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Park, Soohyung; Rice, Amy; Im, Wonpil; Pastor, Richard W.
doi: 10.1002/jcc.27261pmid: 37991280
Peptides and proteins play crucial roles in membrane remodeling by inducing spontaneous curvature. However, extracting spontaneous curvatures from simulations of asymmetric bilayers is challenging because differential stress (i.e., the difference of the leaflet surface tensions) arising from leaflet area strains can vary substantially among initial conditions. This study investigates peptide‐induced spontaneous curvature δc0p in asymmetric bilayers consisting of a single lipid type and a peptide confined to one leaflet; δc0p is calculated from the Helfrich equation using the first moment of the lateral pressure tensor and an alternative expression using the differential stress. It is shown that differential stress introduced during initial system generation is effectively relaxed by equilibrating using P21 periodic boundary conditions, which allows lipids to switch leaflets across cell boundaries and equalize their chemical potentials across leaflets. This procedure leads to robust estimates of δc0p for the systems simulated, and is recommended when equality of chemical potentials between the leaflets is a primary consideration.
Inoue, Nobuki; Watanabe, Yoshihiro; Nakano, Haruyuki
doi: 10.1002/jcc.27251pmid: 37997192
The generalized Foldy–Wouthuysen (GFW) transformation was proposed as a generic form that unifies four types of transformations in relativistic two‐component methods: unnormalized GFW(UN), and normalized form 1, form 2, and form 3 (GFW(N1), GFW(N2), and GFW(N3)). The GFW transformation covers a wide range of transformations beyond the simple unitary transformation of the Dirac Hamiltonian, allowing for the systematic classification of all existing two‐component methods. New two‐component methods were also systematically derived based on the GFW transformation. These various two‐component methods were applied to hydrogen‐like and helium‐like ions. Numerical errors in energy were evaluated and classified into four types: the one‐electron Hamiltonian approximation, the two‐electron operator approximation, the newly defined “picture difference error (PDE),” and the error in determining the transformation, and errors in multi‐electron systems were discussed based on this classification.
Yashmin, Farnaz; Sharma, Rohan; Mazumder, Lakhya J.; Sharma, Pankaz K.
doi: 10.1002/jcc.27253pmid: 37994117
The structure and stability of noble gas (Ng) bound [NHCM]+ complexes (M = Cu, Ag, and Au) were investigated using Quantum chemical calculations. Dissociation energies, enthalpy, and free energy changes were computed to comprehend the stability of these Ng‐bonded complexes. The nature of interactions associated to the bonding between metal and noble gas atoms was studied through the computation of electron density‐based descriptors. Detailed electronic structure study revealed electron donation from the noble gas atoms towards the metal center, resulting in the formation of dative bonds.
Vijay, Sudarshan; H. Heenen, Hendrik; Singh, Aayush R.; Chan, Karen; Voss, Johannes
doi: 10.1002/jcc.27263pmid: 38009447
Kinetic models parameterized by ab‐initio calculations have led to significant improvements in understanding chemical reactions in heterogeneous catalysis. These studies have been facilitated by implementations which determine steady‐state coverages and rates of mean‐field micro‐kinetic models. As implemented in the open‐source kinetic modeling program, CatMAP, the conventional solution strategy is to use a root‐finding algorithm to determine the coverage of all intermediates through the steady‐state expressions, constraining all coverages to be non‐negative and to properly sum to unity. Though intuitive, this root‐finding strategy causes issues with convergence to solution due to these imposed constraints. In this work, we avoid explicitly imposing these constraints, solving the mean‐field steady‐state micro‐kinetic model in the space of number of sites instead of solving it in the space of coverages. We transform the constrained root‐finding problem to an unconstrained least‐squares minimization problem, leading to significantly improved convergence in solving micro‐kinetic models and thus enabling the efficient study of more complex catalytic reactions.
Wada, Satoi; Tsutsumi, Takuro; Saita, Kenichiro; Taketsugu, Tetsuya
doi: 10.1002/jcc.27271pmid: 38009451
Recently, surface‐hopping ab initio molecular dynamics (SH‐AIMD) simulations have come to be used to discuss the mechanisms and dynamics of excited‐state chemical reactions, including internal conversion and intersystem crossing. In dynamics simulations involving intersystem crossing, there are two potential energy surfaces (PESs) governing the motion of nuclei: PES in a spin‐pure state and PES in a spin‐mixed state. The former gives wrong results for molecular systems with large spin‐orbit coupling (SOC), while the latter requires a potential gradient that includes a change in SOC at each point, making the computational cost very high. In this study, we systematically investigate the extent to which the magnitude of SOC affects the results of the spin‐pure state‐based dynamics simulations for the hydride MH2 (M = Si, Ge, Sn, Pb) by performing SH‐AIMD simulations based on spin‐pure and spin‐mixed states. It is clearly shown that spin‐mixed state PESs are indispensable for the dynamics simulation of intersystem crossing in systems containing elements Sn and Pb from the fifth period onward. Furthermore, in addition to the widely used Tully's fewest switches (TFS) algorithm, the Zhu‐Nakamura (ZN) global switching algorithm, which is computationally less expensive, is applied to SH for comparison. The results from TFS‐ and ZN‐SH‐AIMD methods are in qualitative agreement, suggesting that the less expensive ZN‐SH‐AIMD can be successfully utilized to investigate the dynamics of photochemical reactions based on quantum chemical calculations.
Jendoubi, Abir; Arfaoui, Youssef; Palaudoux, Jérôme; Al‐Mogren, Muneerah Mogren; Hochlaf, Majdi
doi: 10.1002/jcc.27270pmid: 38031324
Using density functional theory (DFT), we treat the reaction of coupling of CO2 with aziridine in gas phase, in the presence of water and of a green catalyst (NaBr). Computations show that, in gas phase, this ring‐opening conversions to oxazolidinones initiates by coordinating a CO2 molecule to the nitrogen atom of the aziridine. Then, a nucleophilic interaction between one oxygen atom of the coordinated CO2 and the carbon atom of the aziridine occurs. For methyl substituted aziridine, two pathways are proposed leading either to 4‐oxazolidinone or to 5‐oxazolidinone. Besides, we show that the activation energy of this reaction reduces in aqueous solution, in the presence of a water molecule explicitly or NaBr catalyst. In addition, the corresponding reaction mechanisms and regioselectivity associated with this ring‐opening conversions to oxazolidinones, in the presence of carbon dioxide are found to be influenced by solvent and catalyst. The present findings should allow better designing regioisomer oxazolidinones relevant for organic chemistry, medicinal and pharmacological applications.
Freindorf, Marek; Antonio, Juliana J.; Kraka, Elfi
doi: 10.1002/jcc.27267pmid: 38041830
We investigated the intrinsic strength of distal and proximal FeN bonds for both ferric and ferrous oxidation states of bishistidyl hemoproteins from bacteria, animals, human, and plants, including two cytoglobins, ten hemoglobins, two myoglobins, six neuroglobins, and six phytoglobins. As a qualified measure of bond strength, we used local vibrational force constants ka(FeN) based on local mode theory developed in our group. All calculations were performed with a hybrid QM/MM ansatz. Starting geometries were taken from available x‐ray structures. ka(FeN) values were correlated with FeN bond lengths and covalent bond character. We also investigated the stiffness of the axial NFeN bond angle. Our results highlight that protein effects are sensitively reflected in ka(FeN), allowing one to compare trends in diverse protein groups. Moreover, ka(NFeN) is a perfect tool to monitor changes in the axial heme framework caused by different protein environments as well as different Fe oxidation states.
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