SMD Model Research Articles

DFT investigates the mechanisms of cross-dehydrogenative coupling between heterocycles and acetonitrile

The mechanisms between CH3CN and 1,3-dimethyl-1H-indole, initiated by DCP (dicumyl peroxide), have been studied with the B3LYP-D3 method with def2TZVP basis set for all atoms, and the SMD model was applied to simulate the solvent of acetonitrile. The computational results show that the homolytic process of DCP, catalysed by CuCl or CuI, can decrease the energy barrier, and the recycle procedure of Cu catalyst has been described. Then the Csp3-H activation of CH3CN has been investigated. The introduction of the cyano group is an anti-Markovnikov reaction and region-selectivity would be fulfilled. Localised orbital bonding analysis, localised orbital locator (LOL) isosurfaces, and electron spin density isosurface graphs could be used to interpret the phenomena. The results could provide valuable insights into these types of interactions and related ones. Highlights The homolytic mechanisms of DCP catalyzed by CuCl or CuI are proposed. The anti-Markovnikov's reaction between 1,3-dimethyl-1H-indole and free radical is investigated. Localized orbital bonding analysis, localized orbital locator (LOL) isosurfaces and electron spin density isosurface graphs have been used to interpret the phenomena.

Computational insight into the mechanism and stereoselectivity of cycloaddition between donor-acceptor spirocyclopropane and aldehyde catalyzed by Brønsted acid TsOH.

The mechanism and diastereoselectivity of the cycloaddition reaction between D-A spirocyclopropane and aldehydes, catalyzed by para-toluenesulfonic acid (TsOH) in dichloromethane to produce 2,5-disubstituted tetrahydrofuran-type lignans, have been investigated by density functional theory (DFT) at the M06-2X/6-311+G(d,p)//B3LYP-D3/6-31G(d,p) level combined with the solvation SMD model. Our calculations show that the entire reaction process includes three stages: the activation of the D-A cyclopropane by Brønsted acid, TsOH, the nucleophilic attack of the aldehyde on the spirocyclopropane, and the formation of the final product, 2,5-disubstituted tetrahydrofuran. It was concluded from the conceptual density functional theory (CDFT) reactivity index analysis that aldehydes with electron-rich substituents are more nucleophilic and more favorable for the reaction to proceed. Furthermore, based on the analyses of energetics as well as the noncovalent interaction (NCI) and reduced density gradient (RDG) in the key transition states, the origin of stereoselectivity was revealed to be determined thermodynamically rather than kinetically. The present work explains the experimental phenomenon well, and provides useful theoretical information for the future design of similar reactions.

DFT study on the gold(I)-catalyzed cycloaddition and rearrangement reactions of allene-containing allylic silyl ether.

The DFT calculation at the B3LYP/B3LYP-D3(BJ) level was carried out to explore the reaction mechanism of the synthesis of spirocyclo[4,5]decane skeleton by gold-catalyzed allenyl compounds. The more accurate energy under the CH3CN solvent in the experiment is calculated by the single-point energy of the SMD model. Computational studies have shown that the reaction consists of three main steps: intramolecular cycloaddition of the end group carbon atoms of allenyl and vinyl groups, the semipinacol rearrangement process in which the four-membered ring is reconstructed into the five-membered ring, the elimination reaction releases the catalyst and obtains the product. The calculation results show that Zheng et al. reported that the gold-catalyzed synthesis reaction can easily occur under the experimental conditions due to its low activation free energy (12.07-15.49kcal/mol). Furthermore, it was found that the MOMO(CH2)2 substituent has higher reactivity than the corresponding reactant of the phenyl substituent.

Mechanisms of bromination between thiophenes and NBS: A DFT investigation

Mechanisms for bromination between thiophenes and NBS have been investigated at level of M06-2X-D3/ma-def2-TZVP, and SMD model was taken to simulate the solvent effect of chloroform. The computational results of Gibbs free energy surfaces point out that the paths of forming bromonium ion are favorable. So, Br2 and NBS could provide the source of Br to achieve the bromination process to obtain the final product 2,5-dibromothiophenes. Br2 is trace amount in the reagent of NBS, we speculate that the path with the participation of NBS could happen in large amounts in the reactive system and the path with participation of Br2 could also be occurred in smaller amount. Meanwhile, the relations between the order of forming bromonium ion and energy barriers have been discussed. Fukui function can be used to predict the reactive sites, and frontier orbital theory can analyze the HOMO and LUMO of reactants.

Mechanisms of asymmetric sulfa-Michael additions between phenylacetylene and thiolacetic acid: A DFT investigation

Mechanisms for asymmetric sulfa-Michael additions between phenylacetylene and thiolacetic acid have been investigated with M06-2X-D3/ma-def2-TZVP level, and SMD model was taken to simulate the solvent effect of toluene. The computational results suggest that(E)-S-styryl ethanethioate is the only product, and Gibbs free energy surface points out that the reaction between thiyl radical and terminal carbon atom of phenylacetylene is favorable. The yielded path of S-(1-phenylvinyl) ethanethioatehas a higher barrier and could not happen. Fukui function and dual descriptor can be used to predict the reactive sites, and localized orbital locator isosurfaces and electron spin density isosurface graphs can analyze the structures and reveal the substances.

Mechanisms of Ssp3–H functionalization of thiolacetic acid: A density functional theory investigation

AbstractMechanisms for Ssp3–H functionalization of thiolacetic acid, initiated by AIBN, have been investigated by M06‐2X‐D3/ma‐def2‐TZVP method and basis set, and SMD model was employed to simulate the solvent effect of toluene. The computational results suggest that azodiisobutyronitrile (AIBN), as the radical initiator, would have an intramolecular homolytic reaction; then Ssp3–H activation of thiolacetic acid could be finished via two possible paths; the obtained thiyl radical and diyne would go through electrophilic reaction, ring‐closure reaction, and SN2 reaction to yield 3,4‐fused‐ring‐substituted thiophenes. While in the second part, the mechanism of side reaction has also been investigated, revealing that main reaction has a lower energy barrier. Localized orbital locator isosurfaces and electron spin density isosurface graphs can analyze the structures and reveal the substances.

Multiple-H-bonded-zwitterionic tetramer structure for L-(+)-2-chlorophenylglycine, as investigated by UV, IR and Raman spectroscopy and electronic structure calculations

A DFT tetramer model constructed of multi-H-bonds at B3LYP/6-311G(d,p) level has been proposed for L-(+)-2-Chlorophenylglycine. Motivation in part for the tetramer model comes from the observed IR spectra near 3400−2500 cm−1 showing a very broad sub-band structure spread over ∼ 900 cm−1 without distinct sharp bands; secondly, XRD structures of similar molecular solids show multiple H-bonds among monomers. Therefore, the proposed tetramer consists of fourteen H-bonds arising from a network of inter-/intra-molecularly X−H···Y bonds: N−H···O, C−H···O and Cα−H···Cl bonds, all from four monomer species. The strengths and degree of these H-bonds being covalent, ionic or partial have been determined using topological parameters from AIM calculations. Other weaker van der Waals interactions and steric clashes in relation to the N−H···O, C−H···O and Cα−H···Cl bonds have also been evaluated by the method of ‘non-covalent interactions (NCI)’. Further, the charge transfer from the Y lone pair orbital (donor) to the X−H anti-bonding orbital (acceptor) have been explained on the basis of overlapping of orbitals using NBO analysis. Computed stabilization energies for the X−H···Y bonds have shown the inter-molecular N−H···O bonds to be the strongest of the H-bonds. Concentration-dependent UV spectral analysis aided by TD-DFT-based calculations at B3LYP/6-311G(d,p) with SMD model in water has shown that a strong band at 221 nm, among other bands, blue-shifts to 194 nm with a concomitant arrival of a shoulder band at 219 nm. The bands are assigned to the π→π* transition. This observation has been interpreted to be the result of dissociation of the tetrameric species into monomeric species and is supported by the stabilization of computed ground and excited electronic levels. By the same interpretation, three vibronic bands seen at 260−280 nm also have been explained. Computed vibrational modes of the tetramer fit very well with the experimental IR and Raman band features including low frequency Raman modes below 350 cm−1. It has been shown the consistency among the H-bonding descriptors - H···Y bond distance, change in X−H bond length, X−H frequency shifts, electron density, H-bond energy and stabilization energy by graphical correlations.

Assessing the performances of different continuum solvation models for the calculation of hydration energies of molecules, polymers and surfaces: a comparison between the SMD, VASPsol and FDPB models

Assessing the performances of different continuum solvation models for the calculation of hydration energies of molecules, polymers and surfaces: a comparison between the SMD, VASPsol and FDPB models

The Reaction of Hydrogen Halides with Tetrahydroborate Anion and Hexahydro-closo-hexaborate Dianion.

The mechanism of the consecutive halogenation of the tetrahydroborate anion [BH4]− by hydrogen halides (HX, X = F, Cl, Br) and hexahydro-closo-hexaborate dianion [B6H6]2− by HCl via electrophile-induced nucleophilic substitution (EINS) was established by ab initio DFT calculations [M06/6-311++G(d,p) and wB97XD/6-311++G(d,p)] in acetonitrile (MeCN), taking into account non-specific solvent effects (SMD model). Successive substitution of H− by X− resulted in increased electron deficiency of borohydrides and changes in the character of boron atoms from nucleophilic to highly electrophilic. This, in turn, increased the tendency of the B–H bond to transfer a proton rather than a hydride ion. Thus, the regularities established suggested that it should be possible to carry out halogenation more selectively with the targeted synthesis of halogen derivatives with a low degree of substitution, by stabilization of H2 complex, or by carrying out a nucleophilic substitution of B–H bonds activated by interaction with Lewis acids (BL3).

The vibronic absorption spectrum and electronic properties of Azure B in aqueous solution: TD-DFT/DFT study

The vibronic absorption spectrum of Azure B (AB) in an aqueous solution is calculated using the time-dependent density functional theory (TD-DFT). The results of calculations are analyzed using all hybrid functionals supported by Gaussian16, the 6-31++G(d,p) basis set, and the IEFPCM and SMD solvent models. The solvent model IEFPCM gave significantly underestimated values of λmax in comparison with the experiment. This is a manifestation of the TD-DFT “cyanine failure”. However, the SMD model made it possible to obtain good agreement between the calculation results and experimental data. The best fit was achieved using the X3LYP functional. According to our calculations, the shoulder in the visible absorption spectrum of AB has a vibronic origin. However, the calculated shoulder is weaker than the experimental one. Explicit assignment of two water molecules, which form strong hydrogen bonds with a dye molecule, leads to a shift of the calculated absorption spectrum to longer wavelengths by approximately 17 nm but does not lead to an improvement in its shape. Comparative analysis of the calculated vibronic absorption spectra of Azure B with those obtained earlier for Azure A and methylene blue showed that the presence and intensity of the short-wavelength shoulder are determined by the location of the bands of higher vibronic transitions relative to the band of the 00 → 00 main transitions. Photoexcitation leads to an increase in the dipole moment of the dye molecule. An insignificant photoinduced electron transfer was found in the central ring of the chromophore of the dye molecule.

Mechanisms of Diels‐Alder reactions between pyridines and dienophiles: A DFT investigation

AbstractMechanisms of the Diels‐Alder (D‐A) reactions between N‐alkyl and aryl‐1,2‐dihydropyridines and dienophiles have been investigated by M06‐2X‐D3/6‐31 + G(d,p) basis set, and SMD model was employed to simulate the solvent effect. The computational results show that the productive process of endo‐product is favorable with lower energy barrier. The calculations of substituent effect indicate that there are some relations between the energy barrier and the productivity. The lower energy barrier means the higher productivity, and the barrier of retro D‐A reaction could also have influence on the productivity. Finally, natural bond orbital Fukui function (NOFF) and frontier molecular orbital theory (FMOT) are employed to analyze the structures and reveal the substances of D‐A reactions.

Vibronic absorption spectrum and electronic properties of methylene blue in aqueous solution: TD-DFT study

The vibronic absorption spectrum of methylene blue (MB) in an aqueous solution is calculated using the time-dependent density functional theory (TD-DFT). The results of calculations are analyzed using all hybrid functionals supported by Gaussian16, the 6–31++G(d,p) basis set and the IEFPCM and SMD solvent models. The solvent model IEFPCM gave significantly underestimated values of λmax in comparison with the experiment. This is a manifestation of the TD-DFT “cyanine failure”. However, the SMD model made it possible to obtain good agreement between the calculation results and experimental data. The best fit was achieved using the X3LYP functional. According to our calculations, the shoulder in the visible absorption spectrum of MB has a vibronic origin. Explicit assignment of a water molecule strongly bound to the N10 endocyclic nitrogen atom does not change the shape of the absorption band, but shifts its maximum by 7 nm to the long-wavelength region of the spectrum. The dipole moments and atomic charges of the ground and excited states of the MB molecule have been calculated. Photoexcitation leads to an increase in the dipole moment of the dye molecule. An insignificant photoinduced electron transfer was found in the central ring of the chromophore of the dye molecule. In accordance with our results, the absorption peak of the MB solution in the visible region of the spectrum is due to the π → π* type electronic transition. Vibronic coupling plays a significant role in the absorption spectra of MB.

Aqueous L-alanine molecular interaction from Gibb’s free energy: CPCM and SMD in DFT and ultrasonic studies

L-Alanine (ALA) in water spontaneously forms stable zwitterions. It is observed in a present work that the stimulation to revert can be done by ultrasonic waves. It’s molecular interaction in aqueous system can be found from the Gibb’s free energy. It has been examined experimentally by estimating the Gibb’s free energy using the ultrasonic method for the verification of theoretical result. The theoretical work performed within the computational DFT framework for the different solvation models. This paper deals with two different solvation models, the CPCM and the SMD, which are implemented in a Density Functional Theory preferred with non-hybrid functional and analyzed interaction perspective. The weak interactions by NCI also analyzed for difference. Further, BP86 reported difference in both model. The SMD model is also tested by using B3LYP and PBEh-3 to compare ΔG.

Phenol alkylation under phase transfer catalysis conditions: Insights on the mechanism and kinetics from computations

• Additional phenol improves the partition equilibrium. • The RN4+PhO−(PhOH) complex reacts in the organic phase. • Higher aggregates may be involved for Et4N + and Pr4N+. Experiments reported in the literature involving alkylation of the phenol under phase transfer catalysis conditions support the formation of the RN 4 + PhO ― (PhOH) complex in the organic phase. This complex could be directly involved in the transition state. In the present theoretical study, the phase transfer catalyzed alkylation of phenol was investigated using M06-2X calculations and solvent effect using the SMD model combined with reliable experimental single-ion solvation free energy data in aqueous solution. The analysis was done for tetraethylammonium, tetrapropylammonium and tetrabutylammonium phase transfer catalysts. In the case of tetrabutylammonium ion, the calculations have predicted a reaction kinetics compatible with experimental data. In addition, the BuN 4 + PhO ― (PhOH) complex is calculated to be the active species in the catalysis. For the tetraethylammonium and tetrapropylammonium cations, both the RN 4 + PhO ― and RN 4 + PhO ― (PhOH) complexes are not able to explain the catalysis, suggesting that another more complex aggregate can be involved in the process.

Effect of the anionic center hydration on the activation barrier of intramolecular nucleophilic addition in αβ-unsaturated oximes

The mechanism of intramolecular nucleophilic addition in αβ-unsaturated oximes, as well as the effect of the anionic center hydration with one and two water molecules on the activation barriers of intramolecular cyclization, was studied using the B2PLYP-D2/6-311+G**//B3LYP(D)/6-31+G* method with the solvation effects included within the SMD model. The activation barrier for nucleophilic addition of the anionic center of the oxime group to the carbon skeleton of 3-ethyl-N-hydroxy-5-phenylpenten-3-imine-2 is about 21 kcal/mol. During the hydration of the anionic center with one water molecule, a strong complex is formed, which increases the activation barrier by ∼ 6 kcal / mol. The addition of a second water molecule leads to an even higher activation barrier (ΔG‡ = 28 kcal/mol), but promotes the binding of the leaving hydroxide ion.

Choosing a solvation model for simulating reactions in KOH(KOBut)/DMSO superbasic media

The ability of protocols based on the B2PLYPD/6-311+G**//B3LYP/6-31+G* method with various schemes for accounting for nonspecific solvation to reproduce C-H, N-H, O-H and S-H acidity in a dimethyl sulfoxide medium is considered. For a selected set of 20 compounds, typical reagents for reactions in superbasic media, the IEFPCM scheme with UFF cavity and α = 1.35 multiplier yields better results than the popular SMD model.

Ambiguities in solvation free energies from cluster-continuum quasichemical theory: lithium cation in protic and aprotic solvents.

Gibbs free energies for Li+ solvation in water, methanol, acetonitrile, DMSO, dimethylacetamide, dimethoxyethane, dimethylformamide, gamma-butyrolactone, pyridine, and sulfolane have been calculated using the cluster-continuum quasichemical theory. With n independent solvent molecules S initial state forming the "monomer" thermodynamic cycle, Li+ solvation free energies are found to be on average 14 kcal mol-1 more positive compared to those from the "cluster" thermodynamic cycle where the initial state is the cluster Sn. We ascribe the inconsistency between the "monomer" and "cluster" cycles mainly to the incorrectly predicted solvation free energies of solvent clusters Sn from the SMD and CPCM continuum solvation models, which is in line with the earlier study of Bryantsev et al., J. Phys. Chem. B, 2008, 112, 9709-9719. When experimental-based solvation free energies of individual solvent molecules and solvent clusters are employed, the "monomer" and "cluster" cycles result in identical numbers. The best overall agreement with experimental-based "bulk" scale lithium cation solvation free energies was obtained for the "monomer" scale, and we recommend this set of values. We expect that further progress in the field is possible if (i) consensus on the accuracy of experimental reference values is achieved; (ii) the most recent continuum solvation models are properly parameterized for all solute-solvent combinations and become widely accessible for testing.

Prediction of octanol-water partition coefficients for alkyl-PAHs based on the solvation free energy

Octanol-water partition coefficients (KOW ) are of great importance in assessing the environmental fate and risk of hydrophobic organic pollutants including alkyl-polycyclic aromatic hydrocarbons (alkyl-PAHs). Due to the time-consuming and laborious of experimental determination of KOW , it is desirable to develop a rapid and accurate prediction model for the KOW of alkyl-PAHs. In this study, a prediction model for log KOW of alkyl-PAHs was developed according to the thermodynamic relationship between KOW and the solvation free energy from n-octanol phase to aqueous phase (ΔGOW ). ΔGOW values of alkyl-PAHs were calculated by the SMD model. The effect of dimer formation on the partition behaviour and partition coefficient was explored. After taking the effect of dimer formation into account, the goodness-of-fit, predictive ability, and robustness of the prediction model was significantly improved. The developed model in this study had the superiorities of universal application domain, low dependence on the experimental values and clear model mechanism.

Effects of Reynolds number, plastic number, and flow intensity on the flow and on the heat transfer of a viscoplastic fluid flowing through a planar expansion followed by a contraction

Non-Newtonian fluids are a constant presence in several industrial applications so it becomes interesting to understand their behavior and to optimize their use. One behavior of commercial interest is the viscoplastic behavior characterized by an abrupt change of the apparent viscosity when a certain amount of stress is achieved. The present work performs a study of the effect of Reynolds number, the plastic number, and the flow intensity over flow parameters of industrial interest, namely, mean Nusselt number, displacement efficiency, and head loss. The mechanical model is approximated by a finite volume method implemented by an OpenFOAM® routine developed by the authors. The SMD model was chosen to model the viscoplastic behavior. The adopted geometry is of a planar channel with an abrupt expansion followed by an abrupt contraction. The channel walls are kept insulated and heat transfer occurs only at the cavity formed between the expansion and contraction planes. For the studied range of parameters, mean Nusselt number has a positive dependence on Reynolds number and flow intensity but a negative dependence on plastic number; displacement efficiency has a positive dependence on Reynolds number and flow intensity but a negative dependence on plastic number. The head loss has a negative dependence on Reynolds number and plastic number and an overall positive dependence on flow intensity.

Theoretical investigation of solvent effect on the keto–enol tautomerization of pentane-2,4-dione and a comparison between experimental data and theoretical calculations

The equilibrium constants of stable keto and enol forms of pentane-2,4-dione (known as acetylacetone) are estimated, using the second-order Møller−Plesset (MP2), density functional theory (B3LYP and M06-2X), composite methods (G4, G3, G3B3, CBS-QB3, and G3MP2B3), double-hybrid density functional theory (B2PLYP), and long-range corrected (LC) hybrid functional (ωB97X-D). These methods are integrated with the PCM, CPCM, and SMD models to elucidate the effect of solvent on thermodynamic parameters. The reported measured enol contents in the solutions and gas phase are utilized to benchmark the predictions of different quantum mechanical methods for the keto–enol equilibrium in acetylacetone. In this study, we calculated the enol content in 16 acetylacetone solutions and in the gas phase. Among the applied methods, the MP2 level and the B3LYP level underestimate and overestimate, respectively, the enol content of acetylacetone in the gas phase and solutions. The G3B3 and G3MP2B3 levels give reasonable agreement with the measured data. The best results obtained by calculations at the B2PLYP/6-31+G(2d,p) and CBS-QB3 levels, with mean absolute errors (MAE) relative to experiments of 2.30 and 5.45 and root mean square deviation (RMSD) errors of 0.78 and 1.66, respectively. According to our calculations, one enol and two keto forms (Ket1 and Ket2) coexist in polar solutions. The effect of solvent was more pronounced on the structure and stability of the Ket2 tautomer than others. The strength of the intramolecular hydrogen bond in the enol form of acetylacetone is almost independent of the solvent polarity.