Study of hydrogen bonding interactions relevant to biomolecular structure and function

Ab initio molecular orbital calculations were used to study hydrogen bonding interactions and interatomic distances of a number of hydrogen bonded complexes that are germane to biomolecular structure and function. The calculations were carried out at the STO-3G, 3-21G, 6-31G*, and MP2/6-31G* levels (geometries were fully optimized at each level). For anionic species, 6-31 + G* and MP2/6-31 + G* were also used. In some cases, more sophisticated calculations were also carried out. Whenever possible, the corresponding enthalpy, entropy, and free energy of complexation were calculated. The agreement with the limited quantity of experimental data is good. For comparison, we also carried out semiempirical molecular orbital calculations. In general, AM1 and PM3 give lower interaction enthalpies than the best ab initio results. With regard to structural results, AM1 tends to favor bifurcated structures for O? H-O and N? HO types of hydrogen bonds, but not for hydrogen bonds involving O-H? S and S-H? O, where the usual hydrogen bond patterns are observed. Overall, AM1 geometries are in general in poor agreement with ab initio structural results. On the other hand, PM3 gives geometries similar to the ab initio ones. Hence, from the structural point of view PM3 does show some improvement over AM1. Finally, insights into the formation of cyclic or open formate–water hydrogen bonded complexes are presented. © 1992 by John Wiley & Sons, Inc.     

Comparison of computational studies of internal stabilization of 1‐butadienyllithiums and representative 1‐chloro‐1‐lithio‐2‐phenylalkenes

Comparison of molecular orbital calculations of 1‐butadienyllithiums and representative 1‐chloro‐1‐lithio‐2‐phenylalkenes, carried out by using MNDO and AM1, reveals that the major stabilizing interaction with lithium in these systems is predicted to be agostic bonding between lithium and hydrogen. MNDO and AM1 calculations for 1‐chloro‐1‐lithio‐2‐phenylethenes give evidence for agostic bonding between lithium and the ortho H, such as compressed pertinent bond angles and increased pertinent bond lengths. © 2002 Wiley Periodicals, Inc. Heteroatom Chem 13:263–269, 2002; Published online in Wiley Interscience (www.interscience.wiley.com). DOI 10.1002/hc.10027     

Synthesis and structural studies of N-(p-toluenesulfonyl)-amino acid 3,5-di-tert-butyl-2-phenolamides

This paper describes the synthesis and structural studies of N-(p-toluenesulfonyl)-amino acid 3,5-di-tert-butyl-2-phenolamides by ¹H, ¹³C, and ¹⁵N. The presence of intra- and intermolecular hydrogen bonds were studied by variable temperature NMR spectroscopy. The molecular structure of two amides in the solid state was determined by X-ray diffraction experiments. The results show that tert-butyl substituents in the phenolic ring have important effects in the nature of hydrogen bonds and conformation of these amides. © 2004 Wiley Periodicals, Inc. Heteroatom Chem 15:114–120, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.10223     

Correlation of singlet-triplet gaps for aryl carbenes calculated by MINDO/3, MNDO,AM1, and PM3 with Hammett-type substituent constants

Heats of formation, atomic charges, and geometries of some 110 structures involving substituted singlet and triplet phenyl and 4,4-dimethyl-1,4-dihydronaphthalene carbenes and the corresponding diazomethanes were calculated by MINDO/3, MNDO, AM1, and PM3 semiempirical molecular orbital methods. The singlet-triplet gaps for AM1 and PM3 calculations for the para derivatives in both systems have been successfully correlated with Brown σ⁺ constants. Good correlations with σ⁺ were found for the charges on the carbenic centers of the singlets as well as with the energy barrier for rotation of the aryl group about the C-C single bond in substituted singlet phenylcarbenes. Comparisons of these results with experimental data indicate that AM1 and PM3 are much better than MNDO and MINDO/3 in predicting the intrinsic substituent effects in singlet carbenes.     

Semiempirical study of compounds with intramolecular O?H…︁O hydrogen bonds. II. Further verification of a modified MNDO method

In the forerunner of this article, we described a MNDO modification designed for studies of compounds with intramolecular O? H…?O hydrogen bonds. Here, we report the further verification of the modification by means of its application to 14 compounds not considered in its development. Comparison of the calculated structural parameters and proton transfer characteristics with available experimental or ab initio results, and with those obtained using MNDO, AM1, MNDO/H, MNDO/M, and PM3, supports the validity of the new modification for prediction of hydrogen bond characteristics. © 1994 by John Wiley & Sons, Inc.     

Pyrrolizidine alkaloids necine bases: Ab initio,semiempirical, and molecular mechanics approaches to molecular properties

The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and ¹H-NMR (nuclear magnetic resonance) studies in D₂O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.     

Stereochemical effects in the mass spectra of some cyclopropylsilanes explained by the MNDO molecular orbital method. I. Silicon-oxygen interactions

Large differences have been found between the mass spectra of cis- and trans-1-carbomethoxy-2-trimethylsilylcyclopropane. To help in explaining these differences, quantum chemical calculations were performed by the MNDO method on the neutral molecules, on the vertical and adiabatic molecular ions and also the [M – methyl]⁺ ions. To evaluate the results, heats of formation, bond orders, molecular geometry, spin and charge densities and orbital coefficients were used. These indicate the formation of a very strong bonding interaction between silicon and oxygen in the molecular ion of the cis but not the trans isomer, leading to spontaneous methyl loss and a stabilization energy of ～ 2.6 eV.     

Computational structural determination and energy landscape analysis of the hepatic carcinogen 2-(acetylamino)fluorene

 2-(Acetylamino)fluorene (AAF), a potent mutagen and a prototypical example of the mutagenic aromatic amines, forms covalent adducts to DNA after metabolic activation in the liver. A benchmark study of AAF is presented using a number of the most widely used molecular mechanics and semiempirical computational methods and models. The results are compared to higher-level quantum calculations and to experimentally obtained crystal structures. Hydrogen bonding between AAF molecules in the crystal phase complicates the direct comparison of gas-phase theoretical calculations with experiment, so Hartree–Fock (HF) and Becke–Perdew (BP) density functional theory (DFT) calculations are used as benchmarks for the semiempirical and molecular mechanics results. Systematic conformer searches and dihedral energy landscapes were carried out for AAF using the SYBYL and MMFF94 molecular mechanics force fields; the AM1, PM3 and MNDO semiempirical quantum mechanics methods; HF using the 3-21G*and 6-31G* basis sets; and DFT using the nonlocal BP functional and double numerical polarization basis sets. MMFF94, AM1, HF and DFT calculations all predict the same planar structures, whereas SYBYL, MNDO and PM3 all predict various nonplanar geometries. The AM1 energy landscape is in substantial agreement with HF and DFT predictions; MMFF94 is qualitatively similar to HF and DFT; and the MNDO, PM3 and SYBYL results are qualitatively different from the HF and DFT results and from each other. These results are attributed to deficiencies in MNDO, PM3 and SYBYL. The MNDO, PM3 and SYBYL models may be unreliable for compounds in which an amide group is immediately adjacent to an aromatic ring. Received: 26 May 2002 / Accepted: 12 December 2002 / Published online: 14 February 2003     

Comparative study between ab initio and semiempirical electrostatic potentials on molecular surfaces

The electrostatic potentials of 21 molecules containing different functional groups has been computed at the ab initio RHF/6-31G* level on a series of solvent accessible surfaces and compared with MNDO, AM1, and PM3-derived pontentials. We analyzed in detail the distribution of electrostatic potentials on the surfaces around their maximum and minimum values and found out that consistently MNDO gives results similar to ab initio potentials. The actual values of the MNDO electrostatic potentials show a systematic deviation from the “correct” results, but the pattern of the MEP distribution on the surface is similar to that of the ab initio results. In contrast, PM3 fails in some cases to give even the correct number or distribution of “hot spots” of potential (low MEP) on the surface. AM1 behaves somewhere between these two semiempirical methods. As a conclusion, MNDO would be suggested as the best approach to analyses requiring a fast and efficient mapping of electrostatic potentials on simplified models of molecular surfaces. © 1993 John Wiley & Sons, Inc.     

A comparison of the intramolecular and intermolecular hydrogen bonding of N,N′-ethylenebis(aminobenzylidene) in the solid state with its salen analogue

The crystal structure of H₂amben has been elucidated for the first time. The close NH?N contact between neighbouring molecules supports strongly the notion that intermolecular hydrogen bonding exists within the crystal lattice, creating a series of molecular chains, which are crosslinked in a three-dimensional array. This intermolecular bonding is suggested to account for the anomalously high melting point of H₂amben (176-178 °C) compared to its H₂salen counterpart (126-128 °C). Although strong intramolecular forces are present in both ligands, H₂salen contains no intermolecular hydrogen bonds.     

Improvement of the hydrogen bonding correction to MNDO for calculations of biochemical interest

Recent suggestions for correcting H? Acceptor interactions within MNDO, together with results of crystallographic analysis, were used to modify this SCF semiempirical calculation for multiple hydrogen bonded associations. Thermodynamic profiles for model systems of biochemical interest such as H₂O? H₂O, hydration of neutral and charged molecules, dimerizations and proton transfers show the advantages of this method. Its treatment of charges, bonding, geometries, energetics and vibrational frequencies is shown to be comparable to ab initio calculations with various basis sets. However, basic MNDO deficiencies and criteria applied for H-bonding result in some too high barriers for proton transfers.     

Hydrogen bonds in regioselectively substituted cellulose derivatives

Formation of hydrogen bonds in various cellulose derivatives, 2,3-di-O- and 6-O-substituted cellulose ethers, were characterized by FTIR and solid-state CP/MAS¹³C-NMR. The polymers were synthesized by regioselective substitution of hydroxyl groups and had a uniform structure. Since their three hydroxyl groups (OH) are selectively blocked, the cellulose derivatives appeared to form specific inter- and intramolecular hydrogen bonds. The characteristic OH stretching frequencies in IR spectra and the C-1 chemical shift in CP/MAS spectra of 6-O-substituted cellulose derivatives indicated existence of two equivalent intramolecular hydrogen bonds between ether oxygen and OH groups at 3-OH-O5′ and O6-HO-2′ [Figure 3(C)]. Influence of the substituents at the C-6 position on the formation was not significant except trityl group. Behavior of the hydrogen bonds in 6-O-tritylcellulose were also discussed. © 1994 John Wiley & Sons, Inc.     

A cryptand containing three diiminopyridyl units; aromatic-aromatic interaction and the stability of the complexes

Abstract

The solution properties of a hexaimino cryptand containing 2,6-diiminopyridyl units have been investigated by NMR, UV-VIS absorption and luminescence spectroscopy. The difference in the NMR and UV spectra of the Ba^2- complex and the cryptand is attributed to the conformational change of the diiminopyridyl group. The luminescence spectra of the compounds show near-UV bands and unexpected low-energy bands. The former is attributed to the normal π-π* transition, while the origin of the low-energy bands is discussed in terms of inter- and intra-molecular aromatic-aromatic interactions. The inter-molecular interaction is important in the free ligand, however, intra-molecular interaction is suggested in the Ba²⁺ complex. Further, the specific conformational change of the Ba^2- complex in DMSO-acetonitrile solution is investigated by the measurements of the stability constant of the Ba²⁺ complex in various DMSO concentrations. The large decrease over 4.0 in logK is found only for the Ba²⁺ complex. The behavior is explained by the factors brought about the nature of DMSO and the interactions among the diiminopyridyl units, DMSO and the Ba²⁺ ion.     

Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods

Optimized geometries and total energies of some conformers of alpha- and beta-D-galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of alpha- and beta-D-galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units alpha 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles psi and phi of the glycosidic linkage are considered. In each calculation, at each increment of psi and phi, using a step of 30 degrees from 0 to 330 degrees, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*.     

A combined quantum chemical/molecular mechanical study of hydrogen-bonded systems

A computational approach, which involves the combination of the OPLS force field and molecular orbital MNDO , AM 1, and PM 3 methods, has been developed to describe the effects of a large, molecular mechanically simulated environment on the Hamiltonian of a quantum chemical system. To test the validity of the combined quantum mechanical/molecular mechanical (QM /MM ) potential, a systematic study of the structures and energies of neutral and charged hydrogen-bonded complexes has been carried out, including comparisons with pure semiempirical calculations and available experimental and ab initio data. It is shown that, in many cases, the hybrid QM /MM potential behaves better than do related MNDO /M , AM 1, and PM 3 methods. As a case in point, the draw-back of AM 1 favoring bifurcated H-bonded structures over single ones is not presented in the combined AM 1/OPLS scheme. Possible ways of improvement of the combined QM /MM potential are discussed. © 1992 John Wiley & Sons, Inc.     

Transition from IVR limited vibrational energy transport to bulk heat transport

In a previous paper [M. Schade, P. Hamm, Vibrational energy transport in the presence of intrasite vibrational energy redistribution, J. Chem. Phys. 131 (2009) 044511], it has been shown that on ultrashort length and time scales, the speed of vibrational energy transport along a molecular chain is limited by intrasite vibrational relaxation rather than the actual intersite propagation. However, since intrasite vibrational relaxation is length independent, the intersite propagation rate is expected to become rate-limiting at some length scale, where propagation approaches the bulk limit. In the present paper, we investigate the transition between both regimes. The response of different types of modes may be very different at early times, depending on how much they contribute directly to energy transport. Surprisingly though, when averaging the energy content over all vibrational modes of the various chain sites, the complexity of the intrasite vibrational relaxation process is completely hidden so that energy transport on the nanoscale can be described by an effective propagation rate, that equals the bulk value, even at short times.     

Using of Volatile Release Measurements to Understand Polysaccharide Molecular Interactions: An Example with Guar Gum Study

It is well establishment that polysaccharides are commonly used in many fields of formulation such as food and cosmetic industries as viscosity modifiers or gelling agents. Among the different impacts on the mixture properties, these materials are also known to affect the aroma release or retention thus its sensory perception; the effect depends whether polysaccharide structure induces specific retention or release phenomena from the complex media. Present study deals with studying aroma compounds behaviour from dilute and semi-dilute aqueous polysaccharide solutions consisting of different guar gum samples. Results allow stating that the whole polymer characteristics as determined by means of structural analysis, protein content determination, rheological and surface tension measurements play a major role on the polysaccharide/aroma compound interaction mechanisms. In particular, results evidence a strong Mannose to Galactose (M/G) ratio effect, thus allowing stating the occurrence of hydrophobic intra and intermolecular mechanism. In addition to that, proteins are demonstrated to only slightly affect the volatile retention. More generally, such an original study allows new highlights concerning macromolecular organisation and interactions in solution.