Showing papers on "Solvent effects published in 2006"

Probing the Solvent-Assisted Nucleation Pathway in Chemical Self-Assembly

Abstract: Hierarchical self-assembly offers a powerful strategy for producing molecular nanostructures. Although widely used, the mechanistic details of self-assembly processes are poorly understood. We spectroscopically monitored a nucleation process in the self-assembly of p-conjugated molecules into helical supramolecular fibrillar structures. The data support a nucleation-growth pathway that gives rise to a remarkably high degree of cooperativity. Furthermore, we characterize a helical transition in the nucleating species before growth. The self-assembly process depends strongly on solvent structure, suggesting that an organized shell of solvent molecules plays an explicit role in rigidifying the aggregates and guiding them toward further assembly into bundles and/or gels.

A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution.

Abstract: An effective state specific (SS) model for the inclusion of solvent effects in time dependent density functional theory (TD-DFT) computations of excited electronic states has been developed and coded in the framework of the so-called polarizable continuum model (PCM). Different relaxation time regimes can be treated thus giving access to a number of different spectroscopic properties together with solvent relaxation energies of paramount relevance in electron transfer processes. SS and conventional linear response (LR) models have been compared for two benchmark systems (coumarin 153 and formaldehyde in different solvents) and in the limiting simple case of a dipolar solute embedded in a spherical cavity. The results point out the complementarity of LR and SS approaches and the advantages of the latter model especially for polar solvents. The favorable scaling properties of PCM-TD-DFT models in both SS and LR variants and their availability in effective quantum mechanical codes pave the route for the computation of reliable spectroscopic properties of large molecules of technological and/or biological interest in their natural environments.

Adding Explicit Solvent Molecules to Continuum Solvent Calculations for the Calculation of Aqueous Acid Dissociation Constants

Abstract: Aqueous acid dissociation free energies for a diverse set of 57 monoprotic acids have been calculated using a combination of experimental and calculated gas and liquid-phase free energies. For ionic species, aqueous solvation free energies were calculated using the recently developed SM6 continuum solvation model (Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 1133). This model combines a dielectric continuum with atomic surface tensions to account for bulk solvent effects. For some of the acids studied, a combined approach that involves attaching a single explicit water molecule to the conjugate base (anion), and then surrounding the resulting anion−water cluster by a dielectric continuum, significantly improves the agreement between the calculated pKa value and experiment. This suggests that for some anions, particularly those concentrating charge on a single exposed heteroatom, augmenting implicit solvent calculations with a single explicit water molecule is required, and ...

Mechanisms and free energies of enzymatic reactions.

Abstract: Most enzymatic reactions have very large and remarkably similar apparent second-order rate constants, kcat/KM, at mean values of about 107 M−1 s−1 with kcat in the range of 10–1000 s−1.1–3 In fact, many reactions approach the diffusional encounter rate at the limited enzyme concentration (<10−5 M) in the cell.4 Wolfenden illustrated the catalytic power of enzymes by comparing the rate constant of the catalyzed reaction with that of the same reaction in the absence of the enzyme in aqueous solution, kaq.2,5 Evidently, the most proficient enzymes are those catalyzing the slowest spontaneous reactions, such as the hydrolysis of glycosides and phosphate esters and the decarboxylation reactions of amino acids and of orotidine 5′-monophosphate (OMP), as catalyzed by OMP decarboxylase (ODC).2 In the latter case, the unimolecular rate constant of the spontaneous decarboxylation of OMP is accelerated (kcat/kaq) by 17 orders of magnitude in the active site of ODC.5,6 This reaction also has the distinction of being among the most proficient enzymes in catalyzing reactions without the involvement of cofactors. Significantly, Wolfenden’s experimental approach has been followed and paralleled in computational studies.7 The experiments, along with computational results that we review in this article, provide abundant evidence that the very large observed reductions of the free energy of activation can be achieved through the strong synergism of enzyme and substrate interactions “using ordinary noncovalent forces of attraction”,8 although in other cases enzyme catalysis may involve covalent intermediates9 or a change in reaction mechanism as compared to aqueous solution. Noncovalent attractive forces are mainly electrostatic in nature; they include ion pair interactions, hydrogen bonding, and electronic polarization. The competition between solvent–solvent and solvent–solute interactions contributes to hydrophobic effects (where the “solute” is the substrate or any part of the protein or a coenzyme that participates in the reaction coordinate and the “solvent” is water, spectator residues of the enzyme in the active site, and faraway parts of the protein or protein complex). These interactions all contribute to catalysis. It has been argued insightfully that electrostatic preorganization effects are a key source of enzyme catalysis,10 but the questions remain of what other factors contribute and how preorganization is arranged such that the transition state is stabilized preferentially to the reactant state. To understand enzyme catalysis and mechanism, it is necessary, and often challenging, to elucidate the unique ways in which each enzyme exerts electrostatic and other forces on the substrate and the transition state. In the past 10 years, many computational studies of enzymatic reactions have been carried out, combining quantum mechanical, classical mechanical, and statistical mechanical techniques, coupled with advances in protein structure determination, site-directed mutagenesis, and fast computers and algorithms. All computational studies of atomic scale dynamics must begin with a potential energy surface, and the most promising approach to calculating this surface is to treat the enzyme active site by electronic structure methods11–19 that include the electronic polarization of the reactive species by the dynamical fluctuations of the enzyme–solvent environment through effective sampling of the enzyme conformational space. Although a review necessarily involves only a very limited selection of the reactions that enzymes catalyze in the cell, we can nevertheless conclude7 that each enzyme has its unique characteristics, and enzymes use all possible means to achieve the ultimate objective of reducing the free energy of activation. In addition to providing an enormous rate acceleration, enzymes exercise precise control over the regio- and stereochemistry of the reactions that they catalyze, an aspect of enzyme catalysis that has received relatively little attention in computations (recent studies of triosephosphate isomerase and glyoxal synthase provide a noteworthy exception20). This control is perhaps best illustrated by the reactions catalyzed by terpenoid synthases,21 a large group of enzymes that transform a limited number of linear substrates such as geranyl diphosphate (C10), farnesyl diphosphate (C15), and geranylgeranyl diphosphate (C20) to tens of thousands natural products with a variety of rings and stereocenters, presumably by prefolding the same substrate to a “proper” conformation in the unique binding pocket of each enzyme and subsequently preventing the highly reactive carbocation intermediates from undergoing side reactions and preventing premature terminations of the catalyzed reaction sequences. Both experimental and computational studies appear to point to an important role for the balance of thermodynamic and kinetic factors along the cyclization cascade.22,23 Thus, it is of great interest not only to understand the origin of the enormous catalytic power of enzymes that they achieve by lowering the free energy of activation but also to characterize the detailed mechanism of enzyme actions that control each reaction step and provide the desired regio- and stereospecificity. In this review, we summarize computational studies of the mechanisms and free energies of selected enzymatic reactions. We first highlight computational approaches for enzymatic reactions, with special emphasis on two key elements that affect the computational accuracy, namely, the potential energy function and statistical mechanical sampling of the enzyme system. The potential energy functions may be based on quantum mechanical models, or they may be based on molecular mechanics force fields. In either case, to achieve the required accuracy to understand catalysis, it is essential to parametrize and validate the potential energy functions (or, equivalently, the methods used to calculate them) against model reactions and specific hydrogen bonding interactions in the gas phase. Only when the performance of the potential functions on the intrinsic reactivity of the chemical reactions has been justified can one begin to address the key questions of solvent effects and enzyme catalysis through molecular dynamics and free energy simulations. We then discuss a third element, namely, the choice of the reaction coordinate for determining the free energy of activation to characterize the mechanism of enzymatic processes. Then, we illustrate a variety of factors that have been found to contribute to catalysis in specific enzymatic reactions by lowering the free energy of activation relative to that for the uncatalyzed process in aqueous solution. Finally, we provide a summary of the major conclusions.

Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field

Abstract: The efficient and accurate characterization of solvent effects is a key element in the theoretical and computational study of biological problems. Implicit solvent models, particularly generalized ...

Acceleration of organic reactions through aqueous solvent effects.

Abstract: The parallels between organic reactions conducted with water as the solvent and reactions conducted under high pressure can be understood in light of theories of aqueous solvation and hydrophobic effects. Such parallels provide powerful tools for promoting reactions of nonpolar compounds.

A structural investigation of the N-B interaction in an o-(N,N-dialkylaminomethyl)arylboronate system

Abstract: o-(Pyrrolidinylmethyl)phenylboronic acid (4) and its complexes with bifunctional substrates such as catechol, alpha-hydroxyisobutyric acid, and hydrobenzoin have been studied in detail by X-ray crystallography, (11)B NMR, and computational analysis. The N-B interactions in analogous boronic acids and esters have been extensively cited in molecular recognition and chemosensing literature. The focal point of this study was to determine the factors that are pertinent to the formation of an intramolecular N-B dative bond. Our structural study predicts that the formation of an N-B dative bond, and/or solvent insertion to afford a tetrahedral boronate anion, depends on the solvent and the complexing substrate present. Specifically, from (11)B NMR studies, complexation of 4 with electron-withdrawing and/or vicinally bifunctionalized substrates promotes both the formation of N-B dative bonds and the solvation of sp(2) boron to a tetrahedral sp(3) boronate. In the solid state, the presence of an N-B dative bond in the complex of 4 and catechol (7) depends on the solvent from which it crystallizes. From chloroform, an N-B bond was observed, whereas from methanol, a methoxylated boronate was formed, where the methoxy group is hydrogen-bonded with the neighboring tertiary ammonium ion. The structural optimization of compounds 4 and 7 using density functional theory in a simulated water continuum also predicts that complexation of 4 and catechol promotes either the formation of an N-B bond or solvolysis if 1 equiv of water is present. The conclusion from this study will help in the design of future chemosensing technologies based on o-(N,N-dialkylaminomethyl)arylboronate scaffolds that are targeting physiologically important substances such as saccharides, alpha-hydroxycarboxylates, and catecholamines.

Thioindigo dyes: highly accurate visible spectra with TD-DFT.

Abstract: The structure and visible spectra of a large panel of thioindigo dyes and derivatives have been evaluated using a TD-PBE0/6-311+G(2d,p)//PBE0/6-311G(d,p) approach explicitly taking bulk solvent effects into account by means of the polarizable continuum model. The influence of the solvent characteristics, the trans−cis isomerization, and the chemical substitution on the benzene rings have been investigated. In addition, hemi-thioindigo dyes, thiazine-indigo, chromophore-like molecules, and selenoindigo have been considered. Though the relative oscillator strengths of the two allowed visible transitions in the nonplanar cis isomers are not always correctly reproduced by theory, the agreement between theoretical and experimental results is far above expectations. For the 170 cases studied, we obtained a mean unsigned error on the predicted λmax limited to 6.9 nm or 0.03 eV, with only 6 (4) cases for which the difference exceeds 20 nm (0.10 eV). These errors are 1 order of magnitude smaller than what has prev...

Catalyst Performance in “Click” Coupling Reactions of Polymers Prepared by ATRP: Ligand and Metal Effects

Abstract: CuI-catalyzed azide−alkyne cycloadditions were conducted in organic media under various conditions. The effects of several parameters (ligand, solvent, reducing agent, metal) on these reactions were studied using the step-growth click coupling of low-molecular-weight α,ω-diazido-terminated polystyrene prepared by atom transfer radical polymerization (ATRP). These reactions were typically conducted in DMF, monitored by size exclusion chromatography (SEC), and semiquantitatively analyzed by Gaussian multipeak fitting and subsequent peak integration. Both the electronic properties of the ligand and the number of coordinating atoms had significant influence on the rates of the click coupling reactions. Aliphatic amine ligands led to significantly faster rates as compared to pyridine-based ligands. Faster rates were also observed with tridentate vs tetradentate ligands. A further rate enhancement was observed when the reactions were conducted in a noncoordinating solvent (toluene) vs a coordinating solvent (DM...

A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy

Abstract: A method for modeling infrared solvent shifts using the electrostatic field generated by the solvent is presented. The method is applied to the amide I vibration of N-methyl acetamide. Using ab initio calculations the fundamental frequency, anharmonicity, and the transition dipoles between the three lowest vibrational states are parametrized in terms of the electrostatic field. The generated map, which takes into account the electric field and its gradients at four molecular positions, is tested in a number of common solvents. Agreement of solvent shift and linewidths with experimental Fourier transform infrared (FTIR) data is found to within seven and four wave numbers, respectively, for polar solvents. This shows that in these solvents electrostatic contributions dominate solvation effects and the map is transferable between these types of solvents. The effect of motional narrowing arising from the fast solvent fluctuations is found to be substantial for the FTIR spectra. Also the two-dimensional infrared (2DIR) spectra, simulated using the constructed map, reproduce experimental results very well. The effect of anharmonicity fluctuations on the 2DIR spectra was found to be negligible.

Solvent Controlled Self-Assembly at the Liquid-Solid Interface Revealed by STM

Abstract: The effect of solvent on the two-dimensional (2D) supramolecular ordering of monodendron 1 at the liquid-solid interface has been systematically investigated by means of scanning tunneling microscopy (STM). Solvents range from those with hydrophilic solvating properties, such as alkylated alcohols and acids, to hydrophobic solvents such as alkylated aromatics and alkanes. Dramatic differences in the 2D ordering are observed depending on the nature of the solvent. Of particular interest is the fact that in hydrophobic solvating solvents, such as aliphatic and aromatic hydrocarbons, solvent molecules are coadsorbed in the 2D molecular network while this is not the case for alkylated alcohols or acids. Furthermore, in the case of the coadsorbing solvents, a striking influence of the alkyl chain length has been observed on the 2D pattern formed. The solvent and alkyl chain length dependences are discussed in terms of molecule-molecule interactions (homo and hetero) and molecule-substrate interactions.

Solvent Effect on Organogel Formation by Low Molecular Weight Molecules

Abstract: Solvent−gelator interactions play a key role in mediating organogel formation and ultimately determine the properties of the gel. The effect of solvent on organogel formation was investigated in selected ester, ketone, and alcoholic solvents using unique symmetrical trehalose diesters as gelators. In solvents of the same class the gelation number (defined as the ratio of solvent molecules that gel per gelator molecule) decreased for trehalose 6,6‘-diacetate and 6,6‘-dibutyrate as the solvent Hildebrand solubility parameter increased. The opposite was observed for trehalose 6,6‘-didecanoate and 6,6‘-dimyristate. In general, the gelation numbers for all the gelators studied decreased in the order of esters > ketones > alcohols. Alcohols, which are capable of hydrogen bonding and can make substantial contribution to the total solvent−gelator interaction, significantly compromise gel formation. Optical microscopy and scanning electron microscopy revealed that for systems with high gelation numbers, such as tr...

Sphere, cylinder, and vesicle nanoaggregates in poly(styrene-b-isoprene) diblock copolymer solutions

Abstract: An asymmetric poly(styrene-b-isoprene) diblock copolymer with block molecular weights of 13 000 and 71 000 g/mol, respectively, was dissolved at 1 vol % in a series of solvents with varying selectivity for styrene: dibuthyl phthalate (DBP), diethyl phthalate (DEP), and dimethyl phthalate (DMP). The degree of solvent selectivity was adjusted by mixing DBP/DEP and DEP/DMP in various proportions. With increasing solvent selectivity, the predominant micellar shape changes from spheres to cylinders to vesicles, reflecting the changing interfacial curvature. The detailed micellar morphologies were characterized by small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM). Recently developed form factors were used to characterize the micellar structures in detail, and a vesicle form factor was derived for this system. From the core dimensions, the packing properties, such as the interfacial area per chain and the core chain stretching, were determined. The cryo-TEM results de...

Hydrogen bonding, mobility, and structural transitions in aliphatic polyamides

Abstract: Some salient results in nylon research are reviewed to identify the fundamental principles that are applicable to other strongly interacting or hydrogen-bonded polymers, including proteins. The effects of hydrogen bonds on stress-, heat-, and solvent-induced changes in macroscopic properties are discussed. These data provide a window into the chain mobility and linkages between the crystalline and amorphous domains, both of which are important for any predictive model. The changes in the characteristics of the amorphous phase with the crystallinity and orientation require that it be modeled with at least two components: a rigid/immobile/anisotropic component and a soft/mobile/isotropic component. The deformation and shrinkage behavior of these polymers are discussed in terms of the relative contributions of the amorphous and crystalline domains and of the interactions between them. The premelting crystalline transition is accompanied by the merging of intersheet and intrasheet diffraction peaks in some nylons, as observed by Brill, and not in others even though the underlying mechanism that gives rise to these transitions, the onset of volume-increasing librational motion of the crystalline stems, is the same. Because the effects of the temperature, deformation, and solvent have a common origin associated with mobility, a fictive temperature can be associated with a given solvent activity or stress level. The magnitude of this fictive temperature is the amount by which the glass or Brill transition temperature is reduced in the presence of solvents (∼50 °C) or stress or by which the annealing temperature can be reduced in the presence of a solvent (or active stress) to achieve the same structural state as that of a dry (or static) polymer. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1763–1782, 2006

The Static Dielectric Constant of Ionic Liquids

Abstract: The static dielectric constant of an ionic liquid is not measurable by conventional methods because the samples are largely short-circuited by their intrinsic electrical conductance. It is, however, possible to determine this quantity by recording the frequency-dependent dielectric dispersion curve in the microwave regime, followed by extrapolation to quasi-static conditions. This article compiles the information on static dielectric constants available from such experiments and discusses trends in the cation- and anion-dependence for some widely used imidazolium, pyridinium, pyrrolidinium and alkylammonium salts. The dielectric constant is little sensitive to the nature of the cation, but highly sensitive to the anion. The results classify most ionic liquids as moderately polar solvents with dielectric constants of the order of e = 10-12. Ionic liquids with higher dielectric constants can be designed by introducing highly polar anions such as ethylsulfate. The results are compared with polarity parameters derived from a variety of other experiments, including among others, solvatochromic shifts of probe dyes, polarity parameters deduced from gas chromatography with ionic liquids as stationary phases, and apparent dielectric constants derived from the OH vibrational frequency of dissolved water and from solvent effects on chemical reactions.

Protein-solvent interactions

Abstract: The central importance of solvent interactions in stabilization of specific protein structure has long been recognized. Decades ago, Tanford and Kirkwood treated in detail the interaction of charges with solvent, and showed how desolvation/burial of charges upon protein folding was an important factor in stability 1. The influence of their model, with further elaborations, can still be seen in much subsequent work on protein electrostatics and implicit solvent models. A little later, Kauzmann provided a seminal insight into the second major 'theme' in protein-solvent interaction: The hydrophobic effect and how burial of hydrophobic amino acid side chains could stabilize proteins and play a role in determining their structure2. The view that hydrophobicity is the major contributor to protein stability is widely held 3, although current studies of solvation recognize the importance of other types of solvent-protein interaction, including van der Waals, polar, charged, ionic and hydrogen bonding interactions. The view of solvation as a stabilizing force was further expanded to include the possibility that solvent interactions play a role in specifying structure and function; that water is in effect the ‘21st amino acid’. The field of experimental and theoretical studies, even for this rather specialized topic, is now too vast to be covered in any single review. We have selected four topic for discussion in this review: Peptide-water interactions, New experimental probes of protein hydration, New solvent models for long protein-solvent simulations, and Thermal hysteresis proteins. The selection was guided by the theme of this issue: Protein folding. The rationale for discussing peptides is that the effect of solvent on conformations/nascent folding is best understood in these systems. Peptides have long been used as more experimentally and computationally tractable test systems for studying protein-solvent interactions and developing simulation methods. Thus, much of what is known about the specific and quantitative effects of solvent on proteins is derived from peptide studies. This applies particularly to protein folding. It also goes without saying that many peptides are not simply smaller versions of proteins, but have their own biological importance. New experiments that directly access the hydration of proteins, especially the interior of folded and around unfold proteins, have major implications for how the field views the role of water removal during folding. X-ray crystallography has long been used to analyze water around proteins, and with the routine production of stunningly high resolution structures a wealth of water structure has been revealed. Most X-ray structures, however, are now solved at cryogenic temperatures. This fact, combined with the presence of the crystal lattice makes the relevance of this water structure to biological temperatures and the solution phase problematic at best, and beyond the scope of this review. These concerns and other theoretical issues related to crystallographically observed water have been recently reviewed elsewhere at length. 4–6 In contrast to the rather 'static' picture of protein hydration obtained from crystallography, a 'revised', more dynamic view of protein hydration has resulted from advances in several specific types of spectroscopy, discussed below. Protein folding and unfolding occur on the microsecond to second timescale. Thus very long timescale molecular dynamics (MD) simulations of these events are required. At this point in time, this means one must use implicit solvent models for solvent to be realistically and tractably included. We thus focus on two such implicit models which are currently practical in MD simulations: The Generalized Born (GB) and Poisson Boltzmann (PB) implicit solvent. These two models have changed the way many simulations of proteins in water are done. They have also done much to extend the time scale of routine simulations into the multi-nanosecond to sub-microsecond scale while retaining an accurate treatment of solvent effects. Both these models have been used to study protein electrostatics in a wide variety of applications aside from MD, but this section is not aimed as a general review of GB/PB implicit solvent models. The final topic, thermal hysteresis proteins (THP's), was included because these proteins are unique in their ability to recognize and selectively bind solvent water in its solid phase (i.e. as ice). Study of these proteins is an active area of research. Although the mechanism of thermal hysteresis is not fully understood, study of the unique aspects of THP hydration is leading to qualitatively new information about protein solvation.

exTTF as a Building Block for Fullerene Receptors. Unexpected Solvent-Dependent Positive Homotropic Cooperativity

Abstract: The first exTTF-based receptor for molecular recognition of fullerene is described. Unexpectedly, the receptor shows completely different binding modes in chlorobenzene and CHCl3/CS2 mixtures. In the aromatic solvent, the receptor binds C60 in a noncooperative fashion (nH = 1) with a Kassoc = (2.98 ± 0.12) × 103 M-1, whereas in CHCl3/CS2 mixtures, it shows a marked positive homotropic cooperative effect (nH = 2.7) toward binding of C60, with an apparent binding constant of (3.56 ± 0.16) × 103 M-1. The unique solvent-switchable behavior of our receptor might find use in the controlled self-assembly of exTTF−C60 donor−acceptor ensembles.

Enantioselective arylation of 2-methylacetoacetates catalyzed by CuI/trans-4-hydroxy-L-proline at low reaction temperatures.

Abstract: CuI/trans-4-hydroxy-l-proline-catalyzed coupling reaction of 2-iodotrifluoroacetanilides with 2-methylacetoacetates took place at -45 degrees C to create alpha-aryl all-carbon quaternary centers enantioselectively. Up to 93% ee was achieved when tert-butyl ester was used. The combination of ligand, ortho substituent (participation of NHCOCF3), and solvent effects was shown to account for these unprecedentedly mild reaction conditions.

Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: A computational study of 5-fluorouracil and uracil in acetonitrile and water.

Abstract: The first comprehensive quantum mechanical study of solvent effects on the behavior of the two lowest energy excited states of uracil derivatives is presented. The absorption and emission spectra of uracil and 5-fluorouracil in acetonitrile and aqueous solution have been computed at the time-dependent density-functional theory level, using the polarizable continuum model (PCM) to take into account bulk solvent effects. The computed spectra and the solvent shifts provided by our method are close to their experimental counterpart. The S0/S1 conical intersection, located in the presence of hydrogen-bonded solvent molecules by CASSCF (8/8) calculations, indicates that the mechanism of ground-state recovery, involving out-of-plane motion of the 5 substituent, does not depend on the nature of the solvent. Extensive explorations of the excited-state surfaces in the Franck−Condon (FC) region show that solvent can modulate the accessibility of an additional decay channel, involving a dark n/π* excited state. This ...

Noncovalent Interactions within a Synthetic Receptor Can Reinforce Guest Binding

Abstract: Structural and thermodynamic data are presented on the binding properties of anion receptors containing two covalently linked cyclopeptide subunits that bind sulfate and iodide anions with micromolar affinity in aqueous solution. A synchrotron X-ray crystal structure of the sulfate complex of one receptor revealed that the anion is bound between the peptide rings of the biscyclopeptide. Intimate intramolecular contacts between the nonpolar surfaces of the proline rings of the individual receptor moieties in the complex suggest that hydrophobic interactions within the receptor that do not directly involve the guest contribute to complex stability. This finding is supported by a microcalorimetric analysis of the solvent dependence of complex stability, which showed that increasing the water content of the solvent has only a weak influence on the Gibbs energy of binding. Hence, the increasing amount of energy required for desolvating the binding partners in solutions containing more water is almost compensated by the increasingly favorable hydrophobic interactions. Further observations that suggest that guest-induced intra-receptor interactions contribute to guest binding are (i) anion binding of a monomeric cyclopeptide lacking the covalent linkage between the two rings leads to the formation of 2:1 complexes; (ii) in the crystal structure of the 2:1 iodide complex of this monotopic receptor, a similar arrangement of the two cyclopeptide rings has been found as in the sulfate complex of the biscyclopeptide; (iii) complex formation of the monomeric cyclopeptide in aqueous solution is highly cooperative with a large stability constant corresponding to the formation of the 2:1 complexes from relatively instable 1:1 complexes; (iv) the monomeric cyclopeptide forms only 1:1 anion complexes in DMSO where hydrophobic interactions do not take place; and (v) introducing polar hydroxy groups on the proline rings of the monomeric cyclopeptide disrupts cooperativity causing the formation of only 1:1 complexes even in aqueous solution. Taken together these observations demonstrate that, in addition to direct receptor-substrate interactions, noncovalent interactions between the two subunits of such biscyclopeptides contribute significantly to anion complex stability. Reinforcement of molecular recognition through intra-receptor interactions should be an attractive new strategy to boost host-guest affinities.

Concerning the Relationship between Structural and Growth Synthons in Crystal Nucleation: Solution and Crystal Chemistry of Carboxylic Acids As Revealed through IR Spectroscopy

Abstract: Little is known concerning the precise molecular pathway that links fluid-phase molecules to those in nascent crystal nuclei. In this paper the process of molecular self-assembly has been studied in concentrated solutions using FTIR spectroscopy. Three carboxylic acids, benzoic, tetrolic, and mandelic acids, have been chosen on the basis of their differing crystal chemistries, as reflected in observed hydrogen-bonding motifs. Using the solid-state spectra as a means of unambiguous assignment of carboxyl and hydroxyl vibrations associated with hydrogen bonding, spectroscopic data are reported for solutions as a function of both composition and solvent. In the cases of benzoic acid and tetrolic acid, a link between the growth synthon and the structural synthon is apparent. Mandelic acid, on the other hand, provides a more complex case in which strong solvation effects are evident, leading to the conclusion that significant molecular rearrangement must occur within the developing crystal nuclei.

Mechanism of Oligomerization Reactions of Silica

Abstract: The mechanism of the oligomerization reaction of silica, the initial step of silica formation, has been studied by quantum chemical techniques. The solvent effect is included by using the COSMO model. The formation of various oligomers (from dimer to tetramer) was investigated. The calculations show that the anionic pathway is kinetically preferred over the neutral route. The first step in the anionic mechanism is the formation of the SiO-Si linkage between the reactants to form a five-coordinated silicon complex, which is an essential intermediate in the condensation reaction. The rate-limiting step is water removal leading to the oligomer product. The activation energies for dimer and trimer formation ( approximately 80 kJ/mol) are significantly higher than those of the subsequent oligermerization. The activation energies for the ring closure reaction ( approximately 100 kJ/mol) are even higher. The differences in activation energies can be related to the details in intra- and intermolecular hydrogen bonding of the oligomeric complexes.

The Elusive Mechanism of Olefin Metathesis Promoted by (NHC)Ru-Based Catalysts: A Trade between Steric, Electronic, and Solvent Effects

Abstract: The reaction mechanism operative in olefin metathesis has been and still is a challenging area of research. Here we contribute to the discussion showing that the actual mechanism is a balance of the title effects. In particular, we show that the electronic and solvent effects evidenced by experimental studies can be easily counterbalanced by steric effects.

Substitution and chemical environment effects on the absorption spectrum of indigo.

Abstract: The UV/visible spectra of a series of indigo derivatives have been evaluated by using ab initio methods. The combination of the Polarizable continuum model for estimating bulk solvent effects with the TD-B3LYP∕6-311+G(2d,p)∕∕B3LYP∕6-311G(d,p) level of approximation, leads to an accurate description of the wavelength of maximum absorption of indigoids compounds. Using this procedure, we have assessed the effects of both the surroundings (solvent and solid state) and the substitution pattern. For the latter, we obtained a mean absolute deviation of only 7 nm (0.02 eV) compared to experiment, for a set of 86 molecules/solvents.