Journal of Computational Chemistry最新文献

Doxorubicin (DOX) is a widely used chemotherapeutic agent known for intercalating into DNA. However, the exact modes of DOX interactions with various DNA structures remain unclear. Using molecular dynamics (MD) simulations, we explored DOX interactions with DNA duplexes (dsDNA), G-quadruplex, and nucleosome. DOX predominantly stacks on terminal bases of dsDNA and occasionally binds into its minor groove. In the G-quadruplex, DOX stacks on planar tetrads but does not spontaneously intercalate into these structures. Potential of mean force calculations indicate that while intercalation is the most energetically favorable interaction mode for DOX in dsDNA, the process requires overcoming a significant energy barrier. In contrast, DOX spontaneously intercalates into bent nucleosomal DNA, due to the increased torsional stress. This preferential intercalation of DOX into regions with higher torsional stress provides new insights into its mechanism of action and underscores the importance of DNA tertiary and quaternary structures in therapies utilizing DNA intercalation.

The eXtended Hydrostatic Compression Force Field (X-HCFF) is a mechanochemical approach in which a cavity is used to exert hydrostatic pressure on a target system. The cavity used in this method is set up to represent the van der Waals (VDW) surface of the system by joining spheres sized according to the respective atomic VDW radii. The size of this surface can be varied via a scaling factor, and it can be shown that the compression forces exerted in X-HCFF in its current implementation depend on this factor. To address this dependency, we have developed a rescaling formalism for the applied forces, allowing us to drastically reduce the dependency of the compression forces on the chosen scaling factor. Independency from the scaling factor is important, as the scaling of the VDW spheres is often used to ensure an overlap of cavities in supramolecular complexes, which is necessary for the simulation of chemical reactions. Our rescaling formalism reduces the empiricism of the X-HCFF approach and boosts its applicability in the field of computational high-pressure chemistry.

Corrosion inhibitors are widely used to mitigate safety risks and economic losses in engineering, yet post-adsorption processes remain underexplored. In this study, we employed density functional theory calculations with a periodic model to investigate the dissociation mechanisms of imidazole on the Fe(100) surface. Imidazole was found to adsorb optimally in a parallel orientation, with an adsorption energy of −0.88 eV. We explored two dissociation pathways: CH and NH bond cleavages and found CH dissociation having a lower activation barrier of 0.46 eV. Intriguingly, an alternative indirect route CH dissociation pathway involving a tilted intermediate state was found to be competitive. Both indirect and direct CH dissociation pathways are energetically more favorable than NH cleavage. Molecular dynamics simulations reveal that indirect CH dissociation occurs rapidly. This study proposes an alternative protective mechanism involving dissociated imidazole inhibitors, offering new insights for corrosion inhibitor design.

The energies and geometries of the lowest lying singlet and triplet states of the four diradicals formed by removing two H atoms from thiophene have been characterized. We utilized the highly correlated, multireference methods configuration interaction with single and double excitations with and without the Pople correction for size-extensivity (MR-CISD+Q and MR-CISD) and averaged quadratic coupled cluster theory (MR-AQCC). CAS (8,7) and CAS (10,8) active spaces involving σ, σ*, π, and π* orbitals were employed along with the cc-pVDZ and cc-pVTZ basis sets. The larger active space included the two electrons in the nonbonding sp² hybrid orbital on sulfur. We find that all didehydro isomers exist as planar, stable ground state singlets. The singlet-triplet (S-T) adiabatic gaps range from 15 to 25 kcal/mol while the vertical splittings are 21–35 kcal/mol. The 2,3 isomer has the lowest absolute ground state singlet energy and the largest adiabatic and vertical S-T splitting. The ground states of the 2,3-, and 2,5-didehydrothiophene isomers are predicted to exhibit the smallest and largest diradical character, respectively, based on their electronic structures, spin densities and bonding analysis. To our knowledge, no experimental excitation energies of any of the didehydrothiophene isomers are available, and our computed MR-AQCC/cc-pVTZ data are believed to be among the most accurate computed results. This extensive study shows a competitive performance between MR-AQCC and MR-CISD+Q.

We define an approximation to the internally contracted multireference coupled-cluster method with single and double excitations by a hybrid approach. The rationale is to treat the external pair energy contributions by the coupled-cluster method, which provides accurate results for a large part of the correlation energy while being tractable as the involved pair cluster operators commute. For the internal and semi-internal contributions, for which the coupled-cluster part becomes involved due to non-commuting operators, a linearized approach based on the coupled-electron pair approximation (CEPA) is used. For the latter, the CEPA(0) method, the averaged coupled pair functional (ACPF), the averaged quadratic coupled-cluster (AQCC) method, and the averaged CEPA method are tested. We test the methods concerning size consistency, potential energy curves for C₂, N₂, CN, and O₃ and for the singlet-triplet splitting of ortho-, meta-, and para-benzynes. Our results show that AQCC provides the most accurate results and stable performance. The main drawback of the method is that it shows small violations of size consistency.