The origin of the problems with the PM3 core repulsion function

Quantum chemical assessment of the molecular area corresponding to the onset of the LE-LC phase transition for amphiphilic 2D monolayers at the air/water interface

An approach for the assessment of the area per surfactant molecule in a monolayer at the onset of the LE-LC phase transition (A_c) is proposed based on the quantum chemical approach and a thermodynamic model for amphiphilic monolayers, which takes into account the nonideality of the mixing entropy. The values of the Gibbs' clusterization energy for small surfactant associates, as well as the geometric parameters of the monolayer unit cells, were used, previously calculated using the semiempirical PM3 method for eight classes of amphiphilic compounds: saturated and ethoxylated alcohols, saturated and unsaturated cis-carboxylic acids, α-hydroxylic and α-aminoacids, N-acyl-substituted alanine and dialkyl-substituted melamine. The obtained A_c values are in satisfactory agreement with the available experimental data. This allows using the proposed approach for prognostic purposes in the cases where there are no corresponding π-A isotherms for necessary surfactants, but there are calculated thermodynamic and structural parameters of its clusterization.

Relationship between the Bulk and Surface Basicity of Aliphatic Amines: A Quantum Chemical Approach

To assess the surface basicity constant (pK _b) of aliphatic amine films, the use of a theoretical approach recently developed to evaluate the pK _a of carboxylic acid monolayers on the water surface is tested. The present paper gives a new full picture of the change of acid-base properties of surfactants during their aggregation at the air/water interface. The exploited approach is simple because it does not involve the construction of thermodynamic cycles but uses the Gibbs energies of the formation and dimerization of surfactant monomers in neutral and ionized forms in the aqueous and gaseous phases. The quantum chemical semiempirical PM3 method is applied to perform calculations using a conductor-like screening model, which takes into account the aqueous phase. The calculation shows that aliphatic amines, as well as carboxylic acids, are characterized by a change of the value of the basicity/acidity constant during the film formation. The film formation of surfactants leads to a decrease in their acid-base properties, i.e., the surface pK _a values of carboxylic acids and pK _b values of amines increase. However, unlike carboxylic acids, there is practically no dependence of the surface pK _b value on the alkyl chain length of the aliphatic amine, which is caused by almost identical contributions of one CH₂ fragment to the solvation Gibbs energy of neutral and ionized monomers within the calculation error. The obtained results agree with existing experimental data.

Theoretical Description of Mixed Film Formation at the Air/Water Interface: Carboxylic Acids-Alcohols

The thermodynamic parameters of formation and clusterization of aliphatic alcohols C _n H_2n+1OH and carboxylic acids C _n H_2n+1COOH (n = 6-16) are calculated using the quantum-chemical semiempirical PM3 method. Four types of dimers are constructed in two directions of the spread monolayer comprising the most energetically advantageous monomer structures. The hydrophobic chains of alcohol and carboxylic acid molecules in the regarded dimers are found to be tilted within 12° to the normal of the spread monolayer. The structures of the mixed and pure surfactant dimers are the basis for the mixed alcohol-carboxylic acid monolayers of the following types: two dimensional (2D) film 1 with single distribution of the individual component in the other one, when the molecules of the first component do not interact with each other but are completely surrounded by the molecules of the second component; 2D film 2 with domain structure, when the film consists of "islands" of the individual components. The dependences of the clusterization Gibbs' energy per one monolayer molecule on the molar fraction of the components for the mixed 2D films 1 formed by surfactants with equal alkyl chain length are found to be limited from top to bottom by the corresponding dependences for pure components. This indicates the absence of synergetic interaction between the hydrophilic head groups of carboxylic acids and alcohols and conforms to the available experimental data. The formation of the described types of mixed films is competitive. The preferential formation of 2D films 1 with single distribution of the first component among the molecules of the second one is possible when the length of the carboxylic acid hydrocarbon chain is longer by Δn = 1-2 methylene units than that of the corresponding alcohol alkyl chain. According to the fractionally linear law, the highest possible content of the carboxylic acids in such 2D films 1 depends on the Δn value and does not exceed 33.3%.

Development of Semiempirical Models for Proton Transfer Reactions in Water

This letter presents a method for the parametrization of semiempirical models for proton transfer reactions in water clusters. Two new models are developed: AM1-W, which is a reparameterization of the classic AM1 model, and AM1PG-W, which is a modified AM1-like model including a pairwise correction to the core repulsion function. Both models show good performance on hydrogen-bonding energies and on proton transfer energy profiles, which are of great importance for proton transfer reactions in large water clusters and in proteins. The parametrization method introduced is general and can be used to develop any other system-specific semiempirical models.

Conformational studies of dammarane-type triterpenoids using computational and NMR spectroscopic methods

Natural triterpenoids are of great interest to researchers of various fields as they possess diverse physicochemical and biological properties. In medicinal chemistry, detailed information about the chemical structures of bioactive triterpenoids often helps find new lead compounds. Herein, the low-energy structures of (20S)-protopanaxadiol and (20S)-protopanaxatriol, the aglycones of various triterpenoid saponins found in Panax ginseng, and their (20R)-epimers have been predicted by the geometry optimization of the conformers extracted from molecular dynamics simulations with the self-consistent-charge density functional tight-binding method. By performing quantum mechanical calculations on the low-energy conformers, we have estimated the NMR chemical shifts of the compounds, which display good agreement with the most recently reported experimental values within an expected range of errors. Our results indicate that theoretical estimation of the NMR parameters of a relatively large molecule with a molecular mass of 500 is feasible.

Water interactions with hydrophobic groups: assessment and recalibration of semiempirical molecular orbital methods

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.

Enhanced semiempirical QM methods for biomolecular interactions

Recent successes and failures of the application of 'enhanced' semiempirical QM (SQM) methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) and hydrogen-bond (H) correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D), while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy.

Low-Cost Quantum Chemical Methods for Noncovalent Interactions

The efficient and reasonably accurate description of noncovalent interactions is important for various areas of chemistry, ranging from supramolecular host-guest complexes and biomolecular applications to the challenging task of crystal structure prediction. While London dispersion inclusive density functional theory (DFT-D) can be applied, faster "low-cost" methods are required for large-scale applications. In this Perspective, we present the state-of-the-art of minimal basis set, semiempirical molecular-orbital-based methods. Various levels of approximations are discussed based either on canonical Hartree-Fock or on semilocal density functionals. The performance for intermolecular interactions is examined on various small to large molecular complexes and organic solids covering many different chemical groups and interaction types. We put the accuracy of low-cost methods into perspective by comparing with first-principle density functional theory results. The mean unsigned deviations of binding energies from reference data are typically 10-30%, which is only two times larger than those of DFT-D. In particular, for neutral or moderately polar systems, many of the tested methods perform very well, while at the same time, computational savings of up to 2 orders of magnitude can be achieved.

Temperature effect on the monolayer formation of substituted alkanes at the air/water interface: a quantum chemical approach

An approach to calculation of the threshold temperature for spontaneous clusterization of substituted alkanes (amines, nitriles, alcohols, thioalcohols, saturated and unsaturated carboxylic acids, α-amino acids, carboxylic acid amides, and melamine derivatives) at the air/water interface with dependence on the alkyl chain length was developed. In the framework of this approach, four schemes for the description of the temperature dependencies of the thermodynamic parameters of clusterization of the concerned amphiphilic compounds were proposed. They use the data obtained previously in the framework of quantum chemical semiempirical PM3 method and differ from each other by the degree of their theoretical accuracy. It was shown that the threshold temperature for spontaneous clusterization of the regarded classes of substituted alkanes can be described using a fractionally linear function in dependence on the alkyl chain length. It was found that, in agreement with the presented experimental data, the effect of the alkyl chain elongation of the substituted alkanes by two methylene units correlates with the decrease of the subphase temperature (ΔT) by 10-20 K. The general shape of the obtained dependencies indicates that the difference in the ΔT values for the amphiphilic molecules decreases with increasing alkyl chain length. This implies that the contribution of the intermolecular CH···HC interactions between the alkyl chains of monolayer molecules should be a decisive factor.

Cavity closure dynamics of peracetylated β-cyclodextrins in supercritical carbon dioxide

Structural properties of peracetylated β-cyclodextrin in supercritical carbon dioxide were investigated by means of molecular dynamics simulations. The study indicated a strong reduction of the cavity accessibility to guest molecules, compared to native β-cyclodextrin in water. Indeed, the cavity is self-closed during the largest part of the simulation, which agrees well with suggestions made on the basis on high-pressure NMR experiments. Self-closure happens because one glucose unit undergoes a main conformational change (from chair to skew) that brings one of the acetyl groups in the wide rim of the cyclodextrin to the cavity interior. This arrangement turns out to be quite favorable, persisting for several nanoseconds. In addition to the wide rim self-closure, a narrow rim self-closure may also occur, though it is less likely and exhibits short duration (<1 ns). Therefore, the number of solvent molecules reaching the cavity interior is much smaller than that found in the case of native β-cyclodextrin in water after correction to account for different molar densities. These findings support the weak tendency of the macromolecule to form host-guest complexes in this nonconventional medium, as reported by some experiments. Finally, Lewis acid/base interactions between the acetyl carbonyl groups and the solvent CO(2) molecules were analyzed through ab initio calculations that revealed the existence of a quite favorable four-member ring structure not yet reported. The ensemble of these results can contribute to establish general thermodynamic principles controlling the formation of inclusion complexes in supercritical CO(2), where the hydrophilicity/hydrophobicity balance is not applicable.

Are current semiempirical methods better than force fields? A study from the thermodynamics perspective

The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, were compared on their abilities to reproduce experimental ensemble averages at or near room temperatures for the model system alanine dipeptide in water. Free energy surfaces in the (phi, psi) dihedral angle space, (3)J(H(N),H(alpha)) NMR dipolar coupling constants, basin populations, and peptide-water radial distribution functions (RDF) were calculated from replica exchange simulations and compared to both experiment and fully classical force field calculations using the Amber ff99SB force field. In contrast with the computational chemist's intuitive idea that the more expensive a method the better its accuracy, the ff99SB force field results were more accurate than most of the semiempirical methods, with the exception of RM1. None of the methods, however, was able to accurately reproduce the experimental data. Analysis of the results indicate that the specific QM/MM interactions have little influence on the sampling of free energy surfaces, and the differences are well explained simply by the intrinsic properties of the various QM methods.

A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods

Semiempirical methods could offer a feasible compromise between ab initio and empirical approaches for the calculation of large molecules with biological relevance. A key problem for attempts in this direction is the rather bad performance of current semiempirical methods for noncovalent interactions, especially hydrogen-bonding. On the basis of the recently introduced PM6-DH method, which includes empirical corrections for dispersion (D) and hydrogen-bond (H) interactions, we have developed an improved and transferable H-bonding correction for semiempirical quantum chemical methods. The performance of the improved correction is evaluated for PM6, AM1, OM3, and SCC-DFTB (enhanced by standard empirical dispersion corrections) with several test sets for noncovalent interactions and is shown to reach the quality of current DFT-D approaches for these types of problems.

Experimental and computational structural study of two hindered aminoanthraquinones in crystals and solutions

The crystal and molecular structures of 2-methyl-1-methylamino-anthraquinone (I) and 1-methylphenylamino-anthraquinone (II) were studied by the X-ray single-crystal diffraction and the visible spectra of crystalline specimens and their solutions were recorded. The molecule I is closely planar, whereas in the molecule II the amino group is 58° rotated out of the plane of the anthraquinone skeleton. In both structures the molecules pack in stacks. The comparison of experimental and calculated (on the DFT and AM1 levels) molecular structures, together with the comparison of experimental and INDO/S-calculated electronic spectra, give the evidence that molecular conformations (especially for II) change upon transfer from the solid state to solutions, and the π-delocalisation throughout the whole molecule enhances in the solid state.

Comparison of different force fields for the study of disaccharides

Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying beta-cellobiose, alpha-maltose, and alpha-galabiose [alpha-D-Galp-(1-->4)-alpha-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl, and glycosidic linkage orientations were minimized by the different methods, some at two dielectric constants. By comparing these results and the available crystal structure data and/or higher level density functional theory results, it was concluded that the newer parameterizations for force fields (GROMOS, GLYCAM06, OPLS-2005 and CSFF) give results that are reasonably similar to each other, whereas the older parameterizations for Amber, CHARMM or OPLS were more divergent. However, MM3, an older force field, gave energy and geometry values comparable to those of the newer parameterizations, but with less sensitivity to dielectric constant values. These systems worked better than MM2 variants, which were still acceptable. PM3CARB-1 also gave adequate results in terms of linkage and exocyclic torsion angles. GROMOS, GLYCAM06, and MM3 appear to be the best choices, closely followed by MM4, CSFF, and OPLS-2005. With GLYCAM06 and to a lesser extent, CSFF, and OPLS-2005, a number of the conformers that were stable with MM3 changed to other forms.

Self-consistent polarization neglect of diatomic differential overlap: application to water clusters

Semiempirical self-consistent field (SCF) methods based on the neglect of diatomic differential overlap (NDDO) formalism have the ability to treat the formation and breaking of chemical bonds but have been found to poorly describe hydrogen bonding and weak electrostatic complexes. In contrast, most empirical potentials are not able to describe bond breaking and formation but have the ability to add missing elements of hydrogen bonding by using classical electrostatic interactions. We present a new method which combines aspects of both NDDO-based SCF techniques and classical descriptions of polarization to describe the diffuse nature of the electronic wavefunction in a self-consistent manner. We develop the "self-consistent polarization neglect of diatomic differential overlap" (SCP-NDDO) theory with the additional description of molecular dispersion developed as a second-order perturbation theory expression. The current study seeks to model water-water interactions as a test case. To this end, we have parametrized the method to accurate ab initio complete basis set limit estimates of small water cluster binding energies of Xantheas and co-workers [J. Chem. Phys. 116, 1493 (2002); 120, 823 (2004)]. Overall agreement with the ab initio binding energies (n=2-6, and 8) is achieved with a rms error of 0.19 kcal/mol. We achieve noticeable improvements in the structure, vibrational frequencies, and energetic predictions of water clusters (n< or =21) relative to standard NDDO-based methods.

Photochemical processes induced by vibrational overtone excitations: dynamics simulations for cis-HONO, trans-HONO, HNO3, and HNO3-H2O

Photochemical processes in HNO3, HNO3-H2O, and cis- and trans-HONO following overtone excitation of the OH stretching mode are studied by classical trajectory simulations. Initial conditions for the trajectories are sampled according to the initially prepared vibrational wave function. Semiempirical potential energy surfaces are used in "on-the-fly" simulations. Several tests indicate at least semiquantitative validity of the potential surfaces employed. A number of interesting new processes and intermediate species are found. The main results include the following: (1) In excitation of HNO3 to the fifth and sixth OH-stretch overtone, hopping of the H atom between the oxygen atoms is found to take place in nearly all trajectories, and can persist for many picoseconds. H-atom hopping events have a higher yield and a faster time scale than the photodissociation of HNO3 into OH and NO2. (2) A fraction of the trajectories for HNO3 show isomerization into HOONO, which in a few cases dissociates into HOO and NO. (3) For high overtone excitation of HONO, isomerization into the weakly bound species HOON is seen in all trajectories, in part of the events as an intermediate step on the way to dissociation into OH + NO. This process has not been reported previously. Well-established processes for HONO, including cis-trans isomerization and H hopping are also observed. (4) Only low overtone levels of HNO3-H2O have sufficiently long liftimes to be spectrocopically relevant. Excitation of these OH stretching overtones is found to result in the dissociation of the cluster H hopping, or dissociation of HNO3 does not take place. The results demonstrate the richness of processes induced by overtone excitation of HNO(x) species, with evidence for new phenomena. Possible relevance of the results to atmospheric processes is discussed.

Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach

This work examines the ability of semiempirical methods to describe the structure of liquid water. Particularly, the standard AM1 and PM3 methods together with recently developed PM3-PIF and PM3-MAIS parametrizations have been considered. We perform molecular dynamics simulations for a system consisting of 64 or 216 water molecules in a periodic cubic box. The whole system is described quantum mechanically. Calculations with 64 molecules have been carried out using standard SCF techniques whereas calculations with 216 molecules have been done using the divide and conquer approach. This method has also been used in one simulation case with 64 molecules for test purposes. Within this scope, the molecular dynamics program ROAR have been coupled with a linear scaling semiempirical code (DivCon) implemented in a parallel MPI version. The predicted liquid water structure using either AM1 or PM3 is shown to be very poor due to well-known limitations of these methods describing hydrogen bonds. In contrast, PM3-PIF and PM3-MAIS calculations lead to results in reasonably good agreement with experimental data. The best results for the heat of vaporization are obtained with the PM3-PIF method. The average induced dipole moment of the water molecule in the liquid is underestimated by all semiempirical techniques, which seems to be related to the NDDO approximation and to the use of minimal basis sets. A brief discussion on charge-transfer effects in liquid water is also presented.

Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules

Semi-empirical calculations including an empirical dispersive correction are used to calculate intermolecular interaction energies and structures for a large database containing 156 biologically relevant molecules (hydrogen-bonded DNA base pairs, interstrand base pairs, stacked base pairs and amino acid base pairs) for which MP2 and CCSD(T) complete basis set (CBS) limit estimates of the interaction energies are available. The dispersion corrected semi-empirical methods are parameterised against a small training set of 22 complexes having a range of biologically important non-covalent interactions. For the full molecule set (156 complexes), compared to the high-level ab initio database, the mean unsigned errors of the interaction energies at the corrected semi-empirical level are 1.1 (AM1-D) and 1.2 (PM3-D) kcal mol(-1), being a significant improvement over existing AM1 and PM3 methods (8.6 and 8.2 kcal mol(-1)). Importantly, the new semi-empirical methods are capable of describing the diverse range of biological interactions, most notably stacking interactions, which are poorly described by both current AM1 and PM3 methods and by many DFT functionals. The new methods require no more computer time than existing semi-empirical methods and therefore represent an important advance in the study of important biological interactions.

Interaction energy decomposition in protein-protein association: a quantum mechanical study of barnase-barstar complex

Protein-protein interactions are very important in the function of a cell. Computational studies of these interactions have been of interest, but often they have utilized classical modelling techniques. In recent years, quantum mechanical (QM) treatment of entire proteins has emerged as a powerful approach to study biomolecular systems. Herein, we apply a semi-empirical divide and conquer (DC) methodology coupled with a dielectric continuum model for the solvent, to explore the contribution of electrostatics, polarization and charge transfer to the interaction energy between barnase and barstar in their complex form. Molecular dynamic (MD) simulation was performed to account for the dynamic behavior of the complex. The results show that electrostatics, charge transfer and polarization favor the formation of the complex. Our study shows that electrostatics dominates the interaction between barnase and barstar ( approximately 73%), while charge transfer and polarization are approximately 21% and approximately 6%, respectively. Close inspection of the polarization and charge-transfer effects on the charge distribution of the complex reveals the existence of two, well localized, regions in barstar. The first region includes the residues between P27 and Y47 and the second region is between N65 and D83. Since no such regions could be detected in barnase clearly suggests that barstar is well optimized for efficiently binding barnase. Furthermore, using our interaction energy decomposition scheme, we were able to identify all residues that have been experimentally determined to be important for the complex formation and to suggest other residues never have been investigated. This suggests that our approach will be useful as an aid in further understanding protein-protein contacts for the ultimate goal to produce successful inhibitors for protein complexes.

Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules?

A set of iron parameters for use in the semiempirical PM3 method have been developed to allow the structure and redox properties of the active sites of iron-containing proteins to be accurately modeled, focussing on iron-sulfur, iron-heme, and iron-only hydrogenases. Data computed at the B3LYP/6-31G* level for a training set of 60 representative complexes have been employed. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure and energetics of molecules both within and outside the training set, and overcome the extensive deficiencies of a B3LYP/STO-3G model. Particularly encouraging is the success of the parameters in describing [4Fe-4S] cubanes. The derived parameter set provides a starting point should greater accuracy for a more restricted range of compounds be required.

Development of parameter sets for semi-empirical MO calculations of transition metal systems: Iron parameters for iron–sulfur proteins

A semi-empirical parameter set for iron has been developed which is appropriate for the study of iron-sulfur proteins having a single iron atom, by fitting to density-functional theory (DFT) calculations obtained for a series of small models of iron-containing proteins. These parameters are obtained using a modified BFGS optimisation procedure previously used to obtain semi-empirical parameters for the main group elements. The modifications to this procedure for obtaining parameters for transition metal atoms are outlined. In addition to modifications to the semi-empirical core repulsion function, which yield significant improvements in the calculation of molecular structures, compared to the standard core repulsion function, are outlined. The reported parameters are then tested on a set of model complexes containing a variety of ligands and show good agreement with both DFT and experimental data for these species.

Different chemical dynamics for different conformers of biological molecules: Photoionization of glycine

Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier.

A Model for Double Asymmetric Induction in the Stereocontrolled Reduction of Glycosyl α-Ketoesters with Oxazaborolidines

Experimental diastereoselectivities for the stereocontrolled reduction of glycosyl alpha-ketoesters into the corresponding alpha-hydroxyesters have recently been reported with unexpected results. The process is catalyzed by a chiral oxazaborolidine derivative (the so-called CBS catalyst) and represents the key step in the synthesis of glycosyl alpha-amino acids synthons, a class of compounds that allow preparation of natural glycopeptides analogues exhibiting potential therapeutic relevance. Good to very good diastereomeric excesses have been obtained for a series of reactions with different glucidic derivatives, but surprisingly, the major product obtained does not correspond to that predicted by using Corey's model. In the present work, we carry out a theoretical investigation of these reactions at the density functional level. Separated effects from the catalyst and from the glucidic derivative have been computed to rationalize the observed diastereoselectivities and the double asymmetric induction.

Testing electronic structure methods for describing intermolecular H...H interactions in supramolecular chemistry

In this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2-(2'-hydroxyphenyl)-4-methyloxazole (HPMO) encapsulated in beta-cyclodextrin (beta-CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H. H intermolecular interactions between guest (HPMO) and host (beta-CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H...H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H...H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H...H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(beta-CD)-guest(HPMO) system.

Highly Diastereoselective Hydrogenations Leading to β-Hydroxy δ-Lactones in Hydroxy-Protected Form. A Modified View of δ-Lactone Conformations

Enol MEM ethers 4 and 15 and the corresponding enol acetates were hydrogenated over Pd/C with very high (>99%) diastereoselectivity to saturated delta-lactones. A stereochemical generalization can be formulated thus: trans-5,6-disubstituted 1-oxa-3-cyclohexen-2-ones (e.g. 14 and 15) are hydrogenated over Pd with high selectivity from the side trans to the C(6)-substituent. A mechanistic rationalization of the stereochemical outcome in the Pd-catalyzed hydrogenation of this as well as other types of substituted alpha,beta-unsaturated delta-lactones is presented. An analysis of X-ray crystallographic data for 67 compounds demonstrated a great conformational diversity of the saturated delta-lactone ring. Besides, ab initio calculations (HF/6-31G) indicated a very high conformational mobility. Thus, the lowest calculated transition state for the conversion of the half-chair, most stable, conformer of delta-valerolactone to the boat-type conformer lies only 1.93 kcal/mol above the former. Beside these two conformers, also chair, envelope and skew conformations are accessible; all lie less than 2 kcal/mol above the half-chair. The previous conformational paradigm comprising only boat and half-chair types is incomplete.

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods

Two new semiempirical methods employing a Pairwise Distance Directed Gaussian modification have been developed: PDDG/PM3 and PDDG/MNDO; they are easily implemented in existing software, and yield heats of formation for compounds containing C, H, N, and O atoms with significantly improved accuracy over the standard NDDO schemes, PM5, PM3, AM1, and MNDO. The PDDG/PM3 results for heats of formation also show substantial improvement over density functional theory with large basis sets. The PDDG modifications consist of a single function, which is added to the existing pairwise core repulsion functions within PM3 and MNDO, a reparameterized semiempirical parameter set, and modified computation of the energy of formation of a gaseous atom. The PDDG addition introduces functional group information via pairwise atomic interactions using only atom-based parameters. For 622 diverse molecules containing C, H, N, and O atoms, mean absolute errors in calculated heats of formation are reduced from 4.4 to 3.2 kcal/mol and from 8.4 to 5.2 kcal/mol using the PDDG modified versions of PM3 and MNDO over the standard versions, respectively. Several specific problems are overcome, including the relative stability of hydrocarbon isomers, and energetics of small rings and molecules containing multiple heteroatoms. The internal consistency of PDDG energies is also significantly improved, enabling more reliable analysis of isomerization energies and trends across series of molecules; PDDG isomerization energies show significant improvement over B3LYP/6-31G* results. Comparison of heats of formation, ionization potentials, dipole moments, isomer, and conformer energetics, intermolecular interaction energies, activation energies, and molecular geometries from the PDDG techniques is made to experimental data and values from other semiempirical and ab initio methods.