Journal of Molecular Modeling最新文献

{"title":"Effect of graphene on the key electrical, optical, and magnetic properties of polymethylmethacrylate: a study based on molecular modeling","authors":"Ernesto López-Chávez,&nbsp;Alberto Garcia-Quiroz,&nbsp;José Antonio Irán Díaz-Góngora,&nbsp;J. Antonio López-Barrera,&nbsp;José Alberto Mendoza-Espinoza,&nbsp;Yesica Antonia Peña-Castañeda,&nbsp;Fray de Landa Castillo-Alvarado","doi":"10.1007/s00894-024-06172-z","DOIUrl":"10.1007/s00894-024-06172-z","url":null,"abstract":"<div><h3>Context</h3><p>In this work, a new polymeric structure was designed consisting of a nanometric sheet of graphene (G) and a polymethylmethacrylate (PMMA) repeat unit, which was designated as PMMA-G. Three degrees of polymerization of PMMA-G were considered: monomer (PMMA-G1), dimer (PMMA-G2), and trimer (PMMA-G3). The effect of incorporating a nanometric sheet of graphene into the molecular structure of PMMA on the modification of some of its main optical, magnetic, and electrical properties was investigated. Currently, the study presented here is of great relevance since various areas of technology require new materials with specific properties for the development of new devices. The results of our study reveal that the dielectric constant of PMMA is reduced when graphene is incorporated. However, a percentage increase of 14.48% in the refractive index of PMMA when graphene is inserted to form the nanocomposite is observed. It is found that the absolute value of molar magnetic susceptibility of PMMA increases considerably when reinforced with graphene. Finally, when reinforcing PMMA with graphene to obtain the PMMA-G nanocomposite, the electrical resistivity increases by almost an order of magnitude.</p><h3>Methods</h3><p>We used computational tools under Materials Studio (MS) software. We built a PMMA molecule with three degrees of polymerization, graphene sheet, and polymethylmethacrylate-graphene composite (PMMA-G) was built also with three degrees of polymerization using a concentration of 50% graphene over the PMMA polymer. For each structure, we used computational code DMol³ of MS, which is based on the Density Functional Theory, and the geometry optimization process was carried out to obtain the most stable structures. Finally, using the connectivity indices method together with topological properties of the molecular structures, implemented in Synthia computational code of MS software, we calculated the dielectric constant, magnetic susceptibility, refractive index, and electrical resistivity, for pure PMMA and PMMA-G structures for their three degrees of polymerization. The results were analyzed, and the changes in these properties were discussed in terms of the effect of an electric and magnetic field on the molecular structures of PMMA-G with respect to PMMA.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142434742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ursolic acid interaction with transcription factors BRAF, V600E, and V600K: a computational approach towards new potential melanoma treatments","authors":"Giovanny Aguilera-Durán,&nbsp;Stephanie Hernández-Castro,&nbsp;Brenda V. Loera-García,&nbsp;Alex Rivera-Vargas,&nbsp;J. M. Alvarez-Baltazar,&nbsp;Ma Del Refugio Cuevas-Flores,&nbsp;Antonio Romo-Mancillas","doi":"10.1007/s00894-024-06165-y","DOIUrl":"10.1007/s00894-024-06165-y","url":null,"abstract":"<div><h3>Context</h3><p>Melanoma is one of the cancers with the highest mortality rate for its ability to metastasize. Several targets have undergone investigation for the development of drugs against this pathology. One of the main targets is the kinase BRAF (RAF, rapidly accelerated fibrosarcoma). The most common mutation in melanoma is BRAFV600E and has been reported in 50–90% of patients with melanoma. Due to the relevance of the BRAFV600E mutation, inhibitors to this kinase have been developed, vemurafenib-OMe and dabrafenib. Ursolic acid (UA) is a pentacyclic triterpene with a privileged structure, the pentacycle scaffold, which allows to have a broad variety of biological activity; the most studied is its anticancer capacity. In this work, we reported the interaction profile of vemurafenib-OMe, dabrafenib, and UA, to define whether UA has binding capacity to BRAFWT, BRAFV600E, and BRAFV600K. Homology modeling of BRAFWT, V600E, and V600K; molecular docking; and molecular dynamics simulations were carried out and interactions and residues relevant to the binding of the inhibitors were obtained. We found that UA, like the inhibitors, presents hydrogen bond interactions, and hydrophobic interactions of van der Waals, and π-stacking with I463, Q530, C532, and F583. The Δ<i>G</i> of ursolic acid in complex with BRAFV600K (− 63.31 kcal/mol) is comparable to the Δ<i>G</i> of the selective inhibitor dabrafenib (− 63.32 kcal/mol) in complex to BRAFV600K and presents a Δ<i>G</i> like vemurafenib-OMe with BRAFWT and V600E. With this information, ursolic acid could be considered as a lead compound for design cycles and to optimize the binding profile and the selectivity towards mutations for the development of new selective inhibitors for BRAFV600E and V600K to new potential melanoma treatments.</p><h3>Methods</h3><p>The homology modeling calculations were executed on the public servers I-TASSER and ROBETTA, followed by molecular docking calculations using AutoGrid 4.2.6, AutoDockGPU 1.5.3, and AutoDockTools 1.5.6. Molecular dynamics and metadynamics simulations were performed in the Desmond module of the academic version of the Schrödinger-Maestro 2020–4 program, utilizing the OPLS-2005 force field. Ligand–protein interactions were evaluated using Schrödinger-Maestro program, LigPlot + , and PLIP (protein–ligand interaction profiler). Finally, all of the protein figures presented in this article were made in the PyMOL program.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reaction force constant as a descriptor of the principle of non-perfect synchronization","authors":"César Barrales-Martínez,&nbsp;Danilo J. Carmona,&nbsp;Javier Oller,&nbsp;Andrés F. Flor-Lopez,&nbsp;Kevin Urrutia-Fernández,&nbsp;Sebastián Richter,&nbsp;Agustín Albornoz,&nbsp;Jorge Martínez-Araya,&nbsp;Pablo Jaque","doi":"10.1007/s00894-024-06151-4","DOIUrl":"10.1007/s00894-024-06151-4","url":null,"abstract":"<div><h3>Context</h3><p>In this study, a small set of 1,3-dipolar cycloaddition reactions that proceed at the same exothermicity is presented. Our main objective was to extend the application of the reaction force constant concept to gain an understanding of the reactivity principles. Inspired by a recent article where we show that the Bell-Evans-Polanyi principle is fulfilled under the condition of an equal degree of (a)synchronicity, here, we demonstrate that the reaction force constant is also a suitable descriptor to quantify the principle of non-perfect synchronization proposed by Bernasconi as a way to understand deviations from the Bell-Evans-Polanyi principle.</p><h3>Methods</h3><p>Reaction profiles <span>(V(xi ))</span>, <span>(F(xi ))</span>, and <span>(kappa (xi ))</span> were performed at the B3LYP/6-31G(d,p) level of theory. The stabilizing interactions were characterized using the energy decomposition analysis combined with the natural orbitals for chemical valence, EDA-NOCV, method. The present work was done using Gaussian 09 and Multiwfn programs.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Incrimination and impact on recovery times and effects of BN nanostructures on antineoplastic drug-electronic density study","authors":"T. Aiswarya,&nbsp;K. K. Singh","doi":"10.1007/s00894-024-06167-w","DOIUrl":"10.1007/s00894-024-06167-w","url":null,"abstract":"<div><h3>Context</h3><p>By delivering the drug to the intended cell location, the use of nanomaterials in the drug delivery system may influence how the patient receives the medication and may assist in mitigating severe side effects. Density functional theory was used to assess the use of boron carbon nitride nanocages (BNCNCs), boron nitride (BNNSs), and boron carbon nitride nanosheets (BNCNSs) as melphalan (Mln) drug carriers in both the gaseous and fluid phases. We systematically examined the dipole moment, density of states, frontier molecular orbital, and optimal adsorption energy to understand the targeted drug delivery potential of these nanostructures. Adsorption energy analysis revealed that in both gas and water media, Mln drug adsorption takes place spontaneously on all the conjugated structures. The occurrence of adsorption energy as physisorbed energy suggests that the process is reversible, and desorption can take place with a much lower energy input. This physical contact is appropriate for the unquestionable unloading of Mln medications to the intended location. The reactivity is higher in BNNSs and BNCNSs, while the stability is higher in BNCNCs. The recovery time shows a shorter time for BNNSs and BNCNSs, while BNCNC shows a potential desorption time in higher temperature. These conclusions are corroborated by the results of the quantum theory of atoms in molecules (QTAIM). After the interaction analysis, it was observed that the BNCNCs can act as potential carriers for the melphalan. From dipole moment analysis, all three nanostructures show a high hydrophilic nature but quite higher in BNCNCs after doping in both media. Overall, all the structures show the potential carrier for melphalan drug.</p><h3>Methods</h3><p>The quantum mechanical approach, or DFT, has been used to study the fundamental structural, electrical, thermodynamic, and other aspects of proposed structures to develop an acceptable Mln drug detector. The adsorbate and all adsorbents were optimized via the hybrid B3LYP functional and the 6-311G +  + (2d, p) basis set approach prior to the adsorption process. The Gaussian 09 package was used at 298 K as the constant temperature and 1 atm as the constant pressure. The structures are examined using the same functional models for solvation analysis—6–311 G +  + (2d, p) and B3LYP—as well as the polarized continuum model (PCM) model as the foundation set. Density of states was studied using GaussSum 3.0 software. The interaction studies QTAIM and RDG were studied using VMD and Multiwfn software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shannon entropy variation as a global indicator of electron density contraction at interatomic regions in chemical reactions","authors":"César Barrales-Martínez,&nbsp;Rocío Durán,&nbsp;Julio Caballero","doi":"10.1007/s00894-024-06171-0","DOIUrl":"10.1007/s00894-024-06171-0","url":null,"abstract":"<div><h3>Context</h3><p>The negative of the Shannon entropy derivative is proposed to account for electron density contraction as the chemical bonds are breaking and forming during a chemical reaction. We called this property the electron density contraction index, EDC, which allows identifying stages in a reaction that are dominated by electron contraction or expansion. Four different reactions were analyzed to show how the EDC index changes along the reaction coordinate. The results indicate that the rate of change of Shannon entropy is directly related to the rate of change of the electron density at the bond critical points between all the atomic pairs in the molecular systems. It is expected that EDC will complement the detailed analysis of reaction mechanisms that can be performed with the theoretical tools available to date.</p><h3>Methods</h3><p>Density functional theory calculations at the B3LYP/6-31G(d,p) level of theory were carried out using Gaussian 16 to analyze the reaction mechanisms of the four reactions studied. The reaction paths were obtained via the intrinsic reaction coordinate method, which served as the reaction coordinate to obtain the reaction force and the EDC profiles in each case. Shannon entropy and electron density at the bond critical points were calculated using the Multiwfn 3.7 package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Low-temperature oxidation of methane mediated by Al-doped ZnO cluster and nanowire: a first-principles investigation","authors":"Mehdi D. Esrafili","doi":"10.1007/s00894-024-06168-9","DOIUrl":"10.1007/s00894-024-06168-9","url":null,"abstract":"<div><h3>Context</h3><p>First-principles calculations are performed to investigate the catalytic oxidation of methane by using N₂O as an oxidizing agent over aluminum (Al)-doped Zn₁₂O₁₂ cluster and (Zn₁₂O₁₂)₂ nanowire. The impact of Al impurity on the geometry, electronic structure, and surface reactivity of Zn₁₂O₁₂ and (Zn₁₂O₁₂)₂ is thoroughly studied. Our study demonstrates that Al-doped ZnO systems have a better adsorption ability than the corresponding pristine counterparts. It is found that N₂O molecule is initially decomposed on the Al site to provide the N₂ molecule, and an Al–O intermediate which is an active species for the CH₄ oxidation. The conversion of CH₄ into CH₃OH over AlZn₁₁O₁₂ and (AlZn₁₁O₁₂)₂ requires an activation energy of 0.45 and 0.29 eV, respectively, indicating it can be easily performed at normal temperatures. Besides, the overoxidation of methanol into formaldehyde cannot take place over the AlZn₁₁O₁₂ and (AlZn₁₁O₁₂)₂, due to the high energy barrier needed to dissociate C–H bond of the CH₃O intermediate.</p><h3>Method</h3><p>Dispersion-corrected density functional theory calculations were performed through GGA-PBE exchange–correlation functional combined with a numerical double-ζ plus polarization (DNP) basis set as implemented in DMol³. To include the relativistic effects of core electrons of Zn atoms, DFT-semicore pseudopotentials were adopted. The DFT + D scheme proposed by Grimme was used to involve weak dispersion interactions within the DFT calculations. The reaction energy paths were generated by the minimum energy path calculations using the NEB method.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introducing KICK-MEP: exploring potential energy surfaces in systems with significant non-covalent interactions","authors":"Williams García-Argote,&nbsp;Lina Ruiz,&nbsp;Diego Inostroza,&nbsp;Carlos Cardenas,&nbsp;Osvaldo Yañez,&nbsp;William Tiznado","doi":"10.1007/s00894-024-06155-0","DOIUrl":"10.1007/s00894-024-06155-0","url":null,"abstract":"<div><h3>Context</h3><p>Exploring potential energy surfaces (PES) is fundamental in computational chemistry, as it provides insights into the relationship between molecular energy, geometry, and chemical reactivity. We introduce Kick-MEP, a hybrid method for exploring the PES of atomic and molecular clusters, particularly those dominated by non-covalent interactions. Kick-MEP computes the Coulomb integral between the maximum and minimum electrostatic potential values on a 0.001 a.u. electron density isosurface for two interacting fragments. This approach efficiently estimates interaction energies and selects low-energy configurations at reduced computational cost. Kick-MEP was evaluated on silicon-lithium clusters, water clusters, and thymol encapsulated within Cucurbit[7]uril, consistently identifying the lowest energy structures, including global minima and relevant local minima.</p><h3>Methods</h3><p>Kick-MEP generates an initial population of molecular structures using the stochastic Kick algorithm, which combines two molecular fragments (A and B). The molecular electrostatic potential (MEP) values on a 0.001 a.u. electron density isosurface for each fragment are used to compute the Coulomb integral between them. Structures with the lowest Coulomb integral are selected and refined through gradient-based optimization and DFT calculations at the PBE0-D3/Def2-TZVP level. Molecular docking simulations for the thymol-Cucurbit[7]uril complex using AutoDock Vina were performed for benchmarking. Kick-MEP was validated across different molecular systems, demonstrating its effectiveness in identifying the lowest energy structures, including global minima and relevant local minima, while maintaining a low computational cost.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unimolecular isomerizations of C6H6•+ radical cations: a computational study","authors":"Kiew S. Kharnaior,&nbsp;Asit K. Chandra,&nbsp;R. H. Duncan Lyngdoh","doi":"10.1007/s00894-024-06148-z","DOIUrl":"10.1007/s00894-024-06148-z","url":null,"abstract":"<div><h3>Concept</h3><p>Eighteen concerted isomerization reactions of various C₆H₆^•+ radical cation (RC) species are studied and found to proceed via well-defined transition states, whose relative positions along the reaction pathway generally agree with Hammond’s postulate. From the barrier heights, the rate coefficients of these reactions are estimated by using transition state theory, and the activation energies are computed. Through combination among themselves, these 18 isomerizations yielded 15 multi-step conversion routes of various C₆H₆^•+ species to the lowest energy benzene radical cation isomer <b>1</b>, which routes are compared.</p><h3>Methods</h3><p>Use is made of DFT with the B3LYP and M06-2X functionals, along with the CBS-QB3 approach to arrive at better energies. From the barrier heights for each of the concerted reactions, canonical transition state theory was applied to evaluate rate coefficients <i>k</i> over the temperature range 200–500 K. The Arrhenius activation energies were computed using the plot of ln <i>k</i> vs. 1/<i>T</i>.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-covalent interactions and charge transfer in the CO(_{2}) activation by low-valent group 14 complexes","authors":"Carlos Castillo-Orellana,&nbsp;Esteban Vöhringer-Martinez,&nbsp;Nery Villegas-Escobar","doi":"10.1007/s00894-024-06150-5","DOIUrl":"10.1007/s00894-024-06150-5","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;The CO&lt;span&gt;(_{2})&lt;/span&gt; activation by low-valent group 14 catalysts encompasses the rupture of varied covalent bonds in a single transition state through a concerted pathway. The bond between the central main group atom and the hydride in the complex is elongated to trigger the formation of the C–H bond with CO&lt;span&gt;(_{2})&lt;/span&gt; accompanied by the concomitant formation of the E–O bond between the complex and CO&lt;span&gt;(_{2})&lt;/span&gt; to lead the corresponding formate product. Prior studies have established that besides the apolar nature of CO&lt;span&gt;(_{2})&lt;/span&gt;, its initial interaction with the complex is primarily governed by electrostatic interactions. Notably, other stabilizing interactions and the transfer of charge between catalysts and CO&lt;span&gt;(_{2})&lt;/span&gt; during the initial phases of the reaction have been ignored. In this study, we have quantified the non-covalent interactions and charge transfer that facilitate the activation of CO&lt;span&gt;(_{2})&lt;/span&gt; by group 14 main group complex. Our findings indicate that electrostatic interactions predominantly stabilize the complex and CO&lt;span&gt;(_{2})&lt;/span&gt; in the reactant region. However, induction energy becomes the main stabilizing force as the reaction progresses towards the transition state, surpassing electrostatics. Induction contributes about 50% to the stabilization at the transition state, followed by electrostatics (40%) and dispersion interactions (10%). Atomic charges calculated with the minimal basis iterative stockholder (MBIS) method reveal larger charge transfer for the back-side reaction path in which CO&lt;span&gt;(_{2})&lt;/span&gt; approaches the catalysts in contrast to the front-side approach. Notably, it was discovered that a minor initial bending of CO&lt;span&gt;(_{2})&lt;/span&gt; to approximately &lt;span&gt;(176^circ )&lt;/span&gt; initiates the charge transfer process for all systems. Furthermore, our investigation of group 14 elements demonstrates a systematic reduction in both activation energies and charge transfer to CO&lt;span&gt;(_{2})&lt;/span&gt; while descending in group 14.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;All studied reactions were characterized along the reaction coordinate obtained with the intrinsic reaction coordinate (IRC) methodology at the M06-2X/6-31 g(d,p) level of theory. Gibbs free energy in toluene was computed using electronic energies at the DLPNO-CCSD(T)/cc-pVTZ-SSD(E) level of theory. Vibrational and translational entropy corrections were applied to provide a more accurate description of the obtained Gibbs free energies. To better characterize the changes in the reaction coordinate for all reactions, the reaction force analysis (RFA) has been employed. It enables the partition of the reaction coordinate into the reactant, transition state, and product regions where different stages of the mechanism occur. A detailed characterization of the main non-covalent driving forces in the initial stages of the activation of CO&lt;span&gt;(_{2})&lt;/span&gt; by low-valent group 14 complexes was perfo","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How to search for and reveal a hidden intermediate? The ELF topological description of non-synchronicity in double proton transfer reactions under oriented external electric field","authors":"Vanessa Labet,&nbsp;Antoine Geoffroy-Neveux,&nbsp;Mohammad Esmaïl Alikhani","doi":"10.1007/s00894-024-06163-0","DOIUrl":"10.1007/s00894-024-06163-0","url":null,"abstract":"<div><h3>Context</h3><p>The nature of double intermolecular proton transfer was studied with the ELF topological approach in two model dimers (the formic acid homodimer and the 1,2,3-triazole–guanidine heterodimer) under an oriented external electric field. It has been shown that each of the two dimers can have either a one-step (one transition state structure) or two-step (two transition state structures) reaction path, depending on the intensity and orientation of the external electric field. The presence of a singularly broad shoulder (plateau in the case of homodimer and plateau-like for heterodimer) around the formal transition state structure results from the strong asynchronicity of the reaction. A careful ELF topological analysis of the nature of protons, hydride (localized) or roaming (delocalized) proton, along the reaction path allowed us to unambiguously classify the one-step mechanisms governing the double-proton transfer reactions into three distinct classes: (1) concerted-synchronous, when two events (roaming proton regions) completely overlap, (2) concerted-asynchronous, when two events (roaming proton regions) partially overlap, and (3) two-stage one-step non-concerted, when two roaming proton regions are separated by a “hidden intermediate region”. All the structures belonging to this separatrix region are of the zwitterion form.</p><h3>Methods</h3><p>Geometry optimization of the stationary points on the potential energy surface was performed using density functional theory—wB97XD functional—in combination with the 6–311+ +G(2d, 2p) basis set for all the atoms. All first-principles calculations were performed using the Gaussian 09 quantum chemical packages. We also used the electron localization function (ELF) to reveal the nature of the proton along the reaction path: a bound proton (hydride) becomes a roaming proton (carrying a tiny negative charge ≈ 0.3 e) exchanging with two adjacent atoms via two attractors (topological critical points with (3, − 3) signature). The ELF analyses were performed using the TopMod package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}