Journal of Molecular Modeling最新文献

Context

Single-wall carbon nanotubes (SWCNT) dispersed in water with the help of sodium dodecyl sulfate (SDS) surfactants exhibit a temperature dependent near infrared (NIR) exciton spectrum. Due to their biocompatibility and NIR spectrum falling within the transparent window for biological tissue, SWCNTs hold potential for sensing temperature inside cells. Here, we seek to elucidate the mechanism responsible for this temperature dependence, focusing on changes in the water coverage of the SWCNT as the surfactant structure changes with temperature. We compare optical absorption spectra in the UV–Vis-IR range and fully atomistic molecular dynamics (MD) simulations. The observed temperature dependence of the spectra for various SWCNTs may be attributed to changes in the dielectric environment and its impact on excitons. MD simulations reveal that the adsorbed SDS molecules effectively shield the SWCNT, with ~ 70% of water molecules removed from the first two adlayers; this coverage shows a modest temperature dependence. Although we are not able to directly demonstrate how this influences the NIR spectrum, this represents a potential pathway given the strong influence of the water environment on the excitons in SWCNTs.

Methods

Optical absorption measurements were carried out in the UV–Vis-NIR range using a Varian Cary 5000 spectrophotometer in a temperature-controlled environment. PeakFit™ v. 4.06 was used as peak-fitting program in the spectral range 900–1400 nm (890–1380 meV) as a function of the temperature. Fully atomistic molecular dynamics simulations were conducted using the NAMD2 package. The CHARMM force field comprising two-body bond stretching, three-body angle deformation, four-body dihedral angle deformation, and nonbonded interactions (electrostatic and Lennard–Jones 6–16 potentials) was employed.

Context: The mechanisms for the formation of the first C - C bond and lower olefins on methanol to olefins (MTO) conversion on H-ZSM-5 had been focused in dispute. In this paper, density functional theory has been used to study the reaction mechanisms of methanol to olefins on ZSM-5. The configurations of reactants, intermediates, products and transition state of the numerous reactions involved in such a process have been optimized, as well as the elementary reactions related to these configurations were determined by the calculation of corresponding activation energy barriers and reaction heats. Here, two different kinds of the mechanisms were proposed for the formation of dimethyl ether (DME), one involving an associative interaction of two methanol molecules with the zeolite Brønsted acid sites and the other occurring via a surface methoxy species and a methanol molecule. A critical intermediate of the methoxy methyl cation was theoretically verified by the reaction of the methoxy species and dimethyl ether. Besides, it was found that the first intermediates containing a C - C bond were 1,2-dimethoxyethane and 2-methoxy-ethanolare, in which the former was formed from methoxy species with dimethyl ether and the latter was formed from methanol by onium ions((CH₃)₂O⁺CH₂CH₂OCH₃), respectively. For the whole reaction mechanism, the results in this paper indicated that the ethene formation is more favorable than propylene formation due to the low activation energy barrier for ethene formation (123.49 vs. 162.09 kJ.mol^-1). From these calculations, it would be concluded that ethene is the first alkene product that induces the occurrence of the hydrocarbon pool mechanism.

Methods: All the periodic density function theory (DFT) calculations were performed by the Vienna Ab Initio Simulation package (VASP). The interaction between nucleus and valence electron was described using the pseudopotentials found in the projector augmented wave (PAW) method. PBE-D3 was used in the whole DFT calculations and CI-NEB was used to locate transition state.

Context

Nonlinear optics (NLO) is an interesting field that discloses the interaction between intense light and matter, leading to a deeper understanding of NLO phenomena. Organic chromophores are considered as promising materials for NLO due to their exceptional structural versatility, ease of processing, and rapid response to NLO effects. Functional materials based on thiophene have been indispensable in advancing organic optoelectronics. Specifically, dithiophene-based compounds display weaker aromaticity, reduced steric hindrance, and additional sulfur–sulfur interactions. Hence, by utilizing dithieno[2,3-d:2′,3′-d′]benzo[1,2-b:4,5-b′]dithiophene (DTBDT) as the core structure, designing of a set of organic compounds with D1–π–D2–π–A-type framework, namely ZR1D1–ZR1D8, was carried out in this study. The analysis of frontier molecular orbitals (FMOs) revealed that compound ZR1D2 has the lowest band gap of 1.922 eV among all the investigated chromophores. The correlation of global reactivity parameters (GRPs) with the band gap values indicates that ZR1D2 displays a hardness of 0.961 eV and a softness of 0.520 eV⁻¹. Among the studied compounds, ZR1D2 demonstrated a broad absorption spectrum that extended across the visible region. The maximum absorption wavelengths were observed at 766.470 nm for ZR1D2 and 749.783 nm for ZR1D5. These DTBDT-based dyes exhibit a remarkable NLO response with exceptionally high first hyperpolarizability (β_tot) values. Among them, compound ZR1D2 stands out with the highest average linear polarizability (⟨α⟩ = 3.0 × 10⁻²² esu), first hyperpolarizability (β_tot = 4.1 × 10⁻²⁷ esu), and second hyperpolarizability (γ_tot = 7.5 × 10⁻³² esu) values. In summary, this investigation offers valuable insights into the potential use of DTBDT-based organic chromophores, particularly ZR1D2, for advanced applications in NLO. These findings suggest promising opportunities for researchers to synthesize these molecules and utilize these compounds in hi-tech NLO-based applications.

Methodology

The density functional theory computations were performed at the M06/6-311G(d,p) functional to explore their structural effects on electronic and NLO findings. Various analyses like highest occupied molecular orbital–lowest unoccupied molecular orbital energy gaps, absorption maxima, density of states, open circuit voltage, binding energies of electrons and holes, and transition density matrix are employed to investigate photovoltaic efficiencies of the derivatives. Different software packages like Avogadro, Multiwfn, Origin, GaussSum, PyMOlyze, and Chemcraft were used to deduce conclusions from the output files.

Context: One of the crucial issues related to machine learning potentials is the formation of representative dataset. For multicomponent systems, it is a general methodology to scan the composition range with a certain step. However, there is a lack of information on the compositional transferability of machine learning potentials. In this paper, we extend the knowledge in this area by studying the transferability of deep learning potential over the range of compositions of LiCl-KCl molten mixtures. The training dataset was formed using only the near-eutectic composition of 60% LiCl-40% KCl. Then, we tested the ability of the model to predict physicochemical properties of the melts far from the reference composition. It was found that for the composition range from 0 to 100% of LiCl, the calculated properties concur closely with those of other studies and ab initio calculations. Therefore, the model shows prominent non-intuitive compositional transferability. Moreover, the solid states and solid-liquid coexistence were reproduced. The calculated melting temperatures of LiCl and KCl show the errors of 6.6% and 0.4%, respectively. We argue that such good transferability stems from the local structure configurations that are typical both for pure LiCl and for pure KCl which are implicitly presented in the training dataset because of local fluctuations in composition.

Methods: To collect the data for the initial dataset, density functional theory was employed. Then, the DeePMD package was used to train a neural network potential. To calculate the properties of the melts, standard equilibrium and non-equilibrium molecular dynamic approaches were utilized.

Context: This work reports structure-property correlations of 27 zwitterions Reichardt's types of zwitterions. Focuses are twofold, to see the (1) impacts of metamerism with Reichardt's vs Brooker's types of zwitterions and (2) impacts of monocyclic aromatic rings as bridges. All the molecules considered here have pyridinium (common acceptor: A) and p-phenylene-dicyanomethanide (common donor: D). Fundamental molecular properties like dipole moments (μ), polarizabilities (α), hyperpolarizabilities (β), and adiabatic absorptions were computed only for the Reichardt types and compared with the literature reported respective Brooker's types of zwitterions. As an impact of metamerism, in general 2-3 times enhanced hyperpolarizabilities (β) were observed for Reichardt's compared to Brooker's types. Exceptions were observed with some triazine bridges and furan bridge, where Brooker's types were found to be more efficient. As impacts of aromatic bridges, in general, 6-sevenfold enhanced β compared to well-known traditional bridges and enhanced β were observed compared to D-A directly connected zwitterion (benzene bridge: sixfold enhanced β). Current findings show that the aromatic bridge control with Reichardt's types of zwitterions is more efficient and thus may be employed as an effective strategy for the designing of functional molecular chromophores for various other fundamental areas.

Methods: All computations were performed with Gaussian 09. Geometry optimizations and computations of fundamental properties were carried out with HF, B3LYP, CAM-B3LYP, and ωB97xD methodologies, with 6-31G(d,p) and aug-cc-pVDZ basis sets. For adiabatic excitations, computations were carried out using TDDFT and TDHF approaches. For the computations of the response properties (like the nonlinear optical responses), CPHF approach was used.

Context: The theoretical study investigates the [3 + 2] cycloaddition (32CA) reactions between C, N-diphenyl nitrilimine with 2,3,4,5-tetraphenylcyclopentadienone and benzonitrile oxide with 2,3,4,5-tetraphenylcyclopentadienone. Nitrilimines and nitrile oxides are dipoles used in the synthesis of several heterocyclic compounds, including spiropyrazoline oxindoles and isoxazolines. The derivatives of these compounds are found with different biological activities, such as ion channel blockers, anti-inflammatory and anticancer agents as well as antimalarial. Conceptual density functional theory (CDFT) analysis, along with the activation energies of the 32CA reaction between C, N-diphenyl nitrilimine with 2,3,4,5-tetraphenylcyclopentadienone, demonstrates concordance with the empirical findings. The 32CA reaction is found to proceed through a very polar single-step asynchronous mechanism. While deductions from the activation energies of the 32CA reaction between benzonitrile oxide and 2,3,4,5-tetraphenylcyclopentadienone are found to lead to the experimental product, the parr function analysis could not explain the observed chemo- and regioselectivity. This 32CA reaction is also found to proceed through a one-step asynchronous mechanism, though with a non-polar character. The modulation of substituents positioned at the reactive sites of the reactants is found to influence the kinetics, thermodynamics, and CDFT parameters of the two 32CA reactions, consequently impacting the observed selectivities.

Methods: The 32CA reactions between C, N-diphenyl nitrilimine with 2,3,4,5-tetraphenylcyclopentadienone and benzonitrile oxide with 2,3,4,5-tetraphenylcyclopentadienone have been explored theoretically using the density functional theory method at the hybrid ωB97X-D coupled with the split valence triple-ξ (TZ) basis set as implemented in the Gaussian 09. Solvent effects were taken into account by full optimization of the gas phase geometries through the polarizable continuum model developed within the self-consistent reaction field.

Context: In this study, we detail the synthesis and crystallographic characterization of an unprecedented structure, specifically hypoxanthinium chloride monohydrate ((I) hereafter), which crystallizes in the monoclinic P2₁/c space group. A comparative analysis was conducted with four related hypoxanthinium salts: hypoxanthinium bromide monohydrate (II), 9-methylhypoxanthinium chloride monohydrate (III), hypoxanthinium nitrate monohydrate (IV), and hypoxanthinium perchlorate monohydrate (V). This analysis has focused mainly on their crystal packing, hydrogen-bonding networks, and non-classical intermolecular interactions, as elucidated by comprehensive Hirshfeld surface and topological analyses. Theoretical investigation of the nonlinear optical (NLO) properties of the hypoxanthinium derivatives (I-V) was performed using the Density Functional Theory (DFT).

Methods: The crystalline environment was simulated using the iterative Supermolecule method (SM), and the static and dynamics linear refractive index, linear polarizability, second-order hyperpolarizability, and the third-order nonlinear susceptibility at the DFT/CAM-B3LYP/6-311++G(d,p) level were computed. The results for the macroscopic third-order nonlinear susceptibility of (II) was found to equal ${{\chi }^3=0.81\times 10}^{-20}{m}^2/V^2$ . By replacing the bromine atom in (II) with a chlorine atom as in (III), the ${\chi }^3$ value will be multiplied by 2.16, and therefore these results are large enough to suggest the potential application of these crystals as NLO materials.

Context: Although the crystallization of monosodium urate monohydrate (MSUM) has a crucial role in the occurrence of gout, which is an inflammatory arthritis disease, theoretical models have not been able to describe all features observed in its seeded growth kinetics. In contrast to previous modeling approaches, we show that our model can reproduce qualitative features typically observed in experiments. In particular, our results show that the higher the initial supersaturation and the lower the viscosity, the faster the crystallization kinetics, and they also indicate that there are distinct growth regimes for low and high concentrations of seeds.

Methods: In this work, we introduce an alternative approach based on a master equation that allows us to incorporate hypotheses for the seeded growth crystallization of MSUM in a more transparent way. Such an approach includes not only effects that are related to the finite time-dependent supersaturation and concentration of seeds, but it can also be used to determine how the viscosity of the solution can affect the crystallization kinetics of MSUM molecules.

Context: This study investigates the ethylene insertion reaction mechanism for polymerization catalysis, aiming to discern differences between Ni-α-imine ketone-type catalyst and their SiO₂-supported counterpart. The reaction force analysis unveils a more intricate mechanism with SiO₂ support, shedding light on unexplored factors and elucidating the observed lower catalytic activity. Furthermore, reactivity indexes suggest earlier ethylene activation in the supported catalyst, potentially enhancing overall selectivity. Finally, the reaction electronic flux analysis provides detailed insights into the electronic activity at each step of the reaction mechanism. In sum, this study offers a comprehensive understanding of the ethylene insertion reaction mechanism in both molecular and supported catalysts, underscoring the pivotal role of structural and electronic factors in catalytic processes.

Methods: Density functional theory (DFT) calculations were conducted using the ωB97XD functional and the 6-31 + G(d,p) basis sets with Gaussian16 software. Computational techniques utilized in this study encompassed the IRC method, reaction force analysis, and evaluation of electronic descriptors such as electronic chemical potential, molecular hardness, and electrophilicity reactivity indexes. Additionally, reaction electronic flux analysis was employed to investigate electronic activity along the reaction coordinate.