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Institute
- Institut für Chemie (299) (remove)
The minima on the potential energy surface of 1,2-bis(o-carboxyphenoxy) ethane (CPE) molecule in its electronic ground state were searched by a molecular dynamics simulation performed with MM2 force field. For each of the found minimum-energy conformers, the corresponding equilibrium geometry, charge distribution, HOMO-LUMO energy gap, force field, vibrational normal modes and associated IR and Raman spectral data were determined by means of the density functional theory (DFT) based electronic structure calculations carried out by using B3LYP method and various Pople- style basis sets. The obtained theoretical data confirmed the significant effects of the intra- and inter-molecular hydrogen bonding interactions on the conformational structure, force field, and group vibrations of the molecule. The same data have also revealed that two of the determined stable conformers, both of which exhibit pseudo-crown structure, are considerably more favorable in energy to the others and accordingly provide the major c ntribution to the experimental spectra of CPE. In the light of the improved vibrational spectral data obtained within the "SQM FF" methodology and "Dual Scale Factors" approach for the monomer and dimer forms of these two conformers, a reliable assignment of the fundamental bands observed in the experimental room-temperature IR and Raman spectra of the molecule was given, and the sensitivities of its group vibratb20s to conformation, substitution and dimerization were discussed.
The minima on the potential energy surface of 1,2-bis(o-carboxyphenoxy)ethane (CPE) molecule in its electronic ground state were searched by a molecular dynamics simulation performed with MM2 force field. For each of the found minimum-energy conformers, the corresponding equilibrium geometry, charge distribution, HOMO-LUMO energy gap, force field, vibrational normal modes and associated IR and Raman spectral data were determined by means of the density functional theory (DFT) based electronic structure calculations carried out by using B3LYP method and various Pople-style basis sets. The obtained theoretical data confirmed the significant effects of the intra- and inter-molecular hydrogen bonding interactions on the conformational structure, force field, and group vibrations of the molecule. The same data have also revealed that two of the determined stable conformers, both of which exhibit pseudo-crown structure, are considerably more favorable in energy to the others and accordingly provide the major contribution to the experimental spectra of CPE. In the light of the improved vibrational spectral data obtained within the "SQM FF" methodology and "Dual Scale Factors" approach for the monomer and dimer forms of these two conformers, a reliable assignment of the fundamental bands observed in the experimental room-temperature IR and Raman spectra of the molecule was given, and the sensitivities of its group vibrations to conformation, substitution and dimerization were discussed.
A conformational study of N-acetyl glucosamine derivatives utilizing residual dipolar couplings
(2013)
A conformational study of N-acetyl glucosamine derivatives utilizing residual dipolar couplings
(2011)
The conformational analyses of six non-rigid N-acetyl glucosamine (NAG) derivatives employing residual dipolar couplings (RDCs) and NOEs together with molecular dynamics (MD) simulations are presented. Due to internal dynamics we had to consider different conformer ratios existing in solution. The good quality of the correlation between theoretically and experimentally obtained RDCs show the correctness of the calculated conformers even if the ratios derived from the MD simulations do not exactly meet the experimental data. If possible, the results were compared to former published data and commented.
In C-13 NMR spectroscopy, there are many empirical methods for fast and exact computation of C-13 chemical shifts; comparable procedures for Si-29 NMR chemical shifts are not existing or are older than 20 years. On basis of the largest database of Si-29 chemical shifts available, along this paper a relatively simple procedure for the similarly exact calculation of the Si-29 chemical shifts of disilanes (average margin of error ca. 3.7 ppm) is given. (c) 2005 Elsevier B.V. All rights reserved
The theoretically possible stable conformers of free mn-15S2O3 maleonitrile-dithiacrown ether molecule were searched by means of a conformational study which consists of molecular dynamics and energy minimization calculations performed with MM2 force field and successive geometry optimization + frequency calculations performed first at B3LYP/3- 21G and then at B3LYP/6-31G(d) levels of theory. The obtained calculation results have clearly indicated that the free molecule in electronic ground state is very flexible and accordingly has many possible stable conformers of different conformational properties at room temperature; among them, the one having a macrocyclic ring structure in which all of the ether units oriented toward the center of the ring was determined the energetically most preferable conformer. In addition, the equilibrium geometrical parameters, vibrational normal modes and associated IR spectral data of the determined most stable three conformers of the molecule were calculated at B3LYP/6-31+G(d) and B3LYP/6-31++G(d,p) levels of theory. A successful assignment of the fundamental bands observed in the recorded experimental solid phase and solution phase IR spectra of the molecule was achieved in the light of the theoretical data obtained from these DFT calculations. To fit the calculated harmonic wavenumbers to the experimental ones, two different scaling procedures, referred to as "Scaled Quantum Mechanical Force Field (SQM FF) methodology" and "Scaling wavenumbers with empirical dual scale factors", were proceeded independently.
The ring current effects of aromatic moieties and the anisotropic effects of the C=O and C-X (X = C, N, S) bonds and of the NH=C(NH2)-NH- moiety in the side chains of amino acid residues of proteins were ab initio calculated based on nuclear independent chemical shieldings as employed by P.v.R. Schleyer. Hereby, quantitative information about the spatial extension, sign and scope of the corresponding ring current/anisotropic effects was obtained and they were visualized as iso-chemical-shielding-surfaces. Examining this quantitative information compared with experimental NMR chemical shifts, the role of the corresponding amino acid residues in binding substrates in the binding site of enzymes was studied. (C) 2004 Elsevier B.V. All rights reserved
The C-13 chemical shifts of 20 rigid bicyclic compounds have been calculated with ab initio HF and MP2 methods. The calculations showed very good reproducibility of the experimental values. The molecular orbital interactions in the rigid, nearly planar delta-syn-axial fragments in the isomeric groups of norbornane derivatives 1.x-4.x were studied in detail and were employed to explain the deshielding delta-syn-axial effect in C-13 NMR spectroscopy. (C) 2004 Elsevier B.V. All rights reserved
Equilibria between the Z (tau(1) = 0 degrees) and E (tau(1) = 180 degrees) conformers of p-substituted phenyl acetates 4 and trifluoroacetates 5 (X = OMe, Me, H, Cl, CN, NO2) were studied by ab initio calculations at the HF/6-31G* and MP2/6-31G* levels of theory. The preference for the Z conformer, Delta E(HF), was calculated to be 5.36 kcal mol(-1) and 7.50 kcal mot(-1) for phenyl acetate and phenyl trifluoroacetate (i.e., with X = H), respectively. The increasing electron-withdrawing ability of the phenyl substituent X increases the preference of the Z conformer. An excellent correlation with a negative slope was observed for both series between Delta E of the E-Z equilibrium and the Hammett sigma constant. By using an appropriate isodesmic reaction, it was shown that electron-withdrawing substituents decrease the stability of both conformers, but the effect is higher with the E conformer. Electron-withdrawing phenyl substituents decrease the delocalization of the lone pair of the ether oxygen to the C=O antibonding orbital (n(O) -> pi*(C=O)) in both the E and Z forms and in both series studied; this effect is higher in the E conformer than in the Z conformer. The n(O) -> pi*(C=O) electron donation has a minimum value with tau(1) = 90 degrees and a maximum value with tau(1) = 90 degrees (the Z conformer), the value with tau(1) = 180 degrees (the E conformer) being between these two values, obviously due to steric hindrance. The effects of the phenyl substituents on the reactivity of the esters studied are discussed in terms of molecular orbital interactions. ED/EW substituents adjust the availability of the pi*(C=O) antibonding orbital to interact with the lone pair orbital of the attacking nucleophile and therefore affect the reactivity: EW substituents increase and ED substituents decrease it. Excellent correlations were observed between the rate coefficients of nucleophilic acyl substitutions and pi*(C=O) occupancies of the ester series 4 and
Ab-initio study and semiempirical calculations of keto-enol tautomerism of triazolopyrimidines
(1995)
Through-space NMR shieldings were calculated for trinuclear metal-carbonyl compounds [M-3(CO)(12)] (M = Fe, Ru, Os), employing the nucleus-independent chemical shift approach. The through-space shieldings were visualized as a contour plot of iso-chemical shielding surfaces, and were applied to quantify the overall anisotropic effect of the carbonyl groups, as well as to identify the influence of the transition metal on the scopes of the corresponding anisotropy cones. The shielding surfaces show that the anisotropic effect of the carbonyl groups at equatorial positions changes depending on the metal. This effect was associated with pi-backdonation from the metal to the carbonyl groups in that position, in agreement with geometric data as well as calculated NMR parameters. Therefore, visualization of the through-space NMR shieldings of trinuclear metal-carbonyl compounds of group 8 is able to reflect the distinct arrangements of the carbonyl groups in these organometallic compounds.
The anisotropic effect of the planar nitrate anion NO3- has been ab initio calculated employing the Nucleus- Independent Chemical Shift (NICS) concept of von Ragué Schleyer and visualized as Iso-Chemical-Shielding Surfaces (ICSSs) of various (de)shieldings. Complexation-induced shifts in the 1H NMR spectra of nitrate/metal complexes or nitrate/receptor supramolecules can be separated now into anisotropic influences of the suitably coordinated nitrate anions and effects originating from differential sources.
The spatial magnetic properties (through Space NAIR shieldings, TSNMRSs) of cyclopropane; of the heteroanalogous oxirane, thiirane, and aziridine; and of various substituted dis-, and tris-cyclic analogues have been computed by the GIAO perturbation method employing the nucleus independent chemical shift (NICS) concept and visualized as iso-chemical-shielding surfaces (ICSSs) of various size and direction. The TSNMRS values, thus obtained, can be employed to visualize the anisotropy (ring current) effect of I the cyclopropane ring moiety. This approach has been employed to qualify and quantify substituent influences and contributions of appropriate ring heteroatoms O, NH, and S on the anisotropy (ring current) effect of three-mernbered ring moieties, and to assign the stereochemistry of mono-, bis-, and tris cyclic structures containing cyclopropane as a structural element. Characteristic examples are included.
The nor-halimane diterpenoid tessmannic acid and its methyl, 2-methylisopropyl and 1-methylbutyl esters, the unusual isocoumarins 8-hydroxy-6-methoxy-3-pentylisocoumarin and 7-chloro-8-hydroxy-6-methoxy-3-pentylisocoumarin, and 5- pentyl-3-methoxy-N-butylaniline were isolated from the stem and root bark extracts of Tessmannia densiflora Harms (Caesalpiniaceae) that showed mosquito larvicidal activity. The structures were determined on interpretation of spectroscopic data. Tessmannic acid and its methyl ester exhibited antibacterial and antifungal activity. The compounds also caused high larvae and adult Anopheles gambiae mosquitoe mortality effects, and stronger mosquito repellency than that shown by the standard repellent DEET, hence indicating Tessmannia species to be potential sources of bioactive natural products.
The spatial magnetic properties (through-space NMR shieldings, or TSNMRSs) of the antiaromatic 9-oxaanthracene anion 12(-) and of the corresponding 9-dimeric dianion 11(2-) have been calculated by the gauge-invariant atomic orbitals (GIAO) perturbation method employing the nucleus independent chemical shift (NICS) concept and visualized as iso-chemical-shielding surfaces (ICSSs) of various size and direction. The TSNMRS values, thus obtained, can be employed to indicate antiaromaticity by paratropic ring currents of the anionic compounds of 11(2-) and 12(-) studied and other neutral and ionic antiaromatic molecules from previous studies because anisotropic effects of functional groups in H-1 NMR spectra have quantitatively proven to be the molecular response property of theoretical spatial nucleus independent chemical shieldings (NICS).
The clerodane diterpenoids trans-kolavenolic acid, 18-oxocleroda-3,13(E)-dien-15-oic acid, ent-(18- hydroxycarbonyl)-cleroda- 3,13(E)-dien-15-oate, 2-oxo-ent-cleroda-3,13(Z)-dien-15-oic acid and trans-2-oxo-ent-cleroda- 13(Z)-en-15-oic acid, and the chlorobenzenoid O-(3-hydroxy-4-hydroxycarbonyl-5-pentylphenyl)-3-chloro-4-methoxy-6-pentyl- 2-oxybenzoic acid were isolated from Tessmannia martiniana var pauloi and T. martiniana var matiniana. Structures were established based on interpretation of spectroscopic data. Some of the compounds exhibited significant antimosquito, antifungal and antibacterial activities.