Journal of Chemical Theory and Computation最新文献

{"title":"Linnett is Back: Chemical Bonding through the Lens of Born Maxima.","authors":"María Menéndez-Herrero, Evelio Francisco, Ángel Martín Pendás","doi":"10.1021/acs.jctc.4c01785","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01785","url":null,"abstract":"<p><p>The classical Lewis-Langmuir electron pair model remains central to chemical bonding theories despite its inherent contradictions with quantum mechanical principles such as antisymmetry. This paper revisits the long-forgotten Linnett's double quartet (LDQ) model, which integrates spin considerations into chemical bonding. We demonstrate that the distribution of electrons at the maxima of the square of the wave function (Born maxima) highlights the rigidity of the same-spin electron blocks and validates the LDQ framework in atoms and molecules. A generalized LDQ model accounts for all bond types, including covalent, polar covalent, ionic, dative, and electron-deficient, and directly incorporates electron correlation effects, providing a rigorous yet intuitive approach to bonding. This perspective also reveals fundamental flaws in conventional mean-field descriptions that ignore the correlated motion of electrons. By bridging traditional and quantum paradigms, the generalized LDQ model offers a robust tool for understanding chemical bonding, with implications for education, experimental design, and theoretical advancements.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linear-Scaling Local Natural Orbital-Based Full Triples Treatment in Coupled-Cluster Theory.","authors":"Andy Jiang, Henry F Schaefer, Justin M Turney","doi":"10.1021/acs.jctc.4c01716","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01716","url":null,"abstract":"<p><p>We present an efficient, asymptotically linear-scaling implementation of the canonically <math><mi>O</mi><mrow><mo>(</mo><msup><mi>N</mi><mn>8</mn></msup><mo>)</mo></mrow></math> coupled-cluster method with singles, doubles, and full triples excitations (CCSDT) method. We apply the domain-based local pair natural orbital (DLPNO) approach for computing CCSDT amplitudes. Our method, called DLPNO-CCSDT, uses the converged coupled-cluster amplitudes from a preceding DLPNO-CCSD(T) computation as a starting point for the solution of the CCSDT equations in the local natural orbital basis. To simplify the working equations, we <i>t</i>₁-dress our two-electron integrals and Fock matrices, allowing our equations to take on the form of CCDT. With appropriate parameters, our method can recover more than 99.99% of the total canonical CCSDT correlation energy. In addition, we demonstrate that our method consistently yields sub-kJ mol^-1 errors in relative energies when compared to canonical CCSDT, and, likewise, when computing the difference between CCSDT and CCSD(T). Finally, to highlight the low scaling of our algorithm, we present timings on linear alkanes (up to 30 carbons and 730 basis functions) and water clusters (up to 131 water molecules and 3144 basis functions).</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Medium-Range Order in Iron Phosphate Glass Models Obtained Using Various Randomization Techniques: A Molecular Dynamics Study.","authors":"Shakti Singh, Manan Dholakia, Sharat Chandra","doi":"10.1021/acs.jctc.4c01372","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01372","url":null,"abstract":"<p><p>Glasses are known to have medium-range order (MRO), but their link to any experimentally measurable quantity is still ambiguous. The first sharp diffraction peak (FSDP) in structure factor <i>S</i>(<i>q</i>) obtained from diffraction experiments on glasses has been associated with this MRO (∼7-15 Å), but understanding the fundamental origin of this universal peak is still an open problem. We have addressed this issue for a complex glass, i.e., iron phosphate glass (IPG), through atomistic models generated from a hybrid approach (our in-house-developed MC code + molecular dynamics simulation). IPG is a technologically important glass with applications in waste vitrification, bioactive glass, laser glass material, anode material for batteries, etc., and is seen as a strengthened substitute for borosilicate glasses. We performed a comparative study by generating glass models from different initial configurations and randomization techniques. The developed IPG models were first validated with existing data on short-range order (SRO) and MRO through the study of pair correlation functions, bond angle distributions, and coordination number for SRO and rings distribution, FSDP in structure factor, and void size distribution for MRO. The study of coordination environment of oxygen is specifically shown to aid in understanding glass formation through topological constraint theory. Thereafter, to understand the fundamental origin of FSDP in <i>S</i>(<i>q</i>), structure factors were calculated corresponding to the individual ring sizes present in the model. The relative contribution of these individual <i>S</i>(<i>q</i>)'s in the total experimental <i>S</i>(<i>q</i>) is estimated using an inverse fitting approach. The contributions thus obtained directly correlated with ring size percentages in the models for the considered q-range. In particular, the melt-quenched model obtained from the MC model as an initial structure is found to reproduce most experimental features seen in IPG. Through this exercise, we can connect the rings distribution of an atomistic glass model with an experimentally measurable quantity like FSDP in <i>S</i>(<i>q</i>) for a complex glass-like IPG. This gives physical meaning to the rings distribution while also proving that this structural descriptor is a useful tool for validation of MRO in simulation-produced models of glass.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contextual Subspace Auxiliary-Field Quantum Monte Carlo: Improved Bias with Reduced Quantum Resources.","authors":"Matthew Kiser, Matthias Beuerle, Fedor Šimkovic","doi":"10.1021/acs.jctc.4c01280","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01280","url":null,"abstract":"<p><p>Using trial wave functions prepared on quantum devices to reduce the bias of auxiliary-field quantum Monte Carlo (QC-AFQMC) has established itself as a promising hybrid approach to the simulation of strongly correlated many body systems. Here, we further reduce the required quantum resources by decomposing the trial wave function into classical and quantum parts, respectively treated by classical and quantum devices, within the contextual subspace projection formalism. Importantly, we show that our algorithm is compatible with the recently developed matchgate shadow protocol for efficient overlap calculation in QC-AFQMC. Investigating the nitrogen dimer and the reductive decomposition of ethylene carbonate in lithium-based batteries, we observe that our method outperforms a number of established algorithm for ground state energy computations, while reaching chemical precision with less than half of the original number of qubits.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Algebraic Diagrammatic Construction Theory of Charged Excitations with Consistent Treatment of Spin-Orbit Coupling and Dynamic Correlation.","authors":"Rajat Majumder, Alexander Yu Sokolov","doi":"10.1021/acs.jctc.4c01762","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01762","url":null,"abstract":"<p><p>We present algebraic diagrammatic construction theory for simulating spin-orbit coupling and electron correlation in charged electronic states and photoelectron spectra. Our implementation supports Hartree-Fock and multiconfigurational reference wave functions, enabling efficient correlated calculations of relativistic effects using single-reference (SR-) and multireference-algebraic diagrammatic construction (MR-ADC). We combine the SR- and MR-ADC methods with three flavors of spin-orbit two-component Hamiltonians and benchmark their performance for a variety of atoms and small molecules. When multireference effects are not important, the SR-ADC approximations are competitive in accuracy to MR-ADC, often showing closer agreement with experimental results. However, for electronic states with multiconfigurational character and in nonequilibrium regions of potential energy surfaces, the MR-ADC methods are more reliable, predicting accurate excitation energies and zero-field splittings. Our results demonstrate that the spin-orbit ADC methods are promising approaches for interpreting and predicting the results of modern spectroscopies.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Amber ff24EXP-GA, Based on Empirical Ramachandran Distributions of Glycine and Alanine Residues in Water.","authors":"Athul Suresh, Reinhard Schweitzer-Stenner, Brigita Urbanc","doi":"10.1021/acs.jctc.4c01450","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01450","url":null,"abstract":"<p><p>Molecular dynamics (MD) offers important insights into intrinsically disordered peptides and proteins (IDPs) at a level of detail that often surpasses that available through experiments. Recent studies indicate that MD force fields do not reproduce intrinsic conformational ensembles of amino acid residues in water well, which limits their applicability to IDPs. We report a new MD force field, Amber ff24EXP-GA, derived from Amber ff14SB by optimizing the backbone dihedral potentials for guest glycine and alanine residues in cationic GGG and GAG peptides, respectively, to best match the guest residue-specific spectroscopic data. Amber ff24EXP-GA outperforms Amber ff14SB with respect to conformational ensembles of all 14 guest residues x (G, A, L, V, I, F, Y, D^p, E^p, R, C, N, S, T) in GxG peptides in water, for which complete sets of spectroscopic data are available. Amber ff24EXP-GA captures the spectroscopic data for at least 7 guest residues (G, A, V, F, C, T, E^p) better than CHARMM36m and exhibits more amino acid specificity than both the parent Amber ff14SB and CHARMM36m. Amber ff24EXP-GA reproduces the experimental data on three folded proteins and three longer IDPs well, while outperforming Amber ff14SB on short unfolded peptides.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toward Accurate pH-Dependent Binding Constant Predictions Using Molecular Docking and Constant-pH MD Calculations.","authors":"Mohannad J Yousef, Nuno F B Oliveira, João N M Vitorino, Pedro B P S Reis, Piotr Draczkowski, Maciej Maj, Krzysztof Jozwiak, Miguel Machuqueiro","doi":"10.1021/acs.jctc.4c01291","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01291","url":null,"abstract":"<p><p>pH is an important physicochemical property that modulates proteins' structure and interaction patterns. A simple change in a site's protonation state in an enzyme's catalytic pocket can strongly alter its activity and its affinity to substrate, products, or inhibitors. We addressed this pH effect issue by evaluating its impact on donepezil binding to acetylcholinesterase (AChE). We compared the binding affinities obtained from molecular docking (weighted from the protonation states sampled by constant-pH MD) with those from molecular mechanics/Poisson-Boltzmann surface area and isothermal titration calorimetry data. The computational methods showed a clear trend where donepezil binding to the catalytic cavity is improved with the drug protonation (lowering pH). However, the loss of binding affinity observed experimentally at pH 6.0 indicates that other phenomena eluding our computational approaches are occurring. Possible factors include the shape of the access tunnel to the AChE catalytic pocket (which is captured in our MD time scale) or an entropic penalty difference between neutral and protonated donepezil. Altogether, this work highlighted the need to improve our computational methods to capture the pH effects in protein/drug binding, while also exposing the limitations that will inevitably arise from these new advances.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring Liquid Crystal Properties through the Two-Phase Thermodynamic Model: Structural, Dynamic, and Thermodynamic Properties.","authors":"Juan M Hümöller, Oscar A Oviedo","doi":"10.1021/acs.jctc.4c01350","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01350","url":null,"abstract":"<p><p>This work provides a comprehensive analysis of the structural, dynamic, and thermodynamic properties of liquid crystals (LCs) along with their evolution through phase transitions and mesophases. A model of purely repulsive semiflexible spherocylinders is used in a molecular dynamics scheme through simulations involving NPT and NVT combinations. The two-phase thermodynamic model was used to obtain the translational, rotational, and vibrational density of states as well as the absolute values of thermodynamic parameters. We show evidence that during the isotropic-nematic-smectic-solid transitions, the translational diffusion coefficient becomes anisotropic, initially increasing by 15% in the nematic mesophase with a 129% rise along the director vector. Subsequent transitions result in a reduction of the diffusion coefficient by 42% in the smectic phase and 90% in the crystalline phase. Rotational diffusion decreases across all transitions (12, 35, and 26% for nematic, smectic, and solid transitions), although a notable increase in rotation around the principal axis is observed during the last transition. Thermodynamic analysis reveals that the primary contribution to the Gibbs free energy arises from the mechanical term (PV). With regard to the components, rotational motion is the dominant contribution to the Helmholtz free energy in the first transition, while translational motion dominates in the last transition. For the intermediate transition, translational, rotational, and vibrational contributions are comparable. A thorough analysis has been conducted into the Cartesian projections and the principal axes of rotation, in addition to the \"solid and gas components\" from the two-phase thermodynamic model analysis.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decomposition Analysis for Visualization of Noncovalent Interactions Based on the Fragment Molecular Orbital Method.","authors":"Dmitri G Fedorov, Diego Inostroza, Bastien Courbiere, Fréderic Guegan, Julia Contreras-García, Seiji Mori","doi":"10.1021/acs.jctc.4c01654","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01654","url":null,"abstract":"<p><p>Many-body expansions of the electron density and Fock matrix in the fragment molecular orbital method (FMO) are used to reveal the role of polarization and charge transfer on noncovalent interactions (NCI). In addition to the physicochemical insight gained from these analyses, the use of FMO permits a rapid evaluation of electron densities to study NCI. The developed method is applied to a solvated sodium cation and a small polypeptide, validating the accuracy of the approach with respect to full calculations and revealing the role of polarization and charge transfer in NCI. In order to show the full potential of the approach, the FMO/NCI method is applied to a complex of the Trp-cage (PDB: 1L2Y) protein with a ligand, delivering fruitful insights into binding from both density and energy perspectives. NCI is shown to provide a comprehensive visual picture of interactions that might be missed without it, in particular, interactions between functional groups in a fragment.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient Simulation of Surface-Enhanced Raman Scattering with a Simplified Damped Response Theory.","authors":"Gaohe Hu, Lasse Jensen","doi":"10.1021/acs.jctc.4c01567","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01567","url":null,"abstract":"<p><p>Theoretical studies on enhancement mechanisms of surface-enhanced Raman scattering (SERS) are usually carried out with full quantum mechanical methods to capture the specific interactions between molecules and substrates. However, due to the computational costs of methods like time-dependent density functional theory (TDDFT), simplified model systems are commonly adopted. In the framework of TDDFT, the damped response theory is usually invoked to give a unified description of both on- and off-resonance Raman spectra based on the calculation of polarizability derivatives. However, the computational costs of full TDDFT allow for modeling SERS spectra only using small metal clusters. In this work, we demonstrate the implementation of an efficient method that simplifies the damped response calculations for the simulation of both on- and off-resonance SERS spectra. This simplified damped response method is named as TBAOResponse. We first compare the absorption spectra of a regular small system calculated with TBAOResponse and full TDDFT to benchmark the new method. Then, we demonstrate the efficiency and accuracy of the new method by comparing the on- and off-resonance SERS spectra calculated with different methods. Compared to full TDDFT, while significant improvement of efficiency is achieved, the simplified damped response maintains good accuracy for SERS calculation. We further showcase the efficiency of TBAOResponse by calculating the SERS spectra for a system that is computationally demanding with full TDDFT. This new method is promising for modeling SERS systems when a full quantum mechanical description of both the substrate and the molecule is necessary.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}