Search results for "Intramolecular force"
showing 10 items of 599 documents
The ins and outs of proton complexation
2009
Proton complexation differs from simple protonation by the fact that the coordinated hydrogen atom is bound intramolecularly to more than one donor atom. This is usually achieved by covalent bonding supplemented by hydrogen bonding. In a few cases, however, the complexed proton is hydrogen-bound to all donor atoms, which gives rise to single well (SWHB) and low barrier (LBHB) hydrogen bonds. This tutorial review highlights a full range of proton complexes formed with chelating and "proton-sponge"-type ligands, cryptand-like macropolycycles, and molecules of topological relevance, such as rotaxanes and catenanes. The concept of proton complexation can explain how the smallest cation possible…
Transition structure selectivity in enzyme catalysis: a QM/MM study of chorismate mutase
2001
Two different transition structures (TSs) have been located and characterized for the chorismate conversion to prephenate in Bacillus subtilis chorismate mutase by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) calculations. GRACE software, combined with an AM1/CHARMM24/TIP3P potential, has been used involving full gradient relaxation of the position of ca. 3300 atoms. These TSs have been connected with their respective reactants and products by the intrinsic reaction coordinate (IRC) procedure carried out in the presence of the protein environment, thus obtaining for the first time a realistic enzymatic reaction path for this reaction. Similar QM/MM computational schemes h…
Inter- and intramolecular motions in proteins
1992
The use of 57 Fe Mossbauer radiation allows the study of protein crystal dynamics by a time-resolved analysis of X-ray scattering. In myoglobin crystals, the main source of the root mean squared amplitude of motions come from intramolecular protein dynamics. Segments of the size of an α-helix move collectively. Long-range correlated motions give only a minor contribution. Comparison with Mossbauer absorption spectroscopy shows that protein-specific dynamics is frozaen out below 200 K and the lattice dynamics in mainly responsible for the low-temperature behavior
How Well Can Coarse-Grained Models of Real Polymers Describe Their Structure? The Case of Polybutadiene
2015
Coarse-graining of chemical structure of macromolecules in the melt is investigated using extensive molecular dynamics simulation data which are based on a united atom force-field model of polybutadiene. Systematically increasing the number, n, of the united atoms approximated by an effective coarse-grained monomer, we study the influence of degree of coarse-graining on the structure functions such as the segment-segment intermolecular and intramolecular correlation functions. These results are compared to Monte Carlo simulations of the corresponding coarse-grained bead-spring model and Chen-Kreglewski potential for chain molecules. In contrast to the atomistic chemically realistic model of…
Computer simulations of DNA stretching
2006
Abstract In this chapter we will give short review of computer modelling/simulations of DNA manipulation as a complementary tool to current single molecule manipulation experiments in order to follow the impact on molecular structure during the manipulation experiments. As an example we report molecular dynamics simulations of a 22 base-pair DNA fragment in an explicit water solution with counter-ions to mimic a torsionally unconstrained single-molecule stretching experiment. Positions of the O5′ and O3′ atoms at one end of the 22-mer were fixed while an external linearly increasing tensile force was applied on the corresponding atoms at the other end. Changes in the intramolecular potentia…
ChemInform Abstract: The Ins and Outs of Proton Complexation
2009
Proton complexation differs from simple protonation by the fact that the coordinated hydrogen atom is bound intramolecularly to more than one donor atom. This is usually achieved by covalent bonding supplemented by hydrogen bonding. In a few cases, however, the complexed proton is hydrogen-bound to all donor atoms, which gives rise to single well (SWHB) and low barrier (LBHB) hydrogen bonds. This tutorial review highlights a full range of proton complexes formed with chelating and “proton-sponge”-type ligands, cryptand-like macropolycycles, and molecules of topological relevance, such as rotaxanes and catenanes. The concept of proton complexation can explain how the smallest cation possible…
Association of N-(Pyridin-2-yl),N′-substituted Ureas with 2-Amino-1,8-naphthyridines and Benzoates: NMR and Quantum Chemical Studies of the Substitue…
2013
Association of four N-(pyridin-2-yl),N'-R(1)-ureas (R(1) = ethyl, n-butyl, phenyl, and tert-butyl) with substituted 2-amino-1,8-naphthyridines and benzoates were studied by (1)H NMR spectroscopic titrations and quantum chemical calculations. The benzoates and 2-amino-1,8-naphthyridines were selected as representatives of double and triple hydrogen bonding counterparts, respectively. The classical substituent effect on the association was studied. A prerequisite and a crucial step for the complex formation was the breaking of the intramolecular hydrogen bond in urea derivatives. The QTAIM calculation method was employed to explain the hydrogen bonding within complexes. In the case of benzoat…
Inter/intramolecular Cherenkov radiation energy transfer (CRET) from a fluorophore with a built-in radionuclide.
2014
The Cherenkov radiation (CR) from [(18)F]-FDG, [(177)Lu]-LuCl3 and [(90)Y]-YCl3 was detected and CR energy transfer (CRET) to several fluorophores was examined. Subsequent fluorescence emission was found to be a function of the position of absorption bands with respect to the CR peak, energy of emitted particles, radionuclide/fluorophore loading, and fluorophore brightness. A variant of the best fluorophore with a built-in radionuclide was synthesized to achieve inter- and intra-molecular CRET.
A DFT Study of Inter- and Intramolecular Aryne Ene Reactions
2015
The molecular mechanisms of inter- and intramolecular aryne-ene reactions have been theoretically studied by DFT methods at the MPWB1K/6-311G(d,p) level. These reactions proceed through a one-step mechanism via nearly asynchronous transition states (TSs), in which the C–C single bond formation is slightly more advanced than the hydrogen transfer process. These ene reactions show very low activation enthalpies (<1 kcal/mol) and are strongly exothermic by more than 73 kcal/mol. An electron localisation function (ELF) topological analysis of the changes of electron density during these ene reactions indicates that the bonding changes are nonconcerted. ELF topological analysis of the electron d…
Quantitative characterization of group electrophilicity and nucleophilicity for intramolecular Diels–Alder reactions
2010
In a previous work (L. R. Domingo, M. J. Aurell, P. Perez and R. Contreras, Tetrahedron 2002, 58, 4417) we proposed that the difference in global electrophilicity index be taken as a measure of the polarity at the transition state in intermolecular Diels-Alder reactions. We herein extend this model to deal with intramolecular Diels-Alder (IMDA) processes. The transferability of the empirical reactivity rules established for the intermolecular DA reactions to the IMDA reactions is discussed. The analysis based on group electrophilicity and nucleophilicity in general fails because having two different reactivity patterns within the same molecule hampers a clean classification of electrophilic…