Anne-Marie Kelterer

HF/6‐31G* energy surfaces for disaccharide analogs

The HF/6‐31G* level of theory was used to calculate relaxed potential energy surfaces for 12 analogs of disaccharides. The analogs were made by replacing glucose with tetrahydropyran and fructose with 2‐methyltetrahydrofuran. Molecules had zero, one or two anomeric carbon atoms, and di‐axial, axial‐equatorial, and di‐equatorial linkages. Despite the absence of hydroxyl groups, the surfaces account well for conformations that are observed in crystals of the parent disaccharides. Thus, torsional energy and the simple bulk of ring structures are major factors in determining disaccharide conformation. The contour shapes around the global minima depend on the number of anomeric carbons involved in the linkage, while the presence of alternative minima that have relative energies less than 4 kcal/mol mostly requires equatorial bonds. However, molecules with two adjacent anomeric centers gave exceptions to these rules. Flexibility values related to a partition function show that the di‐axial trehalose analog is the most rigid. The di‐equatorial pseudodisaccharide analog with no anomeric centers is most flexible. Reproduction of these surfaces is proposed as a simple test of force fields for modeling carbohydrates. Also, these surfaces can be used in a simple hybrid method for calculating disaccharide energy surfaces.

Constructing and evaluating energy surfaces of crystalline disaccharides

This paper focuses on the methods used to construct Ramachandran plots for disaccharides. Our recent work based on a hybrid of molecular mechanics and quantum mechanics energies pointed to the need to take extra care when making these maps. Care is also important in the quantitative validation of these energy surfaces with linkage conformations that were determined by crystallography. To successfully predict conformations that have been observed experimentally, the calculation of the energy should include stereoelectronic effects and correctly weight the hydrogen bonding. Technical concerns include the method used to scan the range of conformations, starting geometries, and finding the zero of relative potential energy on a surface where the values were collected at regular intervals. The distributions of observed conformations on energy maps of sucrose, maltose, and laminarabiose at dielectric constants of 1.5 and 7.5 illustrate the effects of an elevated dielectric constant for the MM3 component of the hybrid energy calculations. At dielectric constants of 3.5 and 7.5, the overall average energies of observed conformations of sucrose and seven disaccharides of glucose were less than 1.0 kcal mol-1. The distribution of corresponding energies of the various crystalline conformations conformed well to a Boltzmann-like equation.

A QM/MM analysis of the conformations of crystalline sucrose moieties

Both ab initio quantum mechanics (QM) and molecular mechanics (MM) were used to produce a hybrid energy surface for sucrose that simultaneously provides low energies for conformations that are observed in crystal structures and high energies for most unobserved structures. HF/6-31G* QM energies were calculated for an analogue based on tetrahydropyran (THP) and tetrahydrofuran (THF). Remaining contributions to the potential energy of sucrose were calculated with MM. To do this, the MM surface for the analogue was subtracted from the MM surface for the disaccharide, and the QM surface for the analogue was added. Prediction of the distribution of observable geometries was enhanced by reducing the strength of the hydrogen bonding. Reduced hydrogen-bonding strength is probably useful because many crystalline sucrose moieties do not have intramolecular hydrogen bonds between the fructose and glucose residues. Therefore, hydrogen bonding does not play a large role in determining the molecular conformation. On the hybrid energy surface that was constructed with a dielectric constant of 3.5, the average potential energy of 23 sucrose moieties from crystal structures is 1.16 kcal/mol, and the population of observed structures drops off exponentially as the energy increases.

Intramolecular hydrogen bonding in 2-aminoethanol, 3-aminopropanol and 4-aminobutanol

Abstract Two different intramolecular hydrogen-bonds are formed by 2-aminoethanol, 3-aminopropanol and 4-aminobutanol, both of which lead to cyclic conformations. Results based on ab initio self-consistent field (SCF) calculations for the stronger interaction -N⋯H-O-are presented. The influence of ring size on this interaction is discussed.

Intramolecular interactions in β-alanine, 3-aminopropanal and 3-aminopropanol

Abstract The intramolecular interactions in the local minima on the potential energy surfaces of β-alanine, 3-aminopropanal and 3-aminopropanol are discussed on the basis of electron density maps. The resulting characterization is in agreement with criteria using bond lengths and vibration frequencies. The CO group is found to be the most important structural feature in these compounds.

Coordination of methanol clusters to benzene: A computational study

Benzene-methanol cluster structures were investigated with theoretical chemistry methods to describe the microsolvation of benzene and the benzene-methanol azeotrope. Benzene-methanol (MeOH) clusters containing up to six methanol molecules have been calculated by ab initio [MP2/6-311++G(d,p)//MP2/6-31+G(d,p) + BSSE correction] method. The BSSE was found quite large with this basis set, hence, different extrapolation schemes in combination with the aug-cc-pVxZ basis sets have been used to estimate the complete basis set limit of the MP2 interaction energy [ΔE(MP2/CBS)]. For smaller clusters, n ≤ 3, DFT procedures (DFTB+, MPWB1K, M06-2X) have also been applied. Geometries obtained for these clusters by M06-2X and MP2 calculations are quite similar. Based on the MP2/CBS results, the most stable C(6)H(6)(MeOH)(3) cluster is characterized by a hydrogen bonded MeOH trimer chain interacting with benzene via π···H-O and O···H-C(benzene) hydrogen bonds. Larger benzene-MeOH clusters with n ≥ 4 consist of cyclic (MeOH)(n) subclusters interacting with benzene by dispersive forces, to be denoted by C(6)H(6) + (MeOH)(n). Interaction energies and cooperativity effects are discussed in comparison with methanol clusters. Besides MP2/CBS calculations, for selected larger clusters the M06-2X/6-311++G(d,p)//M06-2X/6-31+G(d,p) procedure including the BSSE correction was also used. Interaction energies obtained thereby are usually close to the MP2/CBS limit. To model the benzene-MeOH azeotrope, several structures for (C(6)H(6))(2)(MeOH)(3) clusters have been calculated. The most stable structures contain a tilted T-shaped benzene dimer interacting by π···H-O and O···H-C (benzene) hydrogen bonds with a (MeOH)(3) chain. A slightly less negative interaction energy results for a parallel displaced benzene sandwich dimer with a (MeOH)(3) chain atop of one of the benzene molecules.

Application of the Quantum Cluster Equilibrium (QCE) model for the liquid phase of primary alcohols using B3LYP and B3LYP-D DFT methods.

The Quantum Cluster Equilibrium (QCE) model was applied to the liquid phase for the first few members of the homologous series of unbranched aliphatic primary alcohols, methanol, ethanol, propan-1-ol, and butan-1-ol. Cluster structures and energies were calculated by density functional theory [B3LYP/6-311++G(2d,2p)]. For butan-1-ol the dispersion interaction was also considered with the B3LYP-D method. In agreement with previous findings, cyclic cluster structures are the most probable ones. In addition, weak C-H...O interactions as well as dispersion interactions between the longer alkyl chains were found to be important in the cluster formation. The reliability of the model was assessed by the calculated constant pressure heat capacity (C(p)) values. Larger deviations between theory and experiment were found for higher homologes (propan-1-ol, butan-1-ol) with the B3LYP method. When the B3LYP-D method was applied for butan-1-ol, adequate agreement was found between experimental and calculated C(p) values.

Theoretical structure investigations of N-acetyl-l-proline amide

Abstract The potential energy surface of N -acetyl-l-proline amide has been investigated via RHF, AM1, and PM3 calculations. The results show significant differences between these methods: seven local minima can be found with RHF, three with AM1, 17 with PM3. The conformation of the RHF/6-31G∗ global minimum corresponds to the γ-turn structure of polypeptides. In contrast to this, the proline conformer that participates in the formation of ten-membered β-turns in peptide chains has a relatively high energy in the dipeptide.

Ab initio SCF investigation of 3-aminopropanol and 3-aminopropanal

Abstract Results of ab initio SCF (4-31G) studies of the potential energy surfaces of 3-aminopropanol and 3-aminopropanal are reported. Geometry data of all local minima are given and various intramolecular interactions are deduced from these data. All reaction paths in the potential energy surface of 3-aminopropanal and selected reaction paths in the potential energy surface of 3-aminopropanol are discussed.

Theoretical Study of Structure, Electronic Properties, and Photophysics of Cyano-Substituted Thiophenes and Terthiophenes

In this paper, quantum chemical calculations for various cyano derivatives of thiophene and terthiophenes at the density functional theory (DFT) and ab initio Møller-Plesset (MP2) levels of theory are presented. In the case of the studied terthiophenes, CN groups located in the central part of the molecule lead to a preference of cis-cis geometry over trans-trans conformation. For alpha-substituted dicyano terthiophene, the investigation of torsional dependences shows that the highest energy barrier occurs at the perpendicular orientation of the aromatic rings. On the other hand, the dicyano substitution in the central part of terthiophene molecule exhibits the lowest energy barrier. Excitation energies were calculated using time-dependent density functional theory (TD-DFT). The obtained theoretical results show that the CN groups in alpha and beta positions have a distinct effect on the excitation energies and corresponding oscillator strengths. A CN group located in the alpha position causes a larger bathochromic shift than a CN group in the beta position. Besides, a CN group in the beta position has negligible influence on the position of the first absorption maximum.