Search results for "Intramolecular force"
showing 10 items of 599 documents
Singlet Excited-State Interactions in Naphthalene-Thymine Dyads
2004
Two thymidine-derived nucleosides 1 and 2 were prepared by attaching a chiral naphthalene to the positions 5′ and 3′ of the sugar. The resulting dyads, which contain key substructures present in drugs and nucleic acids, exhibit different spatial arrangements (transoid or cisoid) of the fluorophore relative to the thymine unit. Emission measurements on these compounds in the presence of ROH molecules revealed a remarkable intramolecular fluorescence quenching for dyad 1. The obtained results are consistent with quenching of the singlet excited state of 1 by hydrogen-bond donor solvents. Thus, a physical deactivation process (vibronically induced internal conversion) would be the pathway resp…
Electrochemical synthesis and structural characterization of Co(II), Ni(II) and Cu(II) complexes of N,N-bis(4,5-dimethyl-2-hydroxybenzyl)-N-(2-pyridy…
2009
The electrochemical oxidation of anodic metal (cobalt, nickel or copper) in a cell containing an acetonitrile solution of the ligand N,N-bis(4,5-dimethyl-2-hydroxybenzyl)-N-(2-pyridylmethyl)amine (H2L) affords complexes [Co2L2].H2O (1), [Ni3L3] (2) and [Cu2L2] 3H2O (4). On using nickel as the anode and the addition to the solution electrolytic phase of the amount of water necessary to saturate the solution, the electrolytic process gave rise to the new compound [Ni2L2(H2O)1.5].CH3CN (3). Compounds 1 and 4 are dimeric and the metal atoms are pentacoordinated. Compound 3 also consists of dimeric neutral molecules with the nickel atoms in both penta- and hexacoordinated environments. The cryst…
Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution
2012
We are presenting a theoretical study of the hydrolysis of a β-lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06-2X functionals. Inclusion of the full molecule of the antibiotic, Cefotaxime, in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate a nucleophilic water molecule. Moreover, the flexibility of the substra…
Dynamic Effects on Reaction Rates in a Michael Addition Catalyzed by Chalcone Isomerase. Beyond the Frozen Environment Approach
2008
We present a detailed microscopic study of the dynamics of the Michael addition reaction leading from 6'-deoxychalcone to the corresponding flavanone. The reaction dynamics are analyzed for both the uncatalyzed reaction in aqueous solution and the reaction catalyzed by Chalcone Isomerase. By means of rare event simulations of trajectories started at the transition state, we have computed the transmission coefficients, obtaining 0.76 +/- 0.04 and 0.87 +/- 0.03, in water and in the enzyme, respectively. According to these simulations, the Michael addition can be seen as a formation of a new intramolecular carbon-oxygen bond accompanied by a charge transfer essentially taking place from the nu…
Alkali metal mediated resorcarene capsules: An ESI-FTICRMS study on gas-phase structure and cation binding of tetraethyl resorcarene and its per-meth…
2002
AbstractElectrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) with additional ab initio calculations were used to examine the alkali metal cation binding selectivity (i.e., molecular recognition) and host properties of tetraethyl resorcarene (1) and its per-methylated derivative (2). The significance of intramolecular hydrogen bonding for the crown conformation was demonstrated. The presence of intramolecular flip-flop hydrogen bonding in 1 was confirmed both with calculations and in ND3-exchange experiments. All the alkali metal cations formed host–guest complexes by docking inside the cavity of the host. Complexation with the larger cations, esp…
Understanding the Mechanism of the Intramolecular Stetter Reaction. A DFT Study
2012
The mechanism of the N-heterocyclic carbene (NHC)-catalyzed intramolecular Stetter reaction of salicylaldehyde 1 to yield chromanone 3 has been theoretically studied at the B3LYP/6-31G** level. This NHC-catalyzed reaction takes place through six elementary steps, which involve: (i) formation of the Breslow intermediate IN2; (ii) an intramolecular Michael-Type addition in IN2 to form the new C-C s bond; and (iii) extrusion of the NHC catalyst from the Michael adduct to yield chromanone 3. Analysis of the relative free energies in toluene indicates that while formation of Breslow intermediate IN2 involves the rate-determining step of the catalytic process, the intramolecular Michael-type addi…
The Molecular and Crystal Structure of tert-Butyl N.ALPHA.-tert-Butoxycarbonyl-L-(S-trityl)cysteinate and the Conformation-Stabilizing Function of We…
2001
The title compound, C31H37NO4S [systematic name: (R)-tert-butyl-2-[(tert-butoxycarbonyl)amino]-3-(tritylsulfanyl)propanoate] is an L-cysteine derivative with three functions: NH2, COOH and SH, blocked by protecting groups tert-butoxycarbonyl, tert-butyl and trityl, respectively. The main chain of the molecule adopts the extended, nearly all-trans C5 conformation with the intramolecular N-H...O=C hydrogen bond. The urethane group is not involved in any intermolecular hydrogen bonding. Only weak intermolecular hydrogen bonds and hydrophobic contacts are observed in the crystal structure. These are C-H...O hydrogen bonds and CH/pi interactions with donor...acceptor distances, C...O ca. 3.5 A a…
Hydrogen and copper ion-induced molecular reorganizations in scorpionand-like ligands. A potentiometric, mechanistic, and solid-state study.
2007
Two aza scorpionand-like macrocycles (L2 and L3) have been prepared. L2 consists of a tren amine with two of its arms cyclizized with a 2,6-bis(bromomethyl)pyridine. In L3, the remaining pendant arm has been further functionalized with a fluorophoric naphthalene group. X-ray data on the compounds [H(L3)]ClO4.H2O (1) and [H3(L3)](H2PO4)3.H2O (2) as well as solution studies (pH-metry, UV-vis, and fluorescence data) show the movement of the pendant arm as a result of the protonation degree of the macrocycles and of the formation of intramolecular hydrogen bonds. X-ray data on the complexes [Cu(L2)](ClO4)2]2.H2O (3) and [Cu(L3)](ClO4)2 (4) and solution studies on Cu2+ coordination show the impl…
β-turn tendency in N-methylated peptides with dehydrophenylalanine residue: DFT study.
2010
The tendency to adopt β-turn conformation by model dipeptides with α,β-dehydrophenylalanine (ΔPhe) residue in the gas phase and in solution is investigated by theoretical methods. We pay special attention to a dependence of conformational properties on the side-chain configuration of dehydro residue and the influence of N-methylation on β-turn stability. An extensive computational study of the conformational preferences of Z and E isomers of dipeptides Ac-Gly-(E/Z)-ΔPhe-NHMe (1a / 1b) and Ac-Gly-(E/Z)-ΔPhe-NMe(2) (2a/2b) by B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) methods is reported. It is shown that, in agreement with experimental data, Ac-Gly-(Z)-ΔPhe-NHMe has a great tendency to adopt …
An "S"-shaped pentanuclear CuII cluster derived from the metal-assisted hydrolysis of pyCOpyCOpy: structural, magnetic and spectroscopic studies.
2007
Reaction of [Cu2(O2CMe)4(H2O)2] with 2,6-di-(2-pyridylcarbonyl)-pyridine (pyCOpyCOpy or dpcp) in MeCN–H2O 10 : 1, led to the pentanuclear copper(II) complex [Cu5(O2CMe)6{pyC(O)(OH)pyC(O)(OH)py}2] (1) which crystallizes in the triclinic P space group. The copper(II) atoms are arranged in an “S”-shaped configuration, and are bridged by the doubly deprotonated bis(gem-diol) form of the ligand, pyC(O)(OH)pyC(O)(OH)py2−. Magnetic susceptibility data indicate the interplay of both ferro- and antiferromagnetic intramolecular interactions stabilizing an S = 3/2 ground state. Fitting of the data according to a next-nearest-neighbour model {Ĥ = −[J1(Ŝ1Ŝ2 + Ŝ1′Ŝ2′) + J2(Ŝ2Ŝ3 + Ŝ3′Ŝ2′) + J3(Ŝ1Ŝ3 + Ŝ3′Ŝ…