Journal of Molecular Modeling最新文献

Context

Single-atom catalytic systems constitute an intriguing research topic due to their inherently different chemical behavior as compared to classic heterogeneous catalysts. In this study, cluster systems representing single late transition metal atoms adsorbed on anatase were constructed starting from previously generated periodic models and subjected to a density functional theory (DFT) benchmark study. The ability of different density functional approximations representing all rungs of the Jacob’s Ladder classification to accurately describe bond lengths and adsorption energies was assessed for these clusters with the aim of revealing the functional that allows to retain the structural characteristics of the initial periodic system, while also delivering reliable energetics. In this regard, our results indicate that optimisation of the clusters with the meta-GGA functionals TPSS or RevTPSS provides the lowest mean unsigned error and root-mean-square deviations with respect to the periodic models. Moreover, these functionals and, to a slightly lesser degree, PW91 were also found to provide adsorption energies that are statistically the least deviating from the CCSD(T) reference data. More complex hybrid functionals appear to be performing less well.

Methods

Cluster geometries were determined at the Kohn–Sham DFT level using the LANL2DZ basis set for the transition metals and the Pople 6-31G(d) basis set for O and H. The density functional approximations considered were SVWN, PBE, BP86, BLYP, PW91, TPSS, RevTPSS, M06L, M11L, B3LYP, PBE0, M06, M06-2X, MN15, ωB97X-D, CAM-B3LYP, M11, and MN12-SX. Reference adsorption energies of the metals on the support cluster were obtained at the CCSD(T)/LANL2TZ (transition metals)/6–311 +  + G(d,p)//RevTPSS/LANLD2DZ (transition metals)/6-31G*. Besides the above-mentioned functionals, energy calculations using the double-hybrid functionals, DSDPBEP86, PBE0-DH, and B2PLYP, were also performed. All adsorption energy calculations were carried out on the RevTPSS geometries.

Context

Describing chemical processes at solid–liquid interfaces as a function of a fixed electron chemical potential presents a challenge for electronic structure calculations and is essential for understanding electrochemical phenomena. Grand Canonical Density Functional Theory (GCDFT) allows treating solid–liquid interfaces in such a way that studying the influence of a fixed electron potential arises naturally. In this work, GCDFT is used to compute the adsorption grand potential (AGP), a key parameter for understanding and predicting the behavior of adsorbates on surfaces. We focused on the adsorption of an OH molecule on three metallic surfaces commonly used in electrochemical processes, such as the oxygen evolution reaction (OER). Our study aims to offer insights into how AGP can be used to compare adsorption strengths under different fixed electron chemical potentials, which is crucial for designing efficient electrode materials. By determining the average number of electrons self-consistently under varying chemical potentials, we showed how one can distinguish between electron acquisition and depletion during the adsorption process, offering a deeper understanding of the adsorbate–surface interactions.

Methods

The approach used in this work employs the Kohn–Sham-Mermin formulation of the Grand Canonical Density Functional Theory. The computations were performed using the periodic open-source density functional theory software, JDFTx, with the Garrity-Bennett-Rabe-Vanderbilt library of ultrasoft pseudopotentials. Calculations were made using truncated Coulomb potentials and the auxiliary Hamiltonian method with the PBE exchange–correlation functional, along with DFT-D2 long-range dispersion corrections. The implicit solvation model CANDLE was used to describe the electrolyte with a 1 M concentration.

Context

The human body contains many different types of transition metal ions, such as Zn²⁺, Cu²⁺, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn²⁺, Cu²⁺, Fe²⁺, and Mn²⁺ and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn²⁺ is combined with two C’s of the benzene ring, Cu²⁺ with four C’s of the benzene ring, and Fe²⁺ and Mn²⁺ with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu²⁺(-294.9 kcal/mol) > Zn²⁺(-261.3 kcal/mol) > Fe²⁺(-247.5 kcal/mol) > Mn²⁺(-220.2 kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O.

Methods

Several initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe.

Context

The 2,4-dioxo-4-phenylbutanoic acid (DPBA) is a subject of interest in pharmaceutical research, particularly in developing new drugs targeting viral and bacterial infections. Complexation with metal ions can improve the stability and solubility of organic compounds. The present study uses quantum chemical calculations to explore the structural and electronic results arising from the interaction between the metal cation (Fe²⁺) and the π-system of DPBA in different solvents. For this purpose, the analyses of atoms in molecules (AIM) and natural bond orbital (NBO) are employed to comprehend the interaction features and the charge delocalization during the process of complexation. The results demonstrate that the strongest/weakest interactions are evident when the complex is situated in non-polar/polar solvents, respectively. In addition, the investigated complex exhibits two intramolecular hydrogen bonds (IMHBs) characterized by the O–H···O motif. The results indicate that the HBs present in the complex fall within the category of weak to medium HBs. Moreover, the O–H···O HBs are influenced by cation–π interactions, which can increase/decrease their strength in polar/non-polar solvents. To enhance understanding of the interactions above, an examination is conducted on various physical properties including the energy gap, electronic chemical potential, chemical hardness, softness, and electrophilicity power.

Method

All calculations are conducted within the density functional theory (DFT) using the ωB97XD functional and 6–311 +  + G(d,p) basis set. The computations are performed using the quantum chemistry package GAMESS, and the obtained results are visualized by employing the GaussView program.

Context

Screening of cocrystals of active pharmaceutical ingredients is important in the development of pharmaceutical compounds because it improves bioavailability, stability, solubility, and many other physicochemical properties. In this work, quantum chemical calculations were utilized for the computational evaluation of the cocrystal screening of benznidazole (BZN) API via hydrogen bonding with four coformers (maleic acid, malonic acid, oxalic acid, and salicylic acid), and they contain carboxylic groups. The nitrogen of the imidazole ring in benznidazole and the carboxylic group of the coformer form a hetero-synthon connected by a strong hydrogen bond. The strength of the hydrogen bonding interaction O–H…N was measured using various tools. It was found that in comparison to BZN cocrystals with malonic acid, oxalic acid, and salicylic acid, the O–H…N interaction in the BZN-maleic acid cocrystal had higher interaction energy, indicating it had stronger hydrogen bonding. The strength of the hydrogen bond O–H…N for synthons was discovered to be more beneficial than the C–H…O interaction, as confirmed by ESP analysis. The BZN-salicylic acid cocrystal was found to be more reactive and polarizable, whereas the BZN-malonic acid cocrystal was more stable. Cocrystals of benznidazole exhibited better physicochemical characteristics than API benznidazole, as indicated by electron transition properties between the most significant orbitals.

Methods

The computational evaluation for the screening of benznidazole cocrystals was performed in Gaussian 16 software using density functional theory (DFT) with the hybrid functional B3LYP and the basis set 6–311 +  + G(d,p). The UV–Vis absorption spectrum in solvent water was analyzed using the TD-DFT/6–311 +  + G(d,p) method to determine the influence of the solvent in cocrystals using a polarizable continuum model. The strength of the hydrogen bonding interactions O–H…N in each of those mentioned cocrystals was used to screen the cocrystals using tools such as thermodynamic probability, ESP analysis, QTAIM analysis, and NBO analysis. The pairing energy of interaction was measured by determining H-bond donor (({alpha }_{text{max}})) and H-bond acceptor ({(beta }_{text{max}})) parameters for hydrogen bonds from maxima and minima on the ESP surface. GaussView 06 software was used to create, visualize, and plot the optimized structure of the cocrystal and HOMO–LUMO orbitals. The AIMALL (10.05.04) software package generated the molecular graph for intra- and intermolecular interactions. The RDG-scatter plot, MEP map, and ELF plot were rendered from Multiwfn 8.0 and VMD 1.9.1 software.

Context

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.

Methods

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.

Context

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 ΔG of ursolic acid in complex with BRAFV600K (− 63.31 kcal/mol) is comparable to the ΔG of the selective inhibitor dabrafenib (− 63.32 kcal/mol) in complex to BRAFV600K and presents a ΔG 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.

Methods

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.

Graphical Abstract

Context

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.

Methods

Reaction profiles (V(xi )), (F(xi )), and (kappa (xi )) 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.

Context

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.

Methods

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.

Context

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.

Methods

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.