of the relative dissociation free energy (RDFE) with the GROMACS molecular dynamics package, based on a novel bidirectional nonequilibrium alchemical approach. The proposed methodology does not require any intervention on the code and allows computing with good accuracy the RDFE between small molecules with arbitrary differences in volume, charge, and chemical topology. The procedure is illustrated for the challenging SAMPL9 batch of host–guest pairs. The article is supplemented by a detailed online tutorial, available at https://procacci.github.io/vdssb_gromacs/NE-RDFE and by a public Zenodo repository available at https://zenodo.org/record/6982932.