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81.
Atkinson CE Aliev AE Motherwell WB 《Chemistry (Weinheim an der Bergstrasse, Germany)》2003,9(8):1714-1723
A binding site optimisation protocol for the design of artificial enzymes based on "small molecule-small molecule" binding studies by diffusion NMR is presented. Since the reaction chosen was the hydrolysis of ester 1 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phenethyl ester), an analogous phosphonate ester 2 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phosphonic phenethyl ester) was selected as a suitable transition state analogue (TSA). The key objective of the NMR studies was to find a unit with functional groups capable of binding to the acidic sites of the TSA. Nine dipeptides, mainly with basic and hydroxyl groups, were used and their affinity to the TSA was studied by measuring the change in the diffusion coefficient, D(pep), upon binding by pulse field gradient NMR. The value of D(pep) at 298 K in D(2)O at pD 5, 7 and 10 was measured both in free solution, and mixtures containing one dipeptide and the TSA. As both components are low molecular weight species with M < 500, a TSA-to-dipeptide ratio of 10:1 was used to detect significant changes in D(pep). The results revealed that dipeptides with basic residues show higher affinity to the TSA than those with hydroxyl or aliphatic side chains in aqueous solutions. The dipeptide showing the most significant relative change in D(pep) was H-Arg-Arg-OH, and the binding constant was estimated to be 86 L M(-1) by measuring D(pep) at varying concentrations of the TSA. In addition, binding of the TSA to a new water-soluble polymer with a polyallylamine backbone and randomly distributed Arg-Arg binding sites was examined, and the binding constant was estimated to be > or =1500 L M(-1). As confirmed by further catalytic activity tests, polymers containing Arg-Arg as a binding site are capable of significant rate accelerations in the hydrolysis of ester 1. 相似文献
82.
The triplet nature of rare long-lived states of d0 metallocenes formed upon ligand-to-metal energy transfer was confirmed by studies of triplet-triplet charge transfer in biscyclopentadienyl
complexes Cp2MCl2 (M = Zr (1), Hf (2)). The interaction between precatalysts and substrates of catalytic polymerization systems, viz., complexes 1 and 2 and unsaturated hydrocarbons (alkenes and dienes), was studied in the region of concentrations close to catalytic values.
For organometallic π-complexes, it has been shown for the first time that, in the case of the unsaturated hydrocarbons, the
efficiency of energy transfer obeys the Perrin equation. The process occurs at distances R
0 close to the diameter of the interacting molecules and is well described by the exchange-resonant mechanism of interaction.
In the case of the cyclopentadiene-Cp2MCl2 (M = Zr, Hf) systems, R
0 = 14.6 Å. A linear relationship between the critical radius of the quenching sphere R
0 and the number of carbon atoms in a linear α-olefin has been revealed for the first time and evidences the formation of a
π-complex between the precatalyst and substrate molecules.
Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 35–39, January, 2007. 相似文献
83.
Schlegel HB 《Journal of computational chemistry》2003,24(12):1514-1527
Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described. 相似文献
84.
Isaac B. Bersuker Natalia N. Gorinchoi Victor Z. Polinger 《Theoretical chemistry accounts》1984,66(3-4):161-172
The vibronic origin of dynamic instability of molecular systems considered earlier, is here given a more complete and rigorous treatment. It is shown that the nonvibronic contribution to the curvature of the adiabatic potential arising due to nuclear displacements under fixed electronic density distribution, is always positive, and hence the only reason for dynamic instability is the pseudo Jahn-Teller effect. For some examples of special interest (planar equilateral NH3, planar square CH4 and linear H
3
+
) the molecular excited states, responsible for the instability of the ground state, are revealed by means of ab initio calculations. 相似文献
85.
We describe and interpret computer simulations of the time evolution of a binary alloy on a cubic lattice, with nearest neighbor interactions favoring like pairs of atoms. Initially the atoms are arranged at random; the time evolution proceeds by random interchanges of nearest neighbor pairs, using probabilities compatible with the equilibrium Gibbs distribution at temperatureT. For temperatures 0.59Tc, 0.81 Tc, and 0.89T
c, with density of A atoms equal to that in the B-rich phase at coexistence, the density C1 of clusters ofl A atoms approximately satisfies the following empirical formulas: C1 w(1 –)3 andC
1, (1 –)4Q1w1 (2 l 10). Herew is a parameter and we defineQ
l
=
K
e
–E(K)
, where the sum goes over all translationally nonequivalentl-particle clusters andE(K) is the energy of formation of the clusterK. Forl > 10,Q
1 is not known exactly; so we use an extrapolation formulaQ
l
Aw
s
–l
l
– exp(–bl
), wherew
s is the value ofw at coexistence. The same formula (withw > w
s) also fits the observed values of C, (for small values ofl) at densities greater than the coexistence density (forT=0.59Tc): When the supersaturation is small, the simulations show apparently metastable states, a theoretical estimate of whose lifetime is compatible with the observations. For higher supersaturation the system is observed to undergo a slow process of segregation into two coexisting phases (andw therefore changes slowly with time). These results may be interpreted as a more quantitative formulation (and confirmation) of ideas used in standard nucleation theory. No evidence for a spinodal transition is found.Supported by AFOSR Grant No. 73-2430D and by ERDA Contract No. EY-76-C-02-3077*000. 相似文献
86.
Laura Gagliardi Giorgio Orlandi Fernando Bernardi Alessandro Cembran Marco Garavelli 《Theoretical chemistry accounts》2004,111(2-6):363-372
In the present paper we report the results of a multiconfigurational computational study on potential-energy curves of azobenzene along the NN twisting to clarify the role of this coordinate in the decay of the S2(*) and S1(n*) states. We have found that there is a singlet state, S3 at the trans geometry, on the basis of the doubly excited configuration n2*2, that has a deep minimum at about 90° of twisting, where it is the lowest excited singlet state. The existence of this state provides an explanation for the short lifetime of S2(*) and for the wavelength-dependence of azobenzene photochemistry. We have characterized the S1(n*) state by calculating its vibrational frequencies, which are found to correspond to the recently observed transient Raman spectrum. We have also computed the potential-energy curve for the triplet T1(n*) at the density functional theory B3LYP level, which indicates that in this state the isomerization occurs along the twisting coordinate.Acknowledgement The financial support from MIUR (project Modellistica delle proprietà spettroscopiche di sistemi molecolari complessi funds ex 60% and project Dinamiche molecolari in sistemi di interesse chimico funds ex 40%), from the University of Bologna (Funds for Selected Research Topics) is gratefully acknowledged.Contribution to the Jacopo Tomasi Honorary Issue 相似文献
87.
Juan Manuel Ortiz-Sánchez Ricard Gelabert Miquel Moreno José M Lluch 《Chemphyschem》2007,8(8):1199-1206
The two isoelectronic bipyridyl derivatives, [2,2'-bipyridyl]-3,3'-diamine and [2,2'-bipyridyl]-3,3'-diol, are experimentally known to undergo very different excited-state double-proton-transfer processes, which result in fluorescence quantum yields that differ by four orders of magnitude. Herein, density functional theory (DFT), time-dependent DFT (TDDFT), and complete active space self-consistent field (CASSCF) calculations are used to study the double-proton-transfer processes in the ground and first singlet pi-->pi* excited state. The quantum-chemistry calculations indicate 1) the existence of only one energy minimum in the ground electronic state corresponding to reactants (thus avoiding the possibility of a fast fluorescent relaxation process from the photoproducts region), 2) an endoergic process of the complete double proton transfer, and 3) the presence of a conical intersection in the excited intermediate region of [2,2'-bipyridyl]-3,3'-diamine. These facts explain the very low fluorescence quantum yield in [2,2'-bipyridyl]-3,3'-diamine compared to [2,2'-bipyridyl]-3,3'-diol. 相似文献
88.
In a previous DFT study a mechanism for the reductive half-reaction of pea seedling amine oxidase (PSAO) was suggested. In many of the suggested steps a lysine at the active site plays an important role. However, this lysine is not found in other amine oxidases. The primary aim of the present DFT study is therefore to investigate alternative mechanisms for those amine oxidases (CAO) where the lysine residue is not present. One of the most important roles suggested for the lysine in PSAO was to protonate the O2-site of TPQ before the critical Cbond;H bond cleavage of the substrate. In the absence of lysine the O2-site of TPQ is now suggested to be protonated by a water ligand on the copper metal complex, in line with experimental suggestions. In other steps the role of lysine is taken over by an asparagine. All results are compared with experimental observations and good agreement is generally found. 相似文献
89.
The absorption spectra and emission spectral band shapes of several polypyridine-ligand (PP) bridged bis-ruthenium(II) complexes imply that the Ru(II)/Ru(III) electronic coupling is weak in their lowest energy metal to ligand charge transfer (MLCT) excited states. Many of these PP-bridging ligands contain pyrazine moieties and the weak electronic coupling of the excited states contrasts to the strong electronic coupling inferred for the correlated mixed-valence ground states. Although the bimetallic complexes emit at significantly lower energy than their monometallic analogs, the vibronic contributions to their 77 K emission spectra are much stronger than expected based on comparison to the monometallic analogs (around twofold in some complexes) and this feature is characteristic of bimetallic complexes in which the mixed-valence excited states are electronically localized. The weaker excited state than ground state donor/acceptor electronic coupling in this class of complexes is attributed to PP-mediated super-exchange coupling in which the mediating orbital of the bridging ligand (PP-LUMO) is partly occupied in the MLCT excited states, but is unoccupied in the ground states; therefore, the vertical Ru(III)-PP− (MLCT) energy is larger and the mixing coefficient smaller in these excited states than is found for Ru(II)-PP in the corresponding ground states. 相似文献
90.
The transition states of intramolecular 1,4 and 1,5 H-atom transfers, from/to primary (p), secondary (s) or tertiary alkyl (t) and primary (p
a), secondary (s
a) or tertiary (t
a) allyl carbon atoms, have been studied at the level of the semiempirical quantum-chemical method AM1 with the UHF approximation. The activation and reaction enthalpies were calculated and compared with experimental data available in the literature and the calculated data obtained for analogous reactions in alkyl radicals. Correlations were found between the activation enthalpies and the dissociation enthalpies of the bonds broken and formed. 相似文献