Charge distribution in the water molecule--a comparison of methods

Approximating quantum many-body intermolecular interactions in molecular clusters using classical polarizable force fields

Many-body intermolecular interaction expansions provide a promising avenue for the efficient quantum mechanical treatment of molecular clusters and condensed-phase systems, but the computationally expensive three-body and higher terms are often nontrivial. When polar molecules are involved, these many-body terms are typically dominated by electrostatic induction effects, which can be approximated relatively easily. We demonstrate an accurate and inexpensive hybrid quantum/classical model in which one- and two-body interactions are computed quantum mechanically, while the many-body induction effects are approximated with a simple classical polarizable force field. Whereas typical hybrid quantum/classical models partition a system spatially into distinct quantum and classical regions, the model demonstrated here partitions based on the order in the many-body interaction series. This enables a spatially homogeneous treatment of the entire system, which could prove advantageous in studying a wide range of condensed-phase molecular systems.

Role of charge transfer in the structure and dynamics of the hydrated proton

Although it has long been recognized that multiple water molecules strongly associate with an extra proton in bulk water, some models and conceptual frameworks continue to utilize the classical hydronium ion (H(3)O(+)) as a fundamental building block. In this work, the nature of the hydronium ion in aqueous systems is examined using an ab initio energy decomposition analysis (EDA) that evaluates both the magnitude of and energetic stabilization due to charge transfer among H(3)O(+) and the surrounding water molecules. The EDA is performed on structures extracted from dynamical bulk-phase simulations and used to determine how frequently the pure hydronium ion, where the excess charge is primarily localized on H(3)O(+), occurs under dynamic conditions. The answer is essentially never. The energetic stabilization of H(3)O(+) due to charge delocalization to neighboring water molecules is found to be much larger (16-49 kcal/mol) than for other ions (even Li(+)) and to constitute a substantial portion (20-52%) of the complex's binding energy. The charge defect is also shown to have intrinsic dynamical asymmetry and to display dynamical signatures that can be related to features appearing in IR spectra.

From monomer to bulk: appearance of the structural motif of solid iodine in small clusters

Formation of iodine clusters in a solid krypton matrix was studied using resonance Raman spectroscopy with a 1 cm(-1) resolution. The clusters were produced by annealing of the solid and recognized by appearance of additional spectral transitions. Two distinct regions, red-shifted from the fundamental vibrational wavenumber of the isolated I(2) at 211 cm(-1), were observed in the signal. The intermediate region spans the range 196-208 cm(-1), and the ultimate region consists of two peaks at 181 and 190 cm(-1) nearly identical to crystalline I(2). The experimental results were compared to DFT-D level electronic structure calculations of planar (I(2))(n) clusters (n = 1-7). The dimer, trimer, and tetramer structures, where the I(2) molecule is complexed from one end, were found to exhibit vibrational shifts corresponding to the intermediate size clusters. The larger, bulklike shift appears when the iodine molecule is coordinated from two opposite directions as in the case of a pentamer and higher clusters. Starting from the pentamer, the structural motif of crystalline iodine is clearly recognized in the clusters.

Selective adsorption of poly(ethylene oxide) onto a charged surface mediated by alkali metal ions

Using a surface force balance, we have measured normal and shear interactions between mica surfaces across pure water and across 0.1 M aqueous solutions of LiNO3, NaNO3, KNO3, and CsNO3, both prior to adding polymer and following addition of 1.5 x 10(-4) w/w poly(ethylene oxide) (PEO, Mw = 170 kD) and overnight incubation. Our results reveal that while the PEO adsorbs strongly from the KNO3 and CsNO3 solutions, unexpectedly it does not adsorb at all from the LiNO3 and NaNO3 salt solutions. We attribute this to the different nature of the hydration layers about the alkali metal ions: these favor liganding to the negatively charged mica surface of the etheric -O- group on the ethylene oxide monomer for the case of the more weakly hydrated K+ and Cs+, but not for the case of Na+ or Li+ with their more strongly bound water. A simple model relating the electrostatic energy changes occurring upon such liganding to the experimentally measured hydration energies of the different alkali metal ions supports this attribution.

Recent synthetic approaches toward non-anomeric spiroketals in natural products

Many natural products of biological interest contain [6,5]- and [6,6]-spiroketal moieties that can adopt various configurations, benefiting or not from anomeric conformation stabilizing effects. The spiroketal fragments are often important for the biological activity of the compounds containing them. Most stable spiroketal stereoisomers, including those benefiting from conformational anomeric effects (gauche conformers can be more stable than anti conformers because of a contra-steric stabilizing effect), are obtained easily under acidic conditions that permit acetal heterolysis (formation of tertiary oxycarbenium ion intermediates). The synthesis of less stable stereoisomers requires stereoselective acetal forming reactions that do not permit their equilibration with their most stable stereoisomers or, in the case of suitably substituted derivatives, concomitant reactions generating tricyclic products that quench the less stable spiroketal conformers. Ingenuous approaches have been recently developed for the synthesis of naturally occurring [6,6]- and [5,6]-nonanomeric spiroketals and analogues. The identification of several parameters that can influence the stereochemical outcome of spirocyclization processes has led to seminal improvements in the selective preparation of the non-anomeric isomers that are discussed herein. This review also gives an up-dated view of conformational anomeric effect which represents a small fraction of the enthalpic anomeric effect that makes gem-dioxy substituted compounds much more stable that their 1,n-dioxy substituted isomers (n > 1). Although models assuming sp3-hybridized oxygen atoms have been very popular (rabbit ears for the two non-bonding electron pairs of oxygen atom), sp2-hybridized oxygen atoms are used to describe the conformational anomeric effect.

Two-state model based on the block-localized wave function method

The block-localized wave function (BLW) method is a variant of ab initio valence bond method but retains the efficiency of molecular orbital methods. It can derive the wave function for a diabatic (resonance) state self-consistently and is available at the Hartree-Fock (HF) and density functional theory (DFT) levels. In this work we present a two-state model based on the BLW method. Although numerous empirical and semiempirical two-state models, such as the Marcus-Hush two-state model, have been proposed to describe a chemical reaction process, the advantage of this BLW-based two-state model is that no empirical parameter is required. Important quantities such as the electronic coupling energy, structural weights of two diabatic states, and excitation energy can be uniquely derived from the energies of two diabatic states and the adiabatic state at the same HF or DFT level. Two simple examples of formamide and thioformamide in the gas phase and aqueous solution were presented and discussed. The solvation of formamide and thioformamide was studied with the combined ab initio quantum mechanical and molecular mechanical Monte Carlo simulations, together with the BLW-DFT calculations and analyses. Due to the favorable solute-solvent electrostatic interaction, the contribution of the ionic resonance structure to the ground state of formamide and thioformamide significantly increases, and for thioformamide the ionic form is even more stable than the covalent form. Thus, thioformamide in aqueous solution is essentially ionic rather than covalent. Although our two-state model in general underestimates the electronic excitation energies, it can predict relative solvatochromic shifts well. For instance, the intense pi-->pi* transition for formamide upon solvation undergoes a redshift of 0.3 eV, compared with the experimental data (0.40-0.5 eV).

Computational Study on the Properties and Structure of Methyl Lactate

A theoretical study on the properties and molecular level structure of the very important green solvent methyl lactate is carried out in the gas phase and methanol and water solutions, with the solvent treated both explicitly and as a continuum. Torsional barriers giving rise to different conformers by rotation of the hydroxyl and methyl groups were analyzed using density functional theory (DFT) to establish the most stable conformer both in gas phase and solution. DFT computations on lactate dimers were also done to study short-range features, and the effect of the surrounding solvent on intra- and intermolecular hydrogen bonding was analyzed according to the polarizable continuum model approach. We have also studied lactate/water and lactate/methanol small clusters together with the corresponding binding energies. Moreover, classical molecular dynamics simulations (MD) were carried out to study medium- and large-range effects at lower computational cost. MD simulations at different pressure and temperature conditions on pure lactate were carried out, and mixtures with water and methanol of different compositions were also studied. Structural information, analyzed through the radial distribution functions, together with dynamic aspects of pure and mixed fluids were considered. The intramolecular hydrogen bonding ability of methyl lactate together with the possibility of homo- and hetero-intermolecular association determines the behavior of this molecule in pure fluids or in mixed.

“Amide Resonance” Correlates with a Breadth of C−N Rotation Barriers

Complete basis set calculations (CBS-QB3) were used to compute the CN rotation barriers for acetamide and eight related compounds, including acetamide enolate and O-protonated acetamide. Natural resonance theory analysis was employed to quantify the "amide resonance" contribution to ground-state electronic structures. A range of rotation barriers, spanning nearly 50 kcal/mol, correlates well to the ground-state resonance weights without the need to account for transition-state effects. Use of appropriate model compounds is crucial to gain an understanding of the structural and electronic changes taking place during rotation of the CN bond in acetamide. The disparate changes in bond length (DeltarCO << DeltarCN) are found to be consonant with the resonance model. Similarly, charge differences are consistent with donation from the nitrogen lone pair electrons into the carbonyl pi* orbital. Despite recent attacks on the resonance model, these findings demonstrate it to be a sophisticated and highly predictive tool in the chemist's arsenal.

Change in a protein's electronic structure induced by an explicit solvent: Anab initio fragment molecular orbital study of ubiquitin

The effect of solvation on the electronic structure of the ubiquitin protein was analyzed using the ab initio fragment molecular orbital (FMO) method. FMO calculations were performed for the protein in vacuo, and the protein was immersed in an explicit solvent shell as thick as 12 A at the HF or MP2 level by using the 6-31G* basis set. The protein's physical properties examined were the net charge, the dipole moment, the internal energy, and the solvent interaction energy. Comparison of the computational results revealed the following changes in the protein upon solvation. First, the positively charged amino acid residues on the protein surface drew electrons from the solvent, while the negatively charged ones transfer electrons to the solvent. Second, the dipole moment of the protein was enhanced as a result of the polarization. Third, the internal energy of the protein was destabilized, but the destabilization was more than compensated for by the generation of a favorable protein-solvent interaction. Finally, the energetic changes were elicited both by the electron correlation effect of the first solvent shell and by the electrostatic effect of more distant solvent molecules. These findings were consistent with the picture of the solvated protein being a polarizable molecule dissolved in a dielectric media.

Can the pH value of water solutions be estimated by quantum chemical calculations of small water clusters?

In the study, various water clusters were explored from the point of view of the proton transfer between H-bonded neighbors. A relatively modest approach--the MP26-31++G(d,p) level--was chosen as acceptable considering the fact that also larger systems have to be included. The tight ion-pair model (with usually three fixed O-O distances) was adopted for the autodissociation process. First, cluster-estimated pH values rapidly decrease as cluster size increases from 2 to 6. For larger clusters in gas phase, the topology of H bonds plays an important role, varying pH from 7 to 13 in hexamers and from 5 to 15 in octamer clusters. The relationship energy/distance was quantified, too. Enhancing our model with the conductorlike screening model (COSMO) approach brought significant improvement in description of the autodissociation reaction with a stable zwitterionic structure. However, when the O-O restrictions were released, the small barrier for backward reaction disappeared, reforming neutral cluster spontaneously. Also Boltzmann weighting procedure was applied, and for the explored clusters in vacuo, the series of pH 25-18-14-13-10 was obtained for cluster sizes n=2, 3, 4, 6, 8. Using the COSMO approach, the analogous series is 15-14-12-10-9. The limit of the series is still about two to three units above the experimentally known pH. In order to reach the size-independent (bulk) value, larger clusters are needed. However, the situation is far from hopeless since (as it was proven in the study) four-coordinated molecules are not involved in the proton transfer process directly; they can only be a part of the surrounding environment.

Unexpected Four-Membered over Six-Membered Ring Formation during the Synthesis of Azaheterocyclic Phosphonates: Experimental and Theoretical Evaluation

The cyclization of functionalized aminophosphonates is studied on both experimental and theoretical grounds. In a recently described route to phosphono-beta-lactams [Stevens C. V.; Vekemans, W.; Moonen, K.; Rammeloo, T. Tetrahedron Lett. 2003, 44, 1619], it was found that starting from an ambident allylic anion only four-membered rings were formed without any trace of six-membered lactams. New anion trapping experiments revealed that the gamma-anion is highly reactive in intermolecular reactions. Ab initio calculations predict higher reaction barriers for the gamma-anion due to restricted rotation about the C-N bond and due to highly strained transition states during ring closure. The sodium or lithium counterion, explicit dimethyl ether solvent molecules, and bulk solvent effects were properly taken into account at various levels of theory.