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doi: 10.1002/jcc.27337pmid: 38459681
In this article, density functional theory computations at the PBE0‐D3/def2‐TZVP level are reported to unveil the type of bonding between β‐D‐glucopyranose—silver ion (1:1) complex ([Ag(C6H12O6)]+) and seven gas molecules, namely, H2, C2H2, C2H4, CO, N2, NO and O2. Moreover, the relative preference of trapping among these molecules within the sight of Ag metal ion in the complex is explored. The nature of interaction of these small molecules with the [Ag(C6H12O6)]+ ion is studied. Exergonic nature of binding is noted with the metal center for all the chosen small molecules except O2. Thermochemical data reveals the binding preference of C2H4 > C2H2 > CO > NO > N2 > H2. Natural bond orbital analysis, contour plot of the Laplacian of electron density, electron density descriptors, and gradient isosurface help in understanding the nature of interactions. Maximum bond formation is noted between the Ag‐complex and CO molecule. Assessed energy decomposition analysis discloses the nature of interaction as mainly orbital between the bound small gas molecules and the Ag‐complex. Frontier molecular orbital pictures further help in understanding the type of interaction as orbital. To disclose the kinetic stability of the gas molecule bound Ag complexes an ab initio molecular dynamics study is done at different temperatures up to 2 ps. These studies help in understanding the type of adsorption. Calculated conceptual density functional theory (CDFT) based reactivity descriptors corroborate well with results. β‐D‐glucopyranose—silver ion (1:1) complex may be used as small gas molecule scavenger.
Wilson, Carter J.; Groot, Bert L.; Gapsys, Vytautas
doi: 10.1002/jcc.27318pmid: 38471815
In a protein, nearby titratable sites can be coupled: the (de)protonation of one may affect the other. The degree of this interaction depends on several factors and can influence the measured pKa. Here, we derive a formalism based on double free energy differences (ΔΔG) for quantifying the individual site pKa values of coupled residues. As ΔΔG values can be obtained by means of alchemical free energy calculations, the presented approach allows for a convenient estimation of coupled residue pKas in practice. We demonstrate that our approach and a previously proposed microscopic pKa formalism, can be combined with alchemical free energy calculations to resolve pH‐dependent protein pKa values. Toy models and both, regular and constant‐pH molecular dynamics simulations, alongside experimental data, are used to validate this approach. Our results highlight the insights gleaned when coupling and microstate probabilities are analyzed and suggest extensions to more complex enzymatic contexts. Furthermore, we find that naïvely computed pKa values that ignore coupling, can be significantly improved when coupling is accounted for, in some cases reducing the error by half. In short, alchemical free energy methods can resolve the pKa values of both uncoupled and coupled residues.
Jia, Lifan; Wang, Yunxia; Song, Lulu; Liu, Ruirui; Li, Longgang; Li, Jisheng; Zhou, Yongquan; Pan, Jianmin; Zhu, Fayan
doi: 10.1002/jcc.27339pmid: 38471809
B6O7OH62− is a highly polymerized borate anion of three six‐membered rings. Limited research on the B6O7OH62− hydrolysis mechanism under neutral solution conditions exists. Calculations based on density functional theory show that B6O7OH62− undergoes five steps of hydrolysis to form H3BO3 and BOH4−. At the same time, there are a small number of borate ions with different degrees of polymerization during the hydrolysis process, such as triborate, tetraborate, and pentaborate anions. The structure of the borate anion and the coordination environment of the bridging oxygen atoms control the hydrolysis process. Finally, this work explains that in existing experimental studies, the reason for the low B6O7OH62− content in solution environments with low total boron concentrations is that it depolymerizes into other types of borate ions and clarifies the borate species. The conversion relationship provides a basis for identifying the possibility of various borate ions existing in the solution. This work also provides a certain degree of theoretical support for the cause of the “dilution to salt” phenomenon.
Maruyama, Yutaka; Yoshida, Norio
doi: 10.1002/jcc.27340pmid: 38472097
Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three‐dimensional extension (3D‐RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D‐RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D‐RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D‐RISM programs for single‐ and multi‐GPU codes written in CUDA would enhance the availability of these hybrid methods because they require the performance of many computationally expensive 3D‐RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io.
D'Anania, Olga; Romano, Eugenio; Barone, Vincenzo; Talarico, Giovanni
doi: 10.1002/jcc.27343pmid: 38470153
Thanks to recent developments in hardware and software, quantum chemical methods are increasingly used for interpreting the complex mechanisms underlying polymerization reaction by homogeneous catalysis. Unfortunately, the dimensions of even the smallest realistic models are too large to permit the use of state‐of‐the‐art composite wave function methods. Under these circumstances, density functional theory still offers the best compromise between cost and accuracy. However, comprehensive benchmarks of different functionals are not yet available for this important research field. The main aim of the present paper is to fill this gap by performing an unbiased comparison of several density functionals and continuum solvent models for the stereo‐control in the propylene polymerization on prototypical catalysts inducing different reaction mechanisms. While it was not possible to define a unique computational protocol providing the best results in all the situations, the B3PW91 functional in conjunction with D3 empirical dispersions and the solvent model density solvent model performs remarkably well for three out of the four investigated catalysts. Under such circumstances, it is recommended to compare the results delivered by different models when approaching additional classes of catalysts.
Xiao, Sian; Ibrahim, Mayar Tarek; Verkhivker, Gennady M.; Zoltowski, Brian D.; Tao, Peng
doi: 10.1002/jcc.27344pmid: 38476039
Avena sativa phototropin 1 light‐oxygen‐voltage 2 domain (AsLOV2) is a model protein of Per‐Arnt‐Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N‐terminal A'α helix in the dark state followed by the unfolding of the C‐terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β‐sheets are identified as crucial components for mediating allosteric signal transmission between the two termini. Through combined experimental and computational investigations, the Hβ and Iβ strands are recognized as the most critical and influential β‐sheets in AsLOV2's allosteric mechanism. To elucidate the role of these β‐sheets, we introduced 13 distinct mutations (F490L, N492A, L493A, F494L, H495L, L496F, Q497A, R500A, F509L, Q513A, L514A, D515V, and T517V) and conducted comprehensive molecular dynamics simulations. In‐depth hydrogen bond analyses emphasized the role of two hydrogen bonds, Asn482‐Leu453 and Gln479‐Val520, in the observed distinct behaviors of L493A, L496F, Q497A, and D515V mutants. This illustrates the role of β‐sheets in the transmission of the allosteric signal upon the photoactivation of the light state.
Koots, Rian; Wang, Yu; Mirahmadi, Marjan; Pérez‐Ríos, Jesús
doi: 10.1002/jcc.27341pmid: 38485218
The three‐body recombination reaction, or ternary association, is a termolecular reaction leading to a molecule after a three‐body encounter that plays a vital role in many relevant scenarios in chemical physics. Here, we introduce the Python 3‐Body Recombination program, which is dedicated to the computation of atomic three‐body recombination rate coefficients. The software is based on a classical trajectory approach in hyperspherical coordinates after mapping the three‐body problem as a single particle in a higher‐dimensional space. This theoretical approach is fully general and applicable to any ion‐atom‐atom or atom‐atom‐atom three‐body process. The predictive power of the methodology has been tested in several different experimental scenarios, reaching a good description of every system. The code structure is presented alongside examples and tests to ensure the software's capacity. In addition, the performance of the software after parallelization is shown.
Zhang, Yueyang; Hu, Gaofeng; Gao, Xueting; Zhang, Zhuxia; Cui, Peng
doi: 10.1002/jcc.27342pmid: 38485224
This study employs grand canonical Monte Carlo (GCMC) simulations to investigate the impact of functional group modifications (CH3, OH, NH2, and OLi) on the adsorption performance of CH4/N2 on Ni‐MOF‐74. The results revealed that functional group modifications significantly increased the adsorption capacity of Ni‐MOF‐74 for both CH4 and N2. The packed methyl groups in CH3‐Ni‐MOF‐74 create an environment conducive to CH4, leading to the highest CH4 adsorption capacity. The electrostatic potential distribution indicates that the strong electron‐donating effect introduced by the alkali metal Li results in the highest electrostatic potential gradient in Li‐O‐Ni‐MOF‐74, leading to the strongest adsorption of N2, this is unfavorable for CH4/N2 separation. At 1500 kPa the selectivity order of adsorbents for mixed gases was as follows: CH3‐Ni‐MOF‐74 > NH2‐Ni‐MOF‐74 > OH‐Ni‐MOF‐74 > Ni‐MOF‐74 > Li‐O‐Ni‐MOF‐74. This study highlights that CH3‐Ni‐MOF‐74 possesses optimal CH4 selectivity and adsorption performance. Given the current lack of research on functionalized MOF‐74 for the separation of CH4 and N2, the findings of this study will serve as a theoretical guide and provide references for the applications of CH4 adsorption and CH4/N2 separation.
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