Henry’s law constant for diatomic and polyatomic Lennard‐Jones molecules

Hydration Free Energies of Polypeptides from Popular Implicit Solvent Models versus All-Atom Simulation Results Based on Molecular Quasichemical Theory

Calculating the hydration free energy of a macromolecule in all-atom simulations has long remained a challenge, necessitating the use of models wherein the effect of the solvent is captured without explicit account of solvent degrees of freedom. This situation has changed with developments in the molecular quasi-chemical theory (QCT)─an approach that enables calculation of the hydration free energy of macromolecules within all-atom simulations at the same resolution as is possible for small molecular solutes. The theory also provides a rigorous and physically transparent framework to conceptualize and model interactions in molecular solutions and thus provides a convenient framework to investigate the assumptions in implicit solvent models. In this study, we compare the results using molecular QCT versus predictions from EEF1, ABSINTH, and GB/SA implicit solvent models for polyglycine and polyalanine solutes covering a range of chain lengths and conformations. The hydration free energies or the differences in hydration free energies between conformers obtained from the implicit solvent models do not agree with explicit solvent results, with the deviations being largest for the group additive EEF1 and ABSINTH models. GB/SA does better in capturing the qualitative trends seen in explicit solvent results. Analysis founded on QCT reveals the critical importance of the cooperativity of hydration that is inherent in the hydrophilic and hydrophobic contributions to hydration─physics that is not well captured in additive models but somewhat better accounted for by means of a dielectric in the GB/SA approach.

Communication: Contact values of pair distribution functions in colloidal hard disks by test-particle insertion

We apply Henderson's method for measuring the cavity distribution function y(r) [J. Henderson, Mol. Phys. 48, 389 (1983)] to obtain the pair distribution function at contact, g(σ⁺). In contrast to the conventional distance-histogram method, no approximate extrapolation to contact is required. The resulting equation of state from experiments and simulations of hard disks agrees well with the scaled particle theory prediction up to high fluid packing fractions. We also provide the first experimental measurement of y(r) inside the hard core, which will allow for a more complete comparison with theory. The method's flexibility is further illustrated by measuring the partial pair distribution functions of binary hard-disk mixtures in simulation. The equation for the contact values can be used to derive familiar results from statistical geometry.

The Application of 3D-QSAR Studies for Novel Cannabinoid Ligands Substituted at the C1‘ Position of the Alkyl Side Chain on the Structural Requirements for Binding to Cannabinoid Receptors CB1 and CB2

A set of 30 novel Delta8-tetrahydrocannabinol and cannabidiol analogues were subjected to three-dimensional quantitative structure-activity relationship studies using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) approaches. Using a combination of molecular modeling techniques and NMR spectroscopy, the putative bioactive conformation of the most potent cannabinoid (CB) ligand in the training set was determined. This conformer was used as the template and CB1 and CB2 pharmacophore models were developed. These models were fitted with experimental binding data and gave high correlation coefficients. Contour maps of the CB1 and CB2 models of CoMFA and CoMSIA approaches show that steric effects dominantly determine the binding affinities. The CoMFA and CoMSIA analyses based on the binding affinity data of CB ligands at the CB1 and CB2 receptors allowed us to deduce the possible optimal binding positions. This information can be used for the design of new CB analogues with enhanced activity and other tailored properties.

Palladium(0)-Catalyzed Trimerization of Arylisocyanates into 1,3,5-Triarylisocyanurates in the Presence of Diimines: A Nonintuitive Mechanism

We show here that palladium(0) (dibenzylideneacetone) complexes bearing 1,10-phenanthroline constitute efficient catalysts for the cyclotrimerization of aromatic isocyanates. For the first time, the mechanism of this reaction has been investigated experimentally and theoretically with group 10 catalysts. This investigation provides a very consistent picture of the catalytic cycle. Notably, we establish that the reaction does not proceed by stepwise cycloadditions or ring insertions involving metallacyclic intermediates, as might have been anticipated. Rather, in our proposal, the initial steps of the mechanism resemble the chain-growth process operative during the anionic polymerization of isocyanates and feature charge-separated intermediates. These steps are then followed by ring closure on the metal center of the last intermediate formed to yield a seven-membered metallacycle that reductively eliminates the cyclotrimer and re-forms the active species. In addition, we conclusively show that the (known) palladacycles that could be isolated during the experimental investigations are not catalytic intermediates but result from catalyst deactivation. Thus, with Pd(0) diimine catalysts, the actual trimerization mechanism appears to be a blend between the two types of mechanisms proposed thus far for the oligomerization of heterocumulenes with very different catalysts. In conclusion, this work contributes to a better understanding of the reactivity of arylisocyanates in the vicinity of late group 10 metal centers in low oxidation state and sheds some light on the detrimental self-poisoning processes observed during the reductive carbonylation of nitroaromatic substrates catalyzed by related catalysts in non-nucleophilic media.

How the Shape of the NH2 Group Depends on the Substituent Effect and H-Bond Formation in Derivatives of Aniline

The geometry and electronic structure of the amino group in aniline and its derivatives are very sensitive to both intramolecular interactions such as substituent effects and intermolecular ones such as H-bonding. An analysis of experimental geometries retrieved from the CSD base and computational modeling of aniline and its derivatives and their H-bonded complexes by use of B3LYP/6-311+G** and MP2/aug-cc-pVDZ showed that the degree of pyramidalization of the amino group depends on H-bonding, which exists in two forms, (i) NH...B (base) and (ii) N...HB (Brønsted acid), both of which affect the shape of the NH2 group. The effect may be significantly enhanced by a substituent through resonance interaction from electron-attracting substituents. The NH...B interactions lead to a substantial planarization of the group, whereas N...HB interactions do not. The natural bond orbital analysis allowed the authors to show that the changes in occupancy of the "lone pair" orbital and in geometry parameters describing pyramidalization of the group depend on the substituent constants.

Degenerate Electron Exchange Reaction of n-Alkane Radical Cations in Solution

The degenerate electron exchange (DEE) reaction involving radical cations (RCs) of n-nonane, n-dodecane, and n-hexadecane in n-hexane solution was studied over the temperature range 253-313 K using the method of time-resolved magnetic field effect in recombination fluorescence of spin-correlated radical ion pairs. In the dilute solutions the rate constant of DEE was found to be 200 times slower than the diffusion limit. Using n-nonane as an example, we showed that two reasons are responsible for the low value of the RC self-exchange rate: (1) conformational variability of molecules and RCs and (2) the activation barrier of DEE reaction. The calculations of the reaction enthalpy performed by the B3LYP/6-31G(d) method indicated that electron transfer can be effective only upon collision of RC with a neutral molecule either in the all-trans conformation or in the conformation differing from the latter by rotation of the end ethyl fragment. The activation barrier of the DEE reaction was estimated using the reorganization energy of the internal degrees of freedom calculated at the B3LYP level and was found to be about 6 kcal/mol. A possible influence of the interaction between RC and a neutral molecule in an encounter complex on DEE rate constant is also discussed.

DFT Study on the Palladium-Catalyzed Allylation of Primary Amines by Allylic Alcohol

The palladium-catalyzed allylation of primary amines has been investigated by DFT calculations (B3PW91, PCM method), and two potential mechanisms were studied. The first mechanism relies on the formation of cationic hydridopalladium complexes. Their formation involves a metal-assisted formal (1,3) shift of a proton from the nitrogen atom of an ammonium to the Cbeta carbon atom. The second part of the cycle relies on a ligand exchange through a pentacoordinated 18VE hydridopalladium complex. The last step likely proceeds through a bimolecular pathway and formally consists of a proton transfer from the allylammonium to the alcohol group of the complex. The second mechanism, which is closer to that currently admitted for nucleophilic allylic substitutions, relies on the decomplexation of the coordinated allylammonium and appears to be favored. This catalytic cycle was recomputed on model complexes varying the ligands, and a charge decomposition analysis was carried out to assess the influence of the electronic properties of the ligands. To compare our results with competitive experiments, CDA calculations were also performed on real ligands. In agreement with experimental observations, this process was found to be strongly ligand dependent, decomplexation being favored by strong pi-acceptor ligands. These calculations led us to show experimentally that complex [Pd(P(OPh)(3))(2)(eta(3)-C(3)H(5))][OTf] is an efficient catalyst for this allylation. Finally, this catalytic process proved to be sensitive to the nature of the amine, with poorly basic amines favoring the re-formation of the catalytic precursor.

Examination of the Excess Thermodynamic Properties of n-Alkane Binary Mixtures: A Molecular Approach

A modification of the statistical associating fluid theory, the so-called Soft-SAFT equation of state, is proposed to predict the excess thermodynamic properties of binary mixtures of n-alkanes. n-Alkane molecules are modeled as fully flexible Lennard-Jones chains. This molecular model accounts for the most important microscopic features of real chainlike molecules: attractive and repulsive interactions between different chemical groups and the connectivity of the segments that form the molecules. In this work we consider an additional microscopic effect that can profoundly affect certain thermodynamic properties, namely, the conformational changes when two different n-alkane molecules are mixed. We propose, following the work of Vega and co-workers [J. Chem. Phys. 1999, 111, 3192], a simple model to account for the conformational changes in molecules. The resulting free energy is combined with the SAFT free energy to describe the excess thermodynamic properties of binary mixtures of n-alkanes. Predictions from the theory are compared with experimental data taken from the literature. The agreement between the experiments and the theoretical predictions is excellent in all cases. This work shows that although minor microscopic effects, such as the conformational changes in the molecules that form the mixtures, have only a very small effect on the usual thermodynamic properties, such as pressure, chemical potential, phase equilibria, and excess volumes, they can contribute significantly to other thermodynamic properties. In fact, one of the main conclusions of this work is that it is essential that conformational effects be taken into account in molecular-based theories if an accurate description of certain excess properties (excess enthalpy for instance) is desired.

Molecular Recognition of Trigonal Oxyanions Using a Ditopic Salt Receptor: Evidence for Anisotropic Shielding Surface around Nitrate Anion

A ditopic, macrobicyclic receptor with adjacent anion and cation binding sites is able to extract a range of monovalent salts into chloroform solution. The structures of the receptor complexed with KAcO, LiNO(3), NaNO(3), KNO(3), and NaNO(2) are characterized in solution by NMR spectroscopy and in the solid state by X-ray crystallography. The sodium and potassium salts are bound to the receptor as contact ion-pairs, with the metal cation located in the receptor's crown ether ring and the trigonal oxyanion hydrogen bonded to the receptor NH residues. The solid-state structure of the LiNO(3) complex has a bridging water molecule between the cation and anion. In all solid-state structures, the trigonal oxyanion is not located symmetrically inside the receptor cavity. It appears that anion orientation is controlled by a complex interplay of steric factors, coordination bonding to the metal cation, and hydrogen bonding with the receptor NH residues. An important feature with this latter effect is the fact that hydrogen bonds directed toward the oxygen lone pairs on a trigonal oxyanion are stronger than hydrogen bonds to the pi-electrons. In solution, the (1)H NMR spectra of the nitrate and nitrite salt complexes are noteworthy because several receptor signals, including the NH protons, undergo unusual upfield movements in chemical shift upon complexation. This is a reflection of the diamagnetic anisotropy of these trigonal oxyanions. The magnetic shielding surface for the NO(3)(-) anion is calculated using density functional theory and shown to have a shielding region directly above the central nitrogen.

Ketene formation in benzdiyne chemistry: ring cleavage versus Wolff rearrangement

In the chemistry toward generating benzdiyne from five benzenetetracarboxylic dianhydride derivatives, ketene formation was exclusively observed in the photolysis of difluorobenzenetetracarboxylic dianhydride in a nitrogen matrix at 13 K. Two ketenes were formed concomitantly with difluorobenzdiyne. These ketenes were identified on the basis of good agreement between the observed and calculated (B3LYP/6-31G level) IR spectra. Neither ketene contained the five-membered-ring moiety as cyclopentadienylideneketene, which is formed by Wolff rearrangement in the benzyne chemistry. The first generated ketene was assigned to a ketene with a cyclopropene moiety, and the second, to a ketene with a butadiyne moiety. The first generated ketene was a major product in the photolysis and was formed by cleavage of the bond connecting the ketene group and the C-F carbon and not the bond connecting the ketene group and the carbene moiety. Thus the structures of these ketenes indicated that a unprecedented ring cleavage, rather than Wolff rearrangement, is the dominant process in the benzdiyne chemistry.

On the calculation of Henry's law constants of chlorinated benzenes in water from semiempirical quantum chemical methods

The Henry's law constants for all 12 polychlorinated benzene congeners were calculated using semiempirical quantum chemical solvation models (SM2, SM2.1, and SM3), and their performances are discussed. The values obtained by the SM3 method are underestimated compared with the experimental values and those calculated by SM2 and SM2.1 methods. This underestimation is larger as the degree of chlorination of the benzenes increases. This bad performance of SM3 to calculate Henry's law constants is attributable to the PM3 Hamiltonian, due to its incapacity to give a good description of electron density in chlorinated benzenes. The best results, within the 95% confidence limit of error of the experimental mean, are obtained using SM2 method. The discussion includes analysis of the different contributions to the free energy of solvation, namely, polarization free energy, cavitation, dispersion, and structural rearrangement of the solvent effects as well as partial atomic charges.

Benzdiynes (1,2,4,5-tetradehydrobenzenes): direct observation by wavelength-selective photolyses of benzenetetracarboxylic dianhydrides in low-temperature nitrogen matrixes

Toward direct observation of benzdiynes, we investigated the wavelength-selective photolyses of five kinds of benzenetetracarboxylic dianhydride derivatives in nitrogen matrixes at 13 K. In the first step of the photolyses, all dianhydrides were converted into benzynedicarboxylic anhydrides with loss of CO and CO2 upon irradiation at 308 nm. In the second step, the benzyne intermediates were photolyzed at 266 nm. In these photolyses, the generation of two kinds of benzdiynes, 3,6-difluoro-1,4-benzdiyne and 3,6-bis(trifluoromethyl)-1,4-benzdiyne, was confirmed by good correspondence between observed and calculated IR spectra. These benzdiynes were converted into the corresponding hexatriynes upon further irradiation at 266 nm. Benzdiynes were not observed in the photolyses of the other three dianhydrides: only hexatriynes were observed as major photoproducts. These results suggested that benzdiynes were generated first and then converted into hexatriynes and that the efficiency of the decomposition of benzdiynes depended on the substituents. The dynamics of the generation and decomposition of benzdiynes in the matrixes was analyzed by using a successive reaction scheme.

Intramolecular 4 + 3 cycloadditions. A theoretical analysis of simple diastereoselectivity in reactions of alkoxyallylic cations and furans

[reaction--see text] A computational examination (B3LYP/6-31+G*//HF/6-31+G* + ZPVE) of an intramolecular 4 + 3 cycloaddition reaction suggests a stepwise process and the likelihood of reversibility in at least one of the pathways examined.