Journal of Computational Chemistry最新文献

Significant amounts of effluents containing pharmaceuticals residues are released each year in the environment. These residues are responsible for the disruption of the metabolism of organisms. In this study, vermiculite, a low-cost and high specific area clay material, is a best and effective way to remove the micro-pollutants by adsorption. Thus, we investigate the adsorption of carbamazepine (CAR), aspirin (ASP), diazepam (DIA), diclofenac (DIC), paracetamol (PAR), and ibuprofen (IBU), the most common pharmaceutical pollutants encountered in wastewater, on the hydrated surface of vermiculite exchanged with magnesium using thermodynamic calculations and density functional theory (DFT). Our results indicate that DIC exhibits the highest affinity for the hydrated surface of vermiculite, followed by PAR, IBU, ASP, CAR, and DIA. Furthermore, it is possible to regenerate the adsorbent after use, just by heating the vermiculite to a temperature of 360 K. The adsorptions are all exothermic, with energies depending upon the structural configuration of the pollutant on the surface.

Precise control over DNA stability and interactions is crucial for successful gene editing technologies. To achieve this, a detailed understanding of individual hydrogen bonds within GC (Watson-Crick) and GC*/GC⁺ (Hoogsteen) base pairs is essential, particularly regarding how strategic substitution of these base pairs modulates their strength and, ultimately, DNA stability. Leveraging the atomic-resolution capabilities of interacting quantum atoms (IQA) and interacting quantum fragments (IQF) analyses, this study investigates the impact of substituent position and electronic nature on individual hydrogen bond strengths in substituted GC (WC), GC* (HG) and GC⁺ (HG) base pairs. Our results reveal how the electronic properties of substituents and their specific location on the base pairs significantly influence the forces governing atomic interactions, ultimately impacting the strength of individual hydrogen bonds within GC (WC), GC* (HG) and GC⁺ (HG) base pairs. While IQA highlights the importance of classical interactions in stabilizing hydrogen bonds, IQF analysis, taking a more holistic perspective, reveals a more significant role for electron sharing, highlighting the intricate dance between these forces in shaping DNA stability. Furthermore, GC⁺ (HG) base pairs consistently exhibit stronger inter-fragment interactions compared to GC (WC) and GC* (HG) base pairs, consistent with their higher energy binding energies. The primary reason for the enhanced stability of the GC⁺ (HG) base pairs compared to the GC (WC) and GC* (HG) base pairs is that cytosine has added a proton to the Hoogsteen geometry, leading to strong inter-fragment interactions. By contrast, GC* (HG) geometries are substantially less favorable than GC (WC) and GC⁺ (HG) geometries. GC* (HG) base pairs consistently show weaker inter-fragment interactions compared to GC (WC) and GC⁺ (HG) bases. This reduction in stability is attributed to the substitution of the cytosine amino group with its imino tautomeric form at the electron-donating site of hydrogen bond a, which leads to a decrease in electron-donating ability and the polarity of the NH bond. Our findings demonstrate the feasibility of tuning the interactions within GC (WC), GC* (HG) and GC⁺ (HG) base pairs through strategic substitution, offering a powerful tool for manipulating DNA stability, function, and interactions with other molecules.

The electrostatic potential at the nucleus of an atom, whether it be in the free state or in a neutral molecule or in an ionic molecular species, is qualitatively a characteristic property of the atom. It changes remarkably little from one molecular environment to another. As has been shown earlier by Politzer, the energies of atoms and molecules can be expressed both rigorously and approximately in terms of the electrostatic potentials at their nuclei. These findings support the validity of the atoms-in-molecules concept; however, without boundaries. This has been further substantiated in recent papers where the authors have shown that the electrostatic potential created by the electrons of all of the other atoms at a particular nucleus in a molecular species, not including those associated with that particular atom itself, is almost identical in magnitude to the potential due to the other nuclei. However, as has been shown by Gadre and Suresh, small differences in the electrostatic potentials at nuclei for interacting atoms in noncovalent interactions have been correlated with their interaction energies. Thus, finding ways to compute these beyond the main group elements is imperative for further exploration. Because of the importance of electrostatic potential at nuclei, in this paper are reported first, for comparison purposes, the electrostatic potentials at nuclei for atoms from Z = 1 to Z = 36 (hydrogen to krypton) using four density functional methods and the 6–311 + G(3df,2p) basis set and then for Z = 1 to Z = 54 (hydrogen to xenon) using six methods and the aHGBSP1-5 basis set. The values are presented and graphically displayed and discussed.

The in-medium similarity renormalization group (IMSRG) approach, based on a continuous unitary transformation, has been applied to closed-shell atoms. The flow equation, which is derived for the Hamiltonian, has been solved along with imaginary-time or White generators using the fourth-order Runge-Kutta and Magnus expansion methods. The behavior of the flow as a function of step size was investigated carefully. Our findings for ground state energy for the $��\text{He}�$ and $��\text{Ne}�$ atoms from the IMSRG calculation are close to those obtained with full configuration interaction. Moreover, it has been observed that the IMSRG calculation based on the Magnus expansion approach, coupled with the White generator, requires the fewest steps to converge.

We studied isomeric conformer effects on the positron affinity (PA) of halogenated hydrocarbons using density functional theory combined with the electron–positron correlation-polarization potential (CPP) model. PA values are computed for 75 halogenated hydrocarbons, including fluorine (F), chlorine (Cl), and bromine (Br) derivatives of methane, ethylene, and ethane molecules. The positive PA values can be described by a linear combination of the dipole moment and polarizability of parent molecules. For Cl-substituted methane derivatives, PA increased with the number of Cl substitutions. Such a trend is consistent with the increase in the polarizability of the Cl-substituted methane derivatives. For Cl-substituted ethylene derivatives, PA differences among C₂H₂Cl₂ isomers (PA(cis-C₂H₂Cl₂) > PA(1,1-C₂H₂Cl₂) > PA(trans-C₂H₂Cl₂)) correlated well with the dipole moments of the respective parent isomers. The isosurfaces of positronic density in the cis isomer revealed that the positron is localized near the halogen atoms, whereas those in the trans isomer are more diffusive due to the spatial separation of the 2 Cl atoms. While a similar overall feature of positron density is observed in Br-substituted C₂H₂Br₂ species, positron densities of C₂H₂Br₂ are more contracted than those of C₂H₂Cl₂, reflecting that PA(Br) > PA(Cl) due to polarizability differences. These tendencies are also found in halogenated ethane species.

In this study, the noncovalent interactions present in microhydrated clusters of the isoelectronic molecules viz. CO₂ and N₂O were investigated by evaluating the energy of individual noncovalent interactions and cooperative contributions using the molecular tailoring approach-based (MTA-based) method. The molecular electrostatic potential (MESP) analysis revealed that CO₂ acts as a better electron acceptor due to a more pronounced electron-deficient region on its C-atom, compared to the central N-atom of N₂O. The energies of the individual tetrel bonds (TBs), pnicogen bonds (PBs), and hydrogen bonds (HBs) observed in CO₂…water and N₂O…water in the dimeric clusters calculated using the MTA-based method align well with the MESP results. As the number of water molecules increases (n = 1–5), the most stable configurations reveal that CO₂ and N₂O preferentially interact with cyclic water clusters, indicating that water…water HBs dominate energetically over CO₂…water and N₂O…water interactions in larger clusters. This is clearly evident from the higher values of water…water HB energies (4.72–9.67 kcal/mol in CO₂(H₂O)_n and 4.50–9.35 kcal/mol in N₂O(H₂O)_n) calculated at the MP2/aug-cc-pVTZ level as compared to the CO₂…water and N₂O…water interactions (range of 0.31–4.05 kcal/mol and 0.04–3.28 kcal/mol, respectively). Based on the calculated energies and cooperative contributions by the MTA-based method, the order of interaction strength in these microhydrated clusters follows: HB in water…water > TB in CO₂…water > PB in N₂O…water > HOH…N of (N₂O) HB > HOH…O of (CO₂) HB > HOH…O of (N₂O) HB. We wish to emphasize here that the present study is the first systematic attempt to establish an energetic hierarchy among various HBs, TBs, and PBs, thereby providing deeper insight into the microhydration networks of two atmospherically relevant isoelectronic molecules. These findings are expected to be crucial for elucidating the subtle interplay of noncovalent interactions in atmospheric and related environments.

In 1976 George A. Olah et al. synthesized the Hückel-aromatic 1,3,5,7-tetramethylcyclo-octatetraene dication 3 under stable ion conditions. As observed by NMR spectroscopy, 3 rearranges at −20°C to the 1,3,5,7-tetramethylbicyclo[3.3.0]-dication 5. This is an unexpected result that has not been commented upon in the original papers or considered in the literature for half a century. We propose a mechanism for the rearrangement of 3 to 5 and discuss the relative instability of the latter with respect to the isomeric 2,4,6,8-tetramethylbicyclo[3.3.0]dication 6. The unknown isomeric dication 6 is predicted to be 34.4 kcal mol⁻¹ lower in energy than 5 and 40.9 kcal mol⁻¹ lower in energy than 3.