Herein, we report the application of quantum chemical topology derived from the Kohn–Sham one-electron potential (KSpot) to open-shell nitrogen-centered radicals. Using 50 representative radicals, the effectiveness of KSpot atomic charges...

Accurate characterization of the complex electrostatic and polarization environments in nucleic acid-based systems is essential for reliable biomolecular simulations, where atomic charges play a central role. In this work, charges derived from the Kohn-Sham one-electron potential (KSpot), characterized by well-defined real-space topological boundaries, are incorporated into the atom-bond electronegativity equalization method (ABEEM) framework to balance quantum chemical accuracy and computational efficiency. Through systematic parametrization using fragment molecules representing diverse chemical environments, we developed a charge model for nucleic acid systems, termed KS-ABEEM. Validation results demonstrate that KS-ABEEM accurately reproduces KSpot real-space topological charges, yielding linear correlation coefficients of 0.9862 and 0.9885 for the training and test sets, respectively. The model also reliably predicts molecular dipole moments and electrostatically dominated intermolecular interaction energies, showing good agreement with quantum chemical calculations. Furthermore, KS-ABEEM avoids the high computational cost associated with conventional real-space topological integration methods. Compared with traditional topological approaches, the proposed KS-ABEEM achieves computational speedups of 102-104 while maintaining favorable computational scaling for large systems. Overall, this work provides an efficient route for extending quantum chemical topology-based charge models toward nucleic acid systems. Validation is presented for representative fragment molecules, hydrated clusters, and base-pair systems, while the computational efficiency and scalability of the approach for large all-atom nucleic acid structures are demonstrated through timing benchmarks, highlighting the potential of real-space topological descriptors for biomolecular simulations and polarizable force field development.

Alkaline-earth metal ions exhibit distinct hydration behaviors that evolve with coordination number and govern their chemical reactivity, transport properties, and biological functions, yet a unified description linking hydration structure, electronic effects, and steric hindrance remains incomplete. In this work, the Molecular Face Theory (MFT) based on the Kohn-Sham one-electron potential (KSpot) was applied to systematically investigate the structural evolution of gas-phase hydrated clusters M[(H2O)(n)](2+) (M = Be, Mg, Ca, Sr, and Ba, n = 1-15). In addition, KSpot was employed to quantify electron density distribution, atomic partitioning, charge transfer, and steric effects during hydration. Across the series, the total water binding energy decreases monotonically with increasing ionic radius (Be2+ > Mg2+ > Ca2+ > Sr2+ > Ba2+), reflecting the dominant role of ionic charge density. The depth of the KSpot at the saddle point along a chemical bond (D-pb) for the metal-oxygen coordination bond exhibits a strong negative correlation with bond length (R = 0.98) and a positive correlation with binding energy (R = 0.99), establishing it as a quantitative descriptor of coordination stability. With the increasing hydration number, the first ionization potential decreases continuously, while the molecular face surface areas and volumes display clear inflection points at n = 6-8, elucidating saturation of the first hydration shell. Charge distribution analysis reveals efficient electrostatic screening by the first-shell water molecules, followed by a pronounced saturation behavior upon shell completion. Stereoselective analysis of calcium ion clusters indicates that seven to eight water molecules mark the structural transition from a monolayer to bilayer hydration, where steric hindrance and electrostatic interactions jointly determine conformational stability and promote second-shell formation. These results provide a unified electronic and stereoselective perspective on alkaline-earth metal ion hydration and its shell-by-shell structural evolution.

Long-time molecular dynamics (MD) simulations of large systems with solvent are a major challenge for theoretical approaches. The popular method is the fragment method, and the challenge of which lies in how to deal with the chemical bonds that are cut and the setting of charges in each subdivision. Dividing the periodic box into subdivisions with their surroundings (DBSS) method has been developed to solve the aforementioned two problems. The DBSS method divides the periodic box or unit of the system into subdivisions according to the atomic coordinates, and solves the charge distribution of each subdivision separately. Partial charges of atoms at the boundary of the subdivision are crucial for computational accuracy. If the cut chemical bond is located in a charged residue, the entire residue is assigned to the subdivision that contains the key atom of the residue. If the cut chemical bond is located in a neutral residue, the partial charge of the bond site is assigned equally between two subdivisions. The total charge of each subdivision is set as the sum of the charges of the charged residues. For non-bonding interactions at the boundary, the DBSS method extends the 4 & Aring; surroundings for each subdivision, which solves the problem of neglecting long-range electrostatic interactions in conventional fragment methods. The ABEEM-DBSS method was applied to perform MD simulations on five trypsin/inhibitor complexes. The ABEEM-7P water model is used for the 3 & Aring; solute surrounding the complexes, and the TIP-3P water model is applied to the distant aqueous solution. The computational efficiency is optimal when each subdivision contains 200-300 atoms. If the system is divided into M subdivisions, the computation time is reduced by a factor of M3 approximately. The size of the simulated system is 100 times larger than that of the original ABEEM method. Compared to the OPLS force field, the deviations of structures are smaller. The predicted sequence of binding energies is consistent with the inhibition constants by photometric assay. It is evident that ABEEM-DBSS is a reliable tool for fast and accurate simulations of macromolecular systems.

Dibenzotriazole (diBTA) ionic liquid was synthesised via a three-pot method, with optimisation of the reaction conditions. Characterisation was conducted using 1H-NMR and mass spectrometry (MS) analyses. Thermal stability was assessed through thermogravimetric analysis, while corrosion inhibition performance was evaluated using static weight loss, electrochemical analysis, and scanning electron microscopy (SEM). Tribological performance was measured using a four-ball machine and compared against base oil, with SEM utilised for surface morphology and elemental analysis. The diBTA ionic liquid demonstrated favourable thermal stability, corrosion inhibition, and lubricating properties. Furthermore, the structural analysis of the diBTA ionic liquid was conducted via quantum chemical methods, exploring molecular structure, charge distribution, orbital energy, atomic coordination binding energy with Cu, and characteristics of coordination compounds. The calculated results aligned with the experimental findings.

Biomolecular aqueous solutions represent a crucial class of condensed matter and serve as the fundamental basis of living organisms. Investigating their structural and chemical properties holds immense scientific and practical significance. Molecular dynamics (MD) simulations are a powerful tool for studying biomolecular systems, where accuracy critically depends on the precision of the molecular force field. Traditional force fields employ fixed atomic charges, neglecting polarization effects and charge transfer. Over recent decades, significant efforts have been devoted to developing polarizable force fields. The atom-bond electronegativity equalization method (ABEEM) polarizable force field effectively captures molecular polarization and charge transfer. This review outlines the ABEEM methodology, with emphasis on the ABEEM-7P water model and the application of the ABEEM polarizable force field is provided. The work has carried out using both the ABEEM-7P water model and the ABEEM polarizable molecular force field for molecular dynamics simulations of biomolecule aqueous systems,and the results have been given by representative case studies.

When I received a phone call from President ZHANG Xi of Jilin University inviting me to write an article for Echoes and Reflection on Graduate Education,Jilin University,I gladly agreed.After a day of contemplation,I realized that what I knew best and remembered most deeply was the education and guidance,which was received at the Department of Chemistry at Jilin University,particularly from my mentor Professor TANG Au-chin.It was under his nurturing that a young man born in Lianhua Nigou Village,Shulan County,Jilin Province,set off on a long and persistent journey in pursuit of science.Many memories began to resurface.

We introduce a quantum chemical topology (QCT) approach using the Kohn-Sham one-electron potential (KSpot) as a scalar function, revealing unique spatial features of atoms in molecules and the chemical bonds. The KSpot and its electron force lines demonstrate that an atom is a 3D basin governed by its nucleus as an attractor. Notably, KSpot atomic charges exhibit less basis set dependence, whose physical reliability is further confirmed through accurate reproduction of electrostatic potentials and dipole moments. To assess performance, we systematically compared KSpot QCT atomic charges with six established methods (QTAIM, Hirshfeld, Mülliken, NPA, CHELPG, and MK) across 20 amino acid dipeptides. KSpot charges have strong correlations with QTAIM and Hirshfeld ones, with correlation coefficients of 0.9207 and 0.9160, respectively. Furthermore, we successfully parameterized the atom bond electronegativity equalization method (ABEEM) using KSpot QCT charges, achieving a good linear agreement between them. These results establish KSpot QCT as a robust tool for molecular structure analysis, electrostatic interaction studies, and force field development.

In additive force fields, the charge is a tunable parameter designed to represent average polarization effects through a mean-field average, which could not accurately respond to different environments. The polarizable force field (PFF) offers enhanced accuracy in representing intermolecular interactions by dynamically capturing electronic polarization effects. The ABEEM PFF for lipids, built on the fluctuating charge model, offers reasonable charge distributions and specific characterization of the hydrogen bonding interaction to improve the electrostatic interactions. The hierarchical parameterization strategy requires optimizing parameters for small molecules of lipid functional groups and subsequently applying these parameters to seven PC lipids, including 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), dimyristoylphosphatidylcholine (DMPC), dilauroylphosphatidylcholine (DLPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), and 1-stearoyl-2-oleoyl-phosphatidylcholine (SOPC). The ABEEM-DBSS method was refined for the specific characteristics of lipid bilayers by charge partitioning calculations for solutes, thereby enhancing the computational efficiency in molecular dynamics (MD) simulations. Results show that the ABEEM PFF can reproduce the quantum mechanical (QM) data of model compounds representing phospholipids as well as the experimental condensed-phase properties of lipid bilayers. In particular, the optimization of dihedral parameters for hydrocarbons has improved the accuracy of the NMR deuterium order parameters of carbon atoms. Based on the advantages of ABEEM PFF, unsupervised machine learning methods were employed to reveal the correlation, which showed the regular impact between the fluctuating charge of phosphorus (P) atoms in lipids and the tilt of the vector between the P and nitrogen (N) atoms in the PC group with respect to the interface plane, as well as the dynamic behavior of water molecules. This work may lay the foundation for further investigations on the structures and properties of membrane proteins in terms of the ABEEM PFF.

Reasonably describing the microscopic interaction mechanisms between calcium ions and water as well as ligand proteins is essential for elucidating the structures and functions of calcium proteins. However, capturing the strong polarization between calcium ligands remains a challenge for classical force fields. In this study, we present a fluctuating charge calcium force field for simulations on calcium proteins and aqueous calcium solutions based on Atom-Bond Electronegativity Equalization Method fused into Molecular Mechanics (ABEEM/MM). To reasonably simulate calcium-ligand interactions, model systems comprising calcium ions with water, ethanol, N-methylacetamide, and propionate as ligands were constructed. The ABEEM/MM parameters were then optimized and determined from quantum mechanical (QM) calculations. The performance of the ABEEM/MM model was evaluated by comparison with QM results for the model molecules as well as the Protein Data Bank (PDB) structures of calcium proteins, demonstrating good agreement in reproducing the charge distributions and structures. Molecular dynamics (MD) simulations were conducted on aqueous calcium solutions and protein segments. The ABEEM/MM adequately reproduces the experimentally observed properties, such as the first radial distribution function peak, reaction rate constants, self-diffusion coefficients, etc. The ABEEM/MM model can more effectively capture the dynamic changes in charge distributions and charge transfer processes of aqueous calcium ions under varying coordination numbers. Additionally, MD simulations were performed on calcium proteins using ABEEM/MM alongside nonpolarizable force fields. Comparative analysis with PDB crystal structures revealed that ABEEM/MM gains lower root-mean-square deviations than do the nonpolarizable force fields. This study may pave the way for further investigations into the structures and properties of aqueous electrolyte solutions and metalloproteins using the ABEEM/MM.

Noncovalent interactions and covalent bonds can be distinguished via quantum chemical topology analysis and molecular face theory, which are based on the potential acting on one electron in a molecule or molecular system (PAEM). A covalent bond forms when a PAEM bond critical point (BCP) occurs on the line connecting two atoms and when their molecular faces contact or fuse together, whereas a noncovalent interaction occurs between two adjacent atoms or chemical species when their molecular faces remain separate. The force acting on one electron within a molecule, which starts at infinity and ends at the BCP, forms nonoverlapping boundary surfaces that partition a molecule into distinct atomic regions. This is demonstrated with the following example reactions: H + H → H2, H + X → HX (X = F, Cl, Br, I), O (1D) + H2 → H2O, and S (1D) + H2 → H2S. The exploration of the physical quantities at PAEM critical points, such as the eigenvalues of the Hessian matrix, ellipticity, and electron interflow frequency, reveals their changing trends during the transition from a noncovalent interaction to a covalent bond or vice versa. These changes can help predict chemical bond formation or breakage, providing insight into chemical bonding.

Magnesium is an essential element involved in diverse life activities. The strong polarization and significant charge transfer effects pose challenges to the traditional fixed charge force fields. Here we establish the ABEEM/MM magnesium force field for proteins and aqueous solutions. The interaction potentials of magnesium with water and proteins are treated as the ABEEM/MM bonded model (ABEEM-BM) in the Morse potential function form. Based on quantum mechanical (QM) results, the related parameters are optimized and determined. The charge distributions of model molecules from ABEEM-BM and the ABEEM/MM nonbonded model (ABEEM-NBM) agree well with the QM results. The potential energy surfaces (PESs) for bond stretching and angle bending between magnesium and ligands by ABEEM-BM have a good consistency with those from QM. Molecular dynamics (MD) simulations of 40 aqueous magnesium protein segments are carried out using ABEEM-BM, ABEEM-NBM, OPLS-AA, AMBER99, and CHARMM22 force fields. The root mean square deviations (RMSDs) for bond length and angle by ABEEM-BM are 0.088 Å and 5.99°, respectively, which are smaller than those from the others. MD simulations of aqueous magnesium solutions are carried out using ABEEM-BM and ABEEM-NBM. The radial and angular distribution functions from ABEEM-BM reproduce the best structural properties, and the rate constant is 4.7 × 105 s− 1. Moreover, the dynamic changing picture of charge transfer and the coordination number (CN) during water exchange processes is presented by ABEEM model. The overall performance of ABEEM models is evidently better than those from fixed charge force fields.

The potential energy acting on one electron in a molecule (PAEM) (i.e., the energy associated with the interactions of one local electron with all nuclei and remaining electrons) is defined and calculated using an ab initio method, and exhibits interesting spatial characteristics. A chemical bond path or bond line (bond bar or stick) is defined or described by a local minimum PAEM line in the vicinity of the path between two adjacent atoms. The strength of a bond is intimately related to the features of the bond center (bc), which corresponds to the PAEM saddle point around the bond path. The PAEM at the bond center along the chemical bond correlates quantitatively with bond length and binding energy. A PAEM-MO diagram is introduced, which clearly distinguishes chemical bonding from nonbonded and/or van der Waals interactions. Furthermore, the electron interflow frequency (EIF) along the bond path at the bc can be defined from the PAEM around the bc; the EIF correlates with the bond-vibration frequency. The properties of the bc along the bond path and the saddle point along the intrinsic reaction coordinate on the potential energy surface are related in a very interesting manner.

In double-stranded DNA, a rapid deprotonation of guanine radical cation (G(center dot+)) hinders the long-distance transfer of positive charge (hole). It is significant to explore the proton transfer of G(center dot+) for designing other DNA structures with high electrical conductivity. The deprotonation of G(center dot+) is explored in the 1H(2)O, 2H(2)O, 3H(2)O, and 9H(2)O models by quantum mechanics (QM) method. The results indicate that the second hydration shell facilitates proton transfer. The QM/molecular mechanics (MM) (ABEEM) method accurately simulates polarization and charge transfer effects through the implementation of the reactive valence-state electronegativity piecewise functions and setting local charge conservation conditions. The QM/MM(ABEEM) method has been developed to investigate the 9H(2)O model. The obtained activation energy (16.3 +/- 0.8 kJ/mol) through molecular dynamics simulations is consistent with experimental data (15.1 +/- 1.5 kJ/mol), demonstrating the accuracy of the QM/MM(ABEEM) method in simulating proton transfer in the DNA system. The deprotonation rate of G(center dot+) in the free base (1.5 x 10(7) s(-1)) is faster than that of G(center dot+) within double-stranded DNA (10(6)-10(7) s(-1)), which indicates that the free G base is an avoidable participant when designing hole transfer carrier due to its rapid deprotonation rate. Concurrently, the relationship between the proton transfer distance and potential barrier is monotone increasing, meaning that the long-range proton transfer corresponds to high energy barrier. The molecule involved in long-range proton transfer of G(center dot+) is more suitable as DNA electronic devices. This research provides valuable microscopic insight into deprotonation to advance the advancement of DNA structures with high electrical conductivity.

The origin of highly efficient asymmetric aminohydroxylation of styrene catalyzed by engineered cytochrome c is investigated by the developed Atom-Bond Electronegativity Equalization Method polarizable force field (ABEEM PFF), which is a combined outcome of electronic and steric effects. Model molecules were used to establish the charge parameters of the ABEEM PFF, for which the bond-stretching and angle-bending parameters were obtained by using a combination of modified Seminario and scan methods. The interactions between carbon-radical Fe-porphyrin (FePP) and waters are simulated by molecular dynamics, which shows a clear preference for the pre-R over the pre-S. This preference is attributed to the hydrogen-bond between the mutated 100S and 101P residues as well as van der Waals interactions, enforcing a specific conformation of the carbon-radical FePP complex within the binding pocket. Meanwhile, the hydrogen-bond between water and the nitrogen atom in the active intermediate dictates the stereochemical outcome. Quantum mechanics/molecular mechanics (QM/MM (ABEEM PFF)) and free-energy perturbation calculations elucidate that the 3RTS is characterized by sandwich-like structure among adjacent amino acid residues, which exhibits greater stability than crowed arrangement in 3STS and enables the R enantiomer to form more favorably. Thus, this study provides mechanistic insight into the catalytic reaction of hemoproteins.

The rapid deprotonation of G˙+ in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G˙+ in the G-tetrad makes it a more suitable carrier for hole conduction. The QM/MM(ABEEM) combined method, which involves the integration of QM and the ABEEM polarizable force field (ABEEM PFF), was developed to investigate the deprotonation of neutral and cation free radicals in the G-tetrad and GGX(8-oxo-G) tetrad (xanthine and 8-oxoguanine dual substituted G-tetrad). By incorporating valence-state electronegativity piecewise functions χ*(r) and implementing charge local conservation conditions, QM/MM(ABEEM) possesses the advantage of accurately simulating charge transfer and polarization effect during deprotonation. The activation energy calculated by the QM method of X˙ is the lowest among other bases in the GGX(8-oxo-G) tetrad, which is supported by the computation of the average electronegativity calculated by ABEEM PFF. By utilizing QM/MM(ABEEM) with a two-way free energy perturbation method, the deprotonation activation energy of X˙ in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol-1, while that of G˙+ in the G-tetrad is 20.7 ± 0.6 kJ mol-1, consistent with the experimental measurement of 20 ± 1.0 kJ mol-1. These results manifest that X˙ in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G˙+ in the G-tetrad, suggesting that the GGX(8-oxo-G) tetrad may serve as a more favorable hole transport carrier. Furthermore, the unequal average electronegativities of bases in the GGX(8-oxo-G) tetrad impede the deprotonation rate. This study provides a potential foundation for investigating the microscopic mechanism of DNA electronic devices.

文章以中国林业科学研究院林产化学工业研究所为例,对中央级公益性科研院所基本科研业务费专项资金的设立背景、管理模式及执行成效进行了阐述和分析,指出基本科研业务费专项资金在推动公益性科研院所科研工作方面发挥的重要作用.指出存在的问题,并提出引入技术管理、改善绩效评价体系以及建立配套绩效奖励机制等建议.

Atomic charge (AC), which is the charge distribution of a molecule, is an important property that is closely associated with structures, reactivities, and intra- and inter-molecular interactions among molecules. Several theoretical models or methods can be used to obtain the magnitudes of AC with different characteristics. These models can be classified into fuzzy-atoms models and models partitioning a molecule into individual atoms with sharp boundaries. The first category includes Mulliken, natural population analysis (NPA), Hirshfeld, Merz-Kollman-Singh (MK), CHELPG, the electronegativity equalization method (EEM), the atom-bond electronegativity equalization method (ABEEM), and atomic polar tensor (APT). The second category is derived from quantum chemical topology (QCT) and includes the quantum theory of atoms in molecules (QTAIM) and QCT analysis based on the potential acting on one electron in a molecule (PAEMQCT). Herein, after giving a bird's-eye view of the population methods of the first category, we specifically describe some features of the second category. We only present the basic framework of QCT for obtaining ACs from QTAIM and PAEMQCT and show their important characteristics. QCT establishes the basis of the following chemical concept: a molecule is spatially partitioned into individual atoms with sharp boundaries. The ACs from QTAIM are close to the atomic valence in chemistry, and ACs from PAEMQCT may be practically suitable for modeling intra- and inter-molecular interactions.

This paper focuses on the development of a quantum mechanics/molecular mechanics method using the ABEEM polarizable force field (QM/MM(ABEEM) method) to investigate the excision reaction mechanism of damaged thymine. This method does not simply combine the QM method with the polarizable force field. A valence electronegativity piecewise function with the distance between atoms as a variable is introduced to describe the atomic partial charges, and changes greatly during the reaction process. At the same time, the charge transfer effect is treated using the condition of local charge conservation. Compared with the traditional QM/MM method, the QM/MM(ABEEM) method can more accurately simulate the polarization effect and charge transfer effect in the reaction process. Focusing on the controversial problems of the excision of damaged bases, six reaction pathways were designed for monofunctional and difunctional deglycosylation of neutral bases and protonated bases. The results show that the QM/MM(ABEEM) method accurately simulates the polarization effect, charge transfer effect, activation energy and other properties of the reaction process. The process in which the active residue Asp activates the nucleophile H2O to attack the protonated base is the preferred path. The average activation energy and free activation energy of the protonated base are 7.00-14.00 kcal mol(-1) lower than that of the neutral base. The study in this paper is helpful to understand the mechanism of repair enzymes in repairing bases.