PCM Model Research Articles

Hydrated Magnesium Ion-Uracil and Magnesium Chloride-Uracil Clusters Revealed by Ab Initio Study.

The study focuses on the interaction between canonical uracil and its rare tautomers with Mg2+ and MgCl2 in the microcosmic water environment and aims to elucidate how ions interact with nucleobase and the cation-anion correlation effect involved using density functional theory calculations. The structures of the Ura-Mg2+(H2O)0-6 and Ura-MgCl2(H2O)0-6 clusters are characterized and show that the water molecules preferentially interact with Mg2+/MgCl2, and Mg2+ adopts a hexacoordination pattern in both Ura-Mg2+(H2O)0-6 and Ura-MgCl2(H2O)0-6 clusters. When uracil interacts with Mg2+ in (H2O)0-6 environments, it tends to favor the formation of keto-enol structures. However, in the presence of Cl- cooperating with Mg2+, the Ura-MgCl2(H2O)0-6 complexes prefer to form diketo structures. The proton transfer mechanism shows that the initial solvation can promote the change from the keto-enol structure to the diketo structure, which is strengthened by the analysis of the Ura-Mg2+(H2O)6 and Ura-MgCl2(H2O)6 structures in the aqueous phase using the PCM model. Additionally, reduced density gradient, atom in molecules, and energy decomposition analysis combined with charge transfer analysis were carried out to obtain the variation law of the interactions between Mg2+ and Ura with the water number increasing, thereby revealing the interaction mechanism of uracil with magnesium ion and the effect of Cl- on the interaction between Mg2+ and uracil.

Hydrogenation of hexene catalyzed by a ruthenium (II) complex with N‐heterocyclic carbene ligands

AbstractIn this study, we investigated the mechanism of the inactivated hexene hydrogenation reaction catalyzed by a ruthenium (II) complex containing “N‐heterocyclic carbene” (NHC) ligands, specifically SIMes and CBA, using DFT calculations. Our focus was on RuH(OSO2CF3)(CO)(SIMes)(CBA), which exhibits excellent catalytic behavior. We tested the B3LYP‐D3, cam‐B3LYP, and TPSSh functionals. The hydrogenation reaction is initiated by the release of SIMes rather than CBA due to the lower associated dissociation energy. Our findings indicate a reaction mechanism consisting of two consecutive steps, each involving one hydrogen atom migration. The first step, considered as the kinetically limiting transition state, exhibits a Gibbs free activation barrier of 12.9 kcal mol−1. This step involves two asynchronous processes. The first one describes the migration of the ruthenium hydride to the internal carbon of the olefine function, transitioning from π to σ coordination mode, which promotes the formation of a bond between ruthenium and the terminal olefinic carbon. The second process involves the oxidation of ruthenium from Ru(II) to Ru(IV). This oxidation is crucial as it enables the decomposition of the H2 molecule into two hydrogen atoms bonded to the ruthenium atom. The geometrical structures of the Hidden Reaction Intermediate Ru(II) complex and the quasi‐transition state of the second process have been determined by means of the RIRC technique. The second step entails the migration of one of the newly formed hydrides of the Ru(IV) complex to the terminal olefinic carbon, resulting in the release of hexane with a weak activation Gibbs free energy of .8 kcal mol−1. Lastly, we explored the use of dichloromethane as a solvent, considering the PCM model. The presence of the solvent significantly decreases the energy dissociation of SIMes from 17.9 to 9.0 kcal mol−1, providing notable benefits.

Quantum chemical framework for designing high-performance ladder-shape NLO molecules and study of implicit vs explicit solvent effects on their NLO properties

Researchers in materials science are greatly fascinated by helicene chemistry due to its excellent optical and structural properties. In this work, we introduced symmetrical substitution of donor and acceptor groups on the [7]helicene ([7]HC-1 to [7]HC-5). DFT analysis is used to explore nonlinear optical (NLO) response for designed compounds. For [7]HC-5, the linear isotropic (αiso) and anisotropic polarizability (αaniso) are 31.59 × 10−24 esu and 59.86 × 10−24 esu, respectively. [7]HC-5 has the highest average third-order NLO polarizability (<γ>) of 47.24 × 10−36 esu which is approximately six times greater than that of para-nitroaniline, a well-known prototype NLO molecule. The effect of implicit and explicit solvents on <γ> and αiso of three selected compounds ([7]HC-1, [7]HC-3, and [7]HC-5) is also evaluated. As compared to explicit and gas phase methods, PCM model predicts an overestimation by an increment of ∼ 4-5 times for selected compounds. TD-DFT calculations show a higher transition dipole moment (4.24) and a lower transition energy (3.414 eV) for [7]HC-5. The higher NLO response is explained based on frontier molecular orbitals (FMOs), electron density difference (EDD), and molecular electrostatic potentials (MEPs). There is a red shift for studied compounds based on UV-visible results. The C-N stretching at 1372 cm-1 for [7]HC-5 indicates the presence of -N(CH3)2. Additionally, we studied photovoltaic parameters and found that [7]HC-5 has the maximum open circuit voltage and the lowest dye regeneration of 2.71 eV and 0.06 eV, respectively.

Optical Rotation Predictions for Rigid Chiral Solute-Achiral Solvent 1:1 Complexes with the PCM Model

We computed specific optical rotations (ORs) in solution for forty-two solute–solvent combinations, involving seventeen chiral solutes and eight achiral solvents, using cam-B3LYP/aug-cc-PVTZ. Explicit solvent effects were considered by calculating Boltzmann-averaged ORs from multiple conformers of a 1:1 solute–solvent complex, with additional implicit solvation. The PCM solvation model correctly predicted OR signs for all combinations, while the “1:1 complex plus PCM“ schemes misjudged it in two cases. Norbornenone in cyclohexane displayed the largest absolute deviation, indicating an inadequate description of the cam-B3LYP functional’s delocalized electronic structure. Incorrect OR signs for fenchone in methanol with the ”1:1 complex plus PCM“ schemes underscored the limitations of our simplistic scheme, which incorporates explicit effects by averaging one-to-one interactions between solute and solvent. Considering computational costs, the ”1:1 complex plus PCM“ scheme may not be the optimal choice for our test set, as the PCM model alone suffices for accurate specific OR calculations in solution.

A comparative analysis on charging performance of triplex-tube heat exchanger under various configurations of composite phase change material

In present work, the melting performance of triplex-tube latent heat thermal energy storage (LHTES) unit was numerically studied using equal volumes of PCM and metal foam composite PCM (CPCM) in various arrangements. For the n-eicosane (as PCM), the study was conducted at the fixed Rayleigh number (Ra) = 4.08x107, Prandtl number (Pr) = 62.9, and Stefan number (Ste) = 0.14. The results showed that positioning the metal foam on the bottom side and distributing segmented CPCM with alternating PCM zones effectively improved the system performance. Moreover, this also prevents the overheating of thermal layers in the LHTES unit. While the model labelled M2 exhibited the highest economic efficiency among all isotropic models, its low dimensionless thermal energy storage (TES) density (i.e., q’ ∼ 0.6) led this study to focus on models falling under the category having a TES density of ∼ 0.8. Compared to a pure PCM model, the configurations under equal volume ratio category demonstrated up to ∼ four times higher TES rate (p’) and the significant reduction of ∼ 75 % in melting time. The optimized isotropic model achieved the highest TES rate per unit cost with peak value of ∼ 3 at a price ratio (N) of 1. Lastly, the testing of metal foam anisotropy on the chosen design showed a substantial increase in melting/heat storage rates. The largest drop of ∼ 33 % in the total melting time was noticed for model M2 as compared to isotropic case.

Study of six coordinated cobalt(III) oxophlorin with different axial ligands: Optimization of geometry and determining of energy and electronic configuration at various spin states by employing of B3LYP, BV86P and M06-2X methods

The six coordinated CoIIIoxophlorin have been studied with imidazole, pyridine and t-butylcyanide as axial ligands using B3LYP, BV86P and MO6-2X methods. Conversion between two isomers [(L)2CoIII(PO)][Formula: see text] and [(L)2CoIII(PO)][Formula: see text] can be occurred at various spin multiplicities, namely singlet, triplet and quintet states. L is employed to show axial ligand namely, imidazole or pyridine. London forces have a basic role in the stability of the mentioned complexes due to non-specific solvent effects. The latter fact has been obtained using the PCM model. Also, it is specified that minimum geometries have not been obtained for some parallel or perpendicular six-coordinated complexes with special axial ligands at a finite spin state. The B3LYP method indicates that one and three [Formula: see text]-electron can be found on the Co atom in every optimized complex at triplet and quintet spin states, respectively. Also, another [Formula: see text]-electron is placed on the ring of oxophlorin. This fact is obtained for different isomers of [(IM2(CoIII(PO)] and [(Py)2CoIII(PO)] at triplet and quintet spin states, while these complexes are optimized using B3LYP. Besides, results obtained from B3LYP show that the most stable state for six coordinated CoIIIoxophlorin with any axial ligand is the singlet state. Based on crystal field theory and molecular orbital theory, electron configuration and hybridization of cobalt in [(IM)2CoIII(PO)] at singlet state can be written as t2g6 eg0 and sp3d2, respectively. Former electronic configuration indicates a strong field with low spin for d orbitals of cobalt, and latter hybridization is expected for a metal with a coordination number of 6 in a complex with Oh symmetry. The results obtained are completely satisfied by NBO analysis.

Parameterization of the IEF PCM model for calculating solvation energies in N-methylpyrrolidone solution

ABSTRACT Theoretical modelling of N-methylpyrrolidone (NMP) solutions, using a polarisable continuum model (IEFPCM), has been carried out with the aim to find the optimal value of a model parameter, a so-called scaling factor (α) for NMP, which should afford an improved modelling of various N-methylpyrrolidone solutions. Our working protocol comprised evaluations of the Gibbs free energy for the dissociation reaction of a set of 22 acids, employing the B2PLYP-D2/6–311+G**//B3LYP/6–31+G* approach, which were then used to calculate the acidity indices by considering the solvation energy at various values of α within the IEFPCM model. The optimal value of α for the N-methylpyrrolidone solvent has been found to amount to 1.40.

Solvation energies of the ferrous ion in water and in ammonia at various temperatures.

The solvation of metal ions is crucial to understanding relevant properties in physics, chemistry, or biology. Therefore, we present solvation enthalpies and solvation free energies of the ferrous ion in water and ammonia. Our results agree well with the experimental reports for the hydration free energy and hydration enthalpy. We obtained [Formula: see text]kJ mol[Formula: see text] for the hydration free energy and [Formula: see text]kJ mol[Formula: see text] for the hydration enthalpy of ferrous ion in water at room temperature. At ambient temperature, we obtained [Formula: see text]kJ mol[Formula: see text] as the [Formula: see text] ammoniation free energy and [Formula: see text]kJ mol[Formula: see text] for the ammoniation enthalpy. In addition, the free energy of solvation is deeply affected when the temperature increases. This pattern can be attributed to the rise of entropy when the temperature rises. Besides, the temperature does not affect the ammoniation enthalpies and the hydration enthalpy of the [Formula: see text] ion. All the geometry optimizations are performed at the MP2 methods associated with the 6-31++g(d,p) basis set of Pople. solvated phase structures of [Formula: see text] ion in water or in ammonia are performed using the PCM model. The [Formula: see text] program suite was used to perform all the calculations. The program TEMPO was also used to evaluate the temperature sensitivity of the different obtained geometries.

Modeling and characterization of lenalidomide-loaded tripolyphosphate-crosslinked chitosan nanoparticles for anticancer drug delivery

Tripolyphosphate-crosslinked chitosan (TPPCS) nanoparticles were employed in the encapsulation of lenalidomide (LND) using a straightforward ionic cross-linking approach. The primary objectives of this technique were to enhance the bioavailability of LND and mitigate inadequate or overloading of hydrophobic and sparingly soluble drug towards cancer cells. In this context, a quantum chemical model was employed to elucidate the characteristics of TPPCS nanoparticles, aiming to assess the efficiency of these nanocarriers for the anticancer drug LND. Fifteen configurations of TPPCS and LND (TPPCS /LND1-15) were optimized using B3LYP density functional level of theory and PCM model (H2O). AIM analysis revealed that the high drug loading capacity of TPPCS can be attributed to hydrogen bonds, as supported by the average binding energy (168 kJ mol−1). The encouraging theoretical results prompted us to fabricate this drug delivery system and characterize it using advanced analytical techniques. The encapsulation efficiency of LND within the TPPCS was remarkably high, reaching approximately 87 %. Cytotoxicity studies showed that TPPCS/LND nanoparticles are more effective than the LND drug. To sum up, TPPCS/LND nanoparticles improved bioavailability of poorly soluble LND through cancerous cell membrane. In light of this accomplishment, the novel drug delivery route enhances efficiency, allowing for lower therapy doses.

Integration and Validation of A Numerical Pcm Model For Building Energy Programs

Integration and Validation of A Numerical Pcm Model For Building Energy Programs

Molecular docking and dynamic simulations of 2-phenoxyaniline and quantum computational, spectroscopic, DFT/TDDFT investigation of electronic states in various solvents

2-phenoxyanline was thoroughly examined using several spectroscopy nuclear magnetic resonance, IR, UV–vis, and quantum mechanical methodologies. D F T with basis set is employed to determine structural optimization and distinct vibration modes. The optimum binding parameters agree closely with the observed binding characteristics. VEDA performed the duties relating to potential energy distribution (PED) satisfactorily. The G I A O approach was adopted to compute chemical shifts in the 13C, 1H- N.M.R and the outcomes were compared to experimental spectra. TD-DFT with PCM model was used to calculate UV–vis with different solvents that, when assessed against observational spectra. The FMO energy provides sufficient proof of such. Molecular docking and dynamic simulations gave a better idea of the interaction of ligands with receptors.

Reactivity of bis(2‐chloroprop‐2‐enyl)sulfide in the system hydrazine hydrate/alkali: A quantum chemical insight

AbstractThe reactivity of bis(2‐chloroprop‐2‐enyl)sulfide in the system hydrazine hydrate/alkali has been studied using quantum‐chemical methods. The B2PLYP‐D2//B3LYP approach shows a good agreement between the relative values of activation barriers compared to high‐precision CBS//Q‐B3. The correction for the entropy change during the transition from the gas phase to the binary solvent hydrazine hydrate is calculated. The IEF PCM model was parameterized for hydrazine hydrate solvent. The studied reaction routes includes (i) a competition between migration of the C=C bond and dehydrochlorination of bis(2‐chloroprop‐2‐enyl)sulfide; (ii) 1,3‐prototropic rearrangements of bis (allenyl)sulfide resulting from a dehydrochlorination; (iii) the possible substitution of sulfur and chlorine atoms with hydrazine. The probable formation of the thiiranium and thiirenium cations formation in the above has also been evaluated.

3,3'-(Phenyl-methyl-ene)bis-(1-ethyl-3,4-di-hydro-1H-2,1-benzo-thia-zine-2,2,4-trione): single-crystal X-ray diffraction study, quantum-chemical calculations and Hirshfeld surface analysis.

The title compound, C27H26N2O6S2, possesses potential anti-microbial, analgesic, and anti-inflammatory activity. This compound has three tautomeric forms, which relative energies were estimated with quantum-chemical calculations. All these tautomers (dienol form 7A, keto-enol form 7B, and diketo form 7C) were optimized by the M06-2X/cc-pVTZ method in a vacuum, using the PCM model with chloro-form and DMSO as solvent. The diketo form of the title compound proved to be the most energetically favourable as compared to the keto-enol or dienol forms. The diketo form can exist as three possible stereoisomers with the same configuration of one stereogenic center and different configurations of the stereogenic centers at two other atoms: ( R , R , R ), (S , R , S ) and ( R , R , S ). The ( R , R , S ) stereoisomer was found in the crystal phase. It was revealed that the thia-zine rings of equivalent benzo-thia-zine fragments have different conformations, (a sofa or a half-chair). The two bicyclic fragments connected through the phenyl-methyl-ene group are oriented almost orthogonal to each other, subtending a dihedral angle of 82.16(7)°.

DFT analysis on the reaction mechanism of Diels-Alder reaction between 2,4-hexane-1-ol and maleic anhydride

Diels Alder reactions are the best method for synthesis of various important molecules. In this work mechanism between maleic anhydride and 2,4-hexadiene-1-ol has been explained by DFT. By using B3LYP method with 6-311G basis set, fukui function, chemical hardness, softness, electrophilicity index, electrochemical potential and thermodynamic properties are calculated. As we vary solvent such as toluene, the gap between product HOMO and LUMO decreases from 0.24 to 0.22 eV in PCM model. Thermodynamic parameters like enthalpy, entropy, internal energy increase by rise in temperature but Gibbs free energy decreases.

Parallel evolution and control method for predicting the effectiveness of non-pharmaceutical interventions in pandemics.

Nonpharmaceutical interventions (NPIs) are important strategies to utilize in reducing the negative systemic impact pandemic disasters have on human health. However, early on in the pandemic, the lack of prior knowledge and the rapidly changing nature of pandemics make it challenging to construct effective epidemiological models that can be used for anti-contagion decision-making. Based on the parallel control and management theory (PCM) and epidemiological models, we developed a Parallel Evolution and Control Framework for Epidemics (PECFE), which can optimize epidemiological models according to the dynamic information during the evolution of pandemics. The cross-application between PCM and epidemiological models enabled us to successfully construct an anti-contagion decision-making model for the early stages of COVID-19 in Wuhan, China. Using the model, we estimated the effects of gathering bans, intra-city traffic blockades, emergency hospitals, and disinfection, forecasted pandemic trends under different NPIs strategies, and analyzed specific strategies to prevent pandemic rebounds. The successful simulation and forecasting of the pandemic showed that the PECFE could be effective in constructing decision models during pandemic outbreaks, which is crucial for emergency management where every second counts. The online version contains supplementary material available at 10.1007/s10389-023-01843-2.

Optoelectronic properties of Portulacaxanthin III (PXIII), GQD/Os-GQD-PXIII nanocomposites, and their coupling with photoanode in dye-sensitized solar cells: Molecular and periodic DFT calculations

In this work, the optoelectronic properties of a naturally occurring dye, Portulacaxanthin III (PXIII), were investigated. To improve the performance of PXIII dye, it was hybridized with graphene quantum dot (GQD) undoped and doped with Os at the central position to form two nanocomposites (PXIII-GQD and Os-GQD-PXIII), and their optoelectronic properties were also investigated. Parameters such as frontier molecular orbital energies and distributions, absorption and emission properties, excited-state lifetimes, and hole and electron reorganization energies were calculated at two molecular (HCTH and CAM-B3LYP) DFT functionals and their counterparts TDDFT functionals in the gas phase and with the PCM model to mimic the effect of the solvent in three solvents: chloroform, acetonitrile, and water. The variation of the abovementioned molecular parameters as a function of media polarities (dielectric constants) was investigated. In addition, the coupling with the photoanode TiO2 anatase (101) with a periodic DFT functional was also investigated. The output from this work demonstrated the better overall performance of the nanocomposites (doped and undoped). Since they have better energy level alignments, red-shifted and broader absorption in the Vis and IR regions, better HOMO and LUMO charge separation, and stronger adsorption on the photoanode.

Vibronic Emission Spectra of Dithiophene and Terthiophene and Their Complexes with H2S and (H2S)2

In this work, the vibronic emission spectra of dithiophene (T2) and terthiophene (T3) molecules and their complexes with hydrogen sulfide and its dimmer were calculated at the TD-DFT / CAM-B3LYP / 6-31G(d) theory level. The solvent was taken into account within the PCM model. Vibronic spectra were calculated considering both the Herzberg-Teller and Duschinsky effects. Good agreement between the computed and experimental spectra was obtained. The vibration promoting modes forming vibronic progressions were found. Vibronic bands for bithiophene and terthiophene were formed by their low-frequency modes (≤370 cm–1), combinations of low-frequency modes with high-frequency modes (1497 and 1672 cm–1 for T2 and 1516 and 1573 cm–1 for T3), and with their composite high-frequency modes. The intensities of vibronic lines for the emission spectra of T2∙∙∙H2S, T3∙∙∙H2S and T2∙∙∙(H2S)2, T3∙∙∙(H2S)2 complexes were shown to decrease 3.7, 2.6 and 5.5, 3.6 times compared to T2 and T3, respectively. The bathochromic shifts of the vibronic bands of dithiophene and terthiophene complexes with H2S and (H2S)2 did not exceed 130 cm–1 for all bands.

Elucidation of the key role of isomerization in the self-assembly and luminescence properties of AIEgens.

Due to the hierarchical nature of the self-assembly process, it is effective to control assembled nanostructures by tuning the spatial configurations of the building blocks through Z-/E-isomerization. A pair of AIE stereoisomers termed (Z)-/(E)-TPE-UPy was reported with different self-assembly mechanisms, morphologies and luminescence properties. In this study, we present a multiscale modeling combining MD simulations, hybrid QM/MM calculations and the PCM model, to systematically clarify the molecular configuration-molecular assembly-photophysical property relationship of (Z)-/(E)-TPE-UPy. Our study shows that (Z)-TPE-UPy follows a concentration-dependent ring-chain polymerization mechanism. At low concentration, (Z)-TPE-UPy tends to form ring-like (Z)-close-dimers with all H-bond sites occupied, while at high concentration, the H-bond backbone in the chain-like structures is more planar and stronger, making the zig-zag chain-like conformations more favorable. For the (E)-isomer, the H-bond backbone is quite planar and rigid, which makes it linearly elongate one-by-one at the whole range of concentrations via the isodesmic polymerization mechanism. (Z)-TPE-UPy oligomers exhibit large flexibility and diverse conformations, leading to sharply enhanced viscosity at high concentration in experiments. Moreover, the fluorescence spectrum of (Z)-/(E)-TPE-UPy aggregate is conformation-dependent and the enhanced emission in the aggregated state is attributed to the restriction of the low-frequency intramolecular rotations of the phenyl rings and the distortion of the CC plane, as well as the reduction of electron-vibration couplings. Our work not only offers valuable insights into the key role of stereoisomerism in assembled morphologies and luminescence properties, but also provides a theoretical basis for the rational design of new building blocks based on stereoisomers.

A Computational Study of the MoO2(acac)2 Catalyzed Epoxidation of Ethylene with Hydrogen Peroxide and t‐Butyl Hydroperoxide

AbstractThe cis‐MoO2(acac)2 catalyzed epoxidation of ethylene by H2O2 or tert‐butyl hydroperoxide (TBHP) was studied by density functional theory at ωB97x–D using the 6‐31G(d,p) and 6‐311G(2d,p) basis sets and the PCM model to include the effect of acetonitril solvation. Three initial MoO2(acac)2⋅H2O2 adducts were identified. An associative pathway with a barrier of 26.7 kcal/mol is favored for H2O2 which inserts first into an acac ligand coordination site of the catalyst. TBHP favors instead a step‐wise mechanism in which a catalyst's Mo=O bond inserts into the oxidant upon which ethylene gets epoxidized by the hepta‐coordinate MoO(OH)(acac)2 (TBHP‐κ2O,O’) intermediate with an activation energy of 33.8 kcal/mol. The reaction barriers for H2O2 and TBHP are both within the typical temperature range (70 °C) used for Mo catalyzed epoxidations. The results indicate that the mechanism depends largely on the nature of the oxidant and the dioxo molybdenum catalysts used.

Solvent Effect on the Chemiluminescence of Acridinium Thioester: A Computational Study.

Chemiluminescent labelling, which is one of the promising procedures of modern immunodiagnostics, is increasingly carried out using acridinium derivatives, an oxidant, and an alkaline aqueous environment. However, the efficiency of the chemiluminescence of luminol or acridinium esters is higher in non-aqueous solvents such as dimethyl sulfoxide or acetonitrile. Therefore, the search for a new environment for the chemiluminescence reaction, especially the one characterized by a higher quantum yield of chemiluminescence, is one of the aims of current research. Using computational methods (DFT and TD DFT with PCM model of solvent), we examined thermodynamic and kinetic data concerning the chemiluminescence and competitive dark pathways. Our results suggest that better characteristics of the chemiluminescence reaction of acridinium thioester are observed in nonpolar solvents, such as methylcyclohexane, n-hexane and n-pentane, than in aqueous media used so far. Further experimental verification is necessary to confirm the possible application of proposed nonpolar solvents in chemiluminescent labelling and hence in immunodiagnostics.