How does halogen bonding behave in solution? A theoretical study using implicit solvation model

A systematic study of halogen bonding interactions in gas phase and in solution was carried out by means of quantum chemical DFT/B3LYP method. Three solvents with different polarities (chloroform, acetone, and water) were selected, and solvation effects were considered using the polarized continuum model (PCM). For charged halogen-bonded complexes, the strength of the interactions tends to significantly weaken in solution, with a concomitant elongation of intermolecular distances. For neutral systems, halogen bond distances are shown to shorten and the interaction energies change slightly. Computations also reveal that in the gas phase the binding affinities decrease in the order Cl(-) > Br(-) > I(-), while in solution the energy gaps of binding appear limited for the three halide anions. According to free energy results, many systems under investigation are stable in solution. Particularly, calculated free energies of formation of the complexes correlate well with halogen-bonding association constants determined experimentally. The differences of the effects of solvent upon halogen and hydrogen bonding were also elucidated. This study can establish fundamental characteristics of halogen bonding in media, which would be very helpful for applying this noncovalent interaction in medicinal chemistry and material design.     

A theoretical study of kinetics and mechanism of the oxa 6π electrocyclization of naphthoquinones as antimalarial drugs

Because of the importance of antimalarial drugs, a theoretical study of kinetics and mechanism of the oxa 6?? electrocyclization of naphthoquinones as antimalarial drugs, was performed using DFT method at B3LYP and HF levels of theory and using 6?C31G and 6?C31G* basis sets. Equilibrium molecular geometries and harmonic vibrational frequencies of the reactant, transition state (TS), and product were calculated. The considered rate constants and activation thermodynamic parameters were calculated. The results showed a fairly agreement with experimental data. Our calculations showed that the reaction proceeds through an asynchronous concerted mechanism.     

A study on the mechanism of reaction between BNAH and chloranil:Evidence for electron transfer

The reaction between chloranil and N-benzyldihydronicotinamide(BNAH)in boratebuffer/DMF was investigated.The reaction mixture gave a strong esr signal,which is consistentwith that of chloranil anion radical,and tetrachlorohydrophenol(QH_2)and N-benzylnicotinamide(BNA~+)were obtained as the sole products.When the reaction was run in benzene solution,a greencoloured charge-transfer complex between the reactants could be isolated,which decomposed in polarsolvents to give BNA-+ and QH_2.Based on kinetic studies by esr spectroscopy by the stopped-flowtechnique,a two-step electron-transfer mechanism for the reactionis proposed in contrast to thehydride-transfer mechanism reported in the literature.     

A DFT investigation of the retro-ene reactions of β-hydroxyacetylenes: concerted or stepwise mechanism

Structural Chemistry - The retro-ene reactions of β-hydroxyacetylene and its 10 derivatives have been investigated theoretically at the B3LYP/6-31+G(d) level. The reactions are found to...     

A quantum chemical study on the mechanism of the consecutive addition of HCN to propionitrile

MINDO/3 MO method has been used to study the mechanism of the consecutive addition of HCN to propionitrile. The results obtained for the first five steps show that the reaction is exothermic, and step 1 is the rate determining step.     

Theoretical study of formation mechanism for 4-methyl-3-phenylbenzonitrile in the course of the Hiyama and Suzuki–Miyaura reactions

A theoretical study on the mechanism of conversion of 3-bromo-4-methylbenzonitrile into 4-methyl-3-phenylbenzo-nitrile in the course of the Suzuki–Miyaura and Hiyama−Denmark cross-coupling reactions has been performed at Cam-B3LYP-D3 level of theory. With the use of Pd–NHC type complex as the catalyst, the Hiyama−Denmark cross-coupling is best suited for this process from both thermodynamic and kinetic aspects.     

Equilibrium and kinetic study of the proton transfer reactions between nitroalkanes and strong organic bases — phosphazenes in tetrahydrofuran solvent

Proton transfer reactions rates between carbon acids 1-nitro-1-(4-nitrophenyl)ethane (NPNE), 2-methyl-1-nitro-1-(4-nitrophenyl)propane (MNPNP)) and phosphazenes (BEMP, BTPP, P₁-t-Oct) in tetrahydrofuran have been measured, and the activation parameters were determined. The results are compared with those previously obtained for P₁-t-Bu phosphazene, guanidines and amidines.      

Intramolecular charge transfer in π-conjugated oligomers: a theoretical study on the effect of temperature and oxidation state

Intramolecular charge transfer (ICT) of gaseous π-conjugated oligo-phenyleneethynylenes (OPE) induced by a homogeneous applied electric field has been theoretically investigated using a combined approach integrating molecular dynamics (MD) simulations and Perturbed Matrix Method calculations. In line with recent investigations, our results indicate the peculiar role of conformational transitions on OPE electronic properties which reflects on a strong temperature effect on ICT. Electron transfer reactions inducing chemical alteration on OPE, also taken into account in this study, revealed extremely important for explaining non-linear ICT effects and probably plays a central role in the mechanisms underlying molecular transport junctions. Our study further points out the necessity of using MD-based approach for modelling molecular electronics, even when relatively rigid molecular systems are concerned.     

A comparative study of the multicomponent Ugi reactions of an oxabicycloheptene-based β-amino acid in water and in methanol

Di-exo-3-amino-7-oxabicyclo[2.2.1]hept-5-ene-2-carboxylic acid 1, five aldehydes and two isocyanides were reacted both in methanol and in water to prepare a 10-membered β-lactam library via a Ugi-4-centre-3-component reaction. The yields were found to be similar in water and methanol. The diastereoselectivities of the aqueous reactions were similar, though in a few cases higher than those in methanol. The benefits of water are the facile isolation of the precipitated product and the shorter reaction time.     

A theoretical study of the copper–cysteine bond in blue copper proteins

 The accuracy of theoretical calculations on models of the blue copper proteins is investigated using density functional theory (DFT) Becke's three-parameter hybrid method with the Lee–Yang–Parr correlation functional (B3LYP) and medium-sized basis sets. Increasing the basis set to triple-zeta quality with f-type functions on all heavy atoms and enlarging the model [up to Cu(imidazole-CH₃)₂(SC₂H₅) (CH₃SC₂H₅)^0/+] has only a limited influence on geometries and relative energies. Comparative calculations with more accurate wave-function–based methods (second-order M?ller–Plesset perturbation theory, complete-active-space second-order perturbation theory, coupled-cluster method, including single and double replacement amplitudes and in addition triple replacement perturbatively) and a variety of basis sets on smaller models indicate that the DFT/B3LYP approach gives reliable results with only a small basis set dependence, whereas the former methods strongly depend on the size of the basis sets. The effect of performing the geometry optimizations in a continuum solvent is quite small, except for the flexible Cu-S_Met bond. The results of this study confirm the earlier results that neither the oxidized nor the reduced copper site in the blue proteins is strained to any significant degree (in energy terms) by the protein surrounding. Received: 7 July 2000 / Accepted: 17 November 2000 / Published online: 21 March 2001     

A theoretical study on the importance of steric effects,electronic properties,interaction and solvation energies in the ‘host–guest’ chemistry of protonated azacryptands and halide anions

It is well known that the selectivity of a receptor for an anion depends on the compatibility of the cavity size of the receptor and the size of the anion. In this work the macrobicyclic [H₆L(X)]⁵⁺ (X⁻=F, Cl, Br); are studied theoretically and compared with [H₆L′(F)]⁵⁺ having a smaller cavity size. It was shown that the ideal match between the sizes of the protonated azacryptand and the fluoride ion exists in the [H₆L′(F)]⁵⁺ complex but the [H₆L]⁶⁺ is a better receptor than [H₆L′]⁶⁺ in solution. Thus the results clearly indicate that in some special cases a better receptor is not one whose cavity size has better compatibility with the anion size.     

How does mechanism of biosorption determine the differences between the initial and equilibrium adsorption states?

The analysis of various models assumed to represent the influence of pH on heavy metals biosorption equilibrium is presented. It shows that all of them lead to the same mathematical expressions (e.g. the Langmuir or the Flory adsorption isotherm equations) when the pH effects are neglected. Even if considering the pH effects, some of them (competitive adsorption and ion-exchange models, for instance) still lead to analogical expressions for sorption isotherm equations. The accepted mechanism of biosorption may, however, influence strongly the differences between the initial and equilibrium states of biosorption system.     

Concurrent cyclopropanation by carbenes and carbanions? A density functional theory study on the reaction pathways

The mechanisms for the addition reactions of phenylhalocarbenes and phenyldihalomethide carbanions with acrylonitrile (ACN) and trimethylethylene (TME) have been investigated using an ab initio BH and HLYP/6-31G (d, p) level of theory. Solvent effects on these reactions have been explored by calculations that included a polarizable continuum model (PCM) for the solvent (THF). These model calculations show that for the addition of phenylhalocarbenes, a TME species may readily undergo addition reactions with carbenes while ACN has a high-energy barrier to overcome. It was also found that phenyldihalomethide carbanions do not readily add to the electron-rich TME. The cyclopropane yields only appear to occur via addition of PhCBr to TME. However, the cyclopropanation proceeds not only via slow addition of phenylhalocarbenes to ACN but also forms through the stepwise reaction of phenyldihalomethide carbanions with ACN. Our calculation results are in good agreement with experimental observations (Moss, R.A.; Tian, J.-Z. J. Am. Chem. Soc. 2005, 127, 8960) that indicate that the cyclopropanation of phenylhalocarbenes and phenyldihalomethide carbanions with ACN are concurrent in THF.     

Energy transfer or electron transfer?—DFT study on the mechanism of [2+2] cycloadditions induced by visible light photocatalysts

The intramolecular [2+2] cycloaddition of 1,3-dienes under visible light irradiation investigated by Yoon and his co-workers shows remarkably high yield and stereoselective differences under different photocatalysts. The reaction was speculated to be induced by energy transfer. However, the origin for these phenomena is still unclear. In this scene, the detailed mechanism for the [2+2] cycloaddition of 1,3-dienes under visible light has been investigated using density functional theory B3LYP and TPSSTPSS methods. The result shows that the reaction not only can be induced by energy transfer between photocatalysts and reactants, but also can be induced by electron transfer between them. The [2+2] cycloaddition induced by energy transfer is carried out along the potential energy surface (PES) of triplet excited states (T₁) firstly, and then goes back to the singlet ground state (S₀) via MECPs (minimum energy crossing points) between the PESs of the S₀ and T₁ states, forming the product in the S₀ state. The [2+2] reaction induced by electron transfer proceeds along the doublet state PES of the cation radical reactant and the neutral four-membered ring product could be obtained by electron transfer from the corresponding reactant or reduced photocatalyst. The origin of stereoselectivity of the [2+2] reaction is attributed to the reaction mechanism difference under different photocatalysts.     

A theoretical study of topomerization of imine systems: Inversion,rotation or mixed mechanisms?

The different mechanisms, rotation, inversion, or intermediate mechanism, by which occur the topomerization of imine systems R₂ CN X have been studied by applying ab initio, B3LYP, and MP2 methods. The effect of a wide variety of substituents R and X on the isomerization pathway have been examined by computing fully optimized structures of the ground and transition states (136 isomers belonging to different imine families were studied and more than 300 transition structures were determined at various levels of theory). Energy barriers have been also obtained and it was found that the groups R and X have a strong influence on the type of mechanism involved and the activation energies. Thus, and depending on the type of substituents, transition state structures related to the following kinds of processes were found: pure inversion, intermediate mechanisms, rotation, and enhanced rotation (hyper‐rotation). In turn, the corresponding activation energies range between very low (<10 kcal/mol) and extremely high (> 70 kcal/mol) values. A simple index that allows us to quantify the percentage of inversion or rotation mechanism is proposed. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Kinetic study of the mass transfer of S-Tr?ger's base in the system cellulose triacetate and ethanol.

A recent study of the mass transfer kinetics of (-)- or S-Tr?ger's base (TB) between ethanol and microcrystalline cellulose triacetate (CTA) allows an analysis of the concentration dependence of the mass transfer rate coefficient (k(m)). S-TB elutes before R-TB. The retention time of the both compounds decreases with increasing temperature. In this study, experimental data measured between 30 and 50 degrees C were analyzed to provide information on the kinetics of several mass transfer processes which take place in the chromatographic column, i.e., axial and intraparticle dispersion, the fluid-to-particle mass transfer, and the kinetics of adsorption/desorption at the actual adsorption sites. Intraparticle diffusion has the dominant contribution to band broadening at high flow-rates. Both intraparticle diffusivity and the surface diffusion coefficient exhibit a small concentration dependence. The positive dependence of k(m) on the concentration of S-TB seems to result from the properties of the adsorption/desorption kinetics and can be interpreted by considering the phase equilibrium properties. A quantitative analysis of the activation energy of the mass transfer kinetics of S-TB in the CTA column was also attempted.