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  • 1
    ISSN: 0948-5023
    Keywords: Keywords NICS, Aromaticity, Molecular orbital theory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Nucleus Independent Chemical Shift (NICS) values, pioneered by Schleyer, provide detailed insights into electronic structures of transition states. These show that the [2+2+2]-cycloaddition transition states, studied early by Schleyer and by us, have aromatic transition structures and that fused cyclopropanes are aromatic in the transition structure, while fused four-membered rings are antiaromatic. The nucleophilic ring-opening of 1- and 2-cyanobicyclo[1.1.0]butanes, studied earlier by Hoz, and ring openings of cyanocyclopropane, cyanocyclobutane, and 2-cyanobicyclo[2.2.0]hexane by hydroxide were investigated at the B3LYP/6-31+G* level. Orbital interactions through bonds explain relative facilities of ring opening.
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  • 2
    ISSN: 0948-5023
    Keywords: Keywords Grignard compounds, Diethylether, Schlenk equilibrium, DFT calculation, Solvent effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Density Functional calculations have been used to study the solvent effect of diethyl ether on the Schlenk equilibrium and the aggregation of Grignard reagents RMgX with R = Me, Et, Ph. Solvent stabilization of the Mg complexes of the first solvent is larger than that of the second one. The solvation energy decreases on going from the dihalides MgX2 to the monohalides RMgX to the diorganyl compounds MgR2. The calculations indicate that the energetic preference of the unsymmetrical species reduces upon solvation. The strong tendency to dimerization of the un- and partly solvated compound vanishes for the higher solvated cases.
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  • 3
    ISSN: 0948-5023
    Keywords: Keywords Nitrene additions, Buckminsterfullerene, C60, NCOOCH3, AM1, B3LYP/6-31G**//AM1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Semiempirical and density functional calculations have been carried out to discuss the origin of the closed [5,6]-aza-bridged adduct obtained as a minor product in the reaction of singlet nitrenes with C60. The results indicated that the most likely source is the direct addition of singlet nitrenes to a [5,6]-bond of C60, in contradiction to the common belief that the [5,6]-bonds are not attacked in cycloaddition reactions to C60.
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  • 4
    ISSN: 0948-5023
    Keywords: Keywords Density functional calculations, Boronium ion, Three center two electron bond
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Structures and energies of XH4 + and XH6 + (X = B, Al and Ga) have been calculated at the density functional theory (DFT) B3LYP/6-311++G(3df,2pd) level. Calculations indicate that although the structure with a three center two electron (3c-2e) bond is the global minimum for BH4 +, the global minima of AlH4 + and GaH4 + are not those with one 3c-2e bond, but those with two 3c-2e bonds. For calibration, both structures of AlH4 + were also calculated at the ab initio CCSD(T)/cc-pVTZ level and results in agreement with the DFT results were found. Similar calculations also indicate that although the C2v symmetrical structure with two 3c-2e bonds is the global minimum for BH6 +, the global minima of AlH6 + and GaH6 + are not the C2v symmetrical structures with two 3c-2e bonds but the C2 symmetrical structures with three 3c-2e bonds.
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  • 5
    ISSN: 0948-5023
    Keywords: Keywords Polyenes, n-doped, B3LYP, Na
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The electronic structures of small, odd-membered, all-trans polyenes doped with one Na atom at various positions have been investigated using Hartree-Fock and density functional (B3LYP) theory with a 6-31G(d) basis set. Two distinctly different structural motifs have been identified. In one motif, the dopant atom interacts with an allylic polyene unit in a 4π-electron interaction that results in a planar polyene backbone. The other motif has the dopant atom interacting with a pentadienyl polyene unit in a 6π-electron interaction, which produces a significantly warped polyene backbone. Independent of structural motif at the doping site, the portion of the polyene structure outside the interaction region remains largely undisturbed in terms of planarity and bond length alternation. For a particular formula unit and potential energy surface, the stationary points corresponding to minima and transition states are remarkably close in energy despite the pronounced changes that occur in the dihedral angles of the polyene backbone at the dopant sites. Whereas internal and external instabilities are found in the Hartree-Fock wavefunctions for NaC7H9 and NaC9H11 structures, the restricted B3LYP wavefunctions are stable for all structures investigated.
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  • 6
    ISSN: 0948-5023
    Keywords: KeywordsAb initio calculation, Isomerism, Lithium, Solid-state structure, Sulphur
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Reaction of o-mercaptopyridine (o-MPH) and trithiocyanuric acid (TTCyH3) with one equivalent of BunLi in the presence of HMPA yields the mono-lithiated salts MPLi.HMPA (1) and TTCyH2Li.2HMPA (2) respectively, which have been characterised by NMR spectroscopy and X-ray crystallography. Reaction of three equivalents of BunLi with anhydrous TTCyH3 in THF yields the tri-lithiated species TTCyLi3.4THF (3). In all three compounds the lithium centres have N,S-bridged coordination modes. Whereas 1 is dimeric in the solid state, 2 has an unusual monomeric structure and 3, which is a very rare example of a structurally characterised tri-lithiated compound, has an unprecedented polymeric structure incorporating (NCSLi) n (n = 1, 2) rings. The structural diversities displayed by 1 and 2 have been probed, and thereby in part rationalised, by ab initio (6-31G*/RHF, 6-31G**/RHF and 6-31G*/MP2 levels) MO calculations on both their thio-keto and thiol isomers and on their uncomplexed and complexed lithiated derivatives. In particular, the optimised structures predict and reproduce the N,S-bridging coordination modes found for lithium and explain why structure 1 is dimeric whereas 2 is monomeric.
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  • 7
    ISSN: 0948-5023
    Keywords: KeywordsAb initio, Boron compounds, Crystal structure, Homoaromatics, Three center two electron bond
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Bishomotriborirane anions with a B-H-B bridge, 7, have been synthesized by a) protonation and b) methylation of bishomodianions, 3, as well as by c) hydride addition to 1,2,4-triboracyclopentanes, 15. Compounds 7 were characterized by 1H, 13C and 11B NMR spectroscopy and X-ray diffraction analyses. The suggested mechanism for the formation of 7 is supported by MP4SDTQ/6-311++G**//MP2(fc)/6-31+G* computations on [C2B3H8]- model compounds. Classical 1,2-dibora-4-borata-cyclopentane intermediates 16 undergo an intramolecular hydrogen shift to the B-B unit in their envelope conformation to give intermediates 17, which easily isomerize to 7. Relative energies for the parent compounds, 16u, 17u, 7u and the transition structures, TS-16/17u and TS-7/17u are predicted to be 30.7, 14.5, 0.0, 32.6 and 23.5 kcal mol-1, respectively. The terms classical and non-classical homobridges are suggested for methylene and hydrogen bridges in 7 and in related compounds on the grounds of common building principles. The strength of homoaromaticity in 7u was estimated to be at least 23.5 kcal mol-1, neglecting the much higher strain in 7u compared to TS-7/17u without a 3c2e bond.
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  • 8
    ISSN: 0948-5023
    Keywords: Proteins ; Davydov Model ; Special Cases ; Expansion of Exact Solutions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract For the Davydov Hamiltonian several special cases are known which can be solved analytically. Starting from these cases we show that the initial state for a simulation using Davydov′s |D1〉 approximation has to be constructed from a given set of initial lattice displacements and momenta in form of a coherent state with its amplitudes independent of the lattices site, corresponding to Davydov′s |D2〉 approximation. In the |D1〉 ansatz the coherent state amplitudes are site dependent. The site dependences evolve from this initial state exclusively via the equations of motion. Starting the |D1〉 simulation from an ansatz with site dependent coherent state amplitudes leads to an evolution which is different from the analytical solutions for the special cases. Further we show that simple construction of such initial states from the expressions for displacements and momenta as functions of the amplitudes leads to results which are inconsistent with the expressions for the lattice energy. The site-dependence of coherent state amplitudes can only evolve through the exciton-phonon interactions and cannot be introduced already in the initial state. Thus also in applications of the |D1〉 ansatz to polyacetylene always |D2〉 type initial states have to be used in contrast to our previous suggestion [W. Förner, J. Phys.: Condens. Matter 1994, 6, 9089-9151, on p. 9105]. Further we expand the known exact solutions in Taylor serieses in time and compare expectation values in different orders with the exact results. We find that for an approximation up to third order in time (for the wave function) norm and total energy, as well as displacements and momenta are reasonably correct for a time up to 0.12-0.14 ps, depending somewhat on the coupling strengh for the transportless case. For the oscillator system in the decoupled case the norm is correct up to 0.6-0.8 ps, while the expectation values of the number operators for different sites are reasonably correct up to roughly 0.6 ps, when calculated from the third order wave function. The most important result for the purpose to use such expansions for controlling the validity of ansatz states is, however, that the accuracy of S(t) and H(t) (constant in time, exact values known in all cases) is obviously a general indicator for the time region in which a given expansion yields reliable values also for the other, physically more interesting expectation values.
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular modeling 2 (1996), S. 103-135 
    ISSN: 0948-5023
    Keywords: Proteins ; Davydov Model ; Nonlinear Dynamics ; Expansion of Exact Solutions ; Ansätze
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We performed long time simulations using the |D1〉 approximation for the solution of the Davydov Hamiltonian. In addition we computed expectation values of the relevant operators with the state (Ĥ D /J)|D 1〉 and the deviation |δ〉 from the exact solution over long times, namely 10 ns. We found that in the very long time scale the |D1〉 ansatz is very close to an exact solution, showing expectation values of the relevant physical observables in the state (Ĥ D /J)|D 1〉 being about 5-6 orders of magnitudes larger than in the deviation state |δ〉. In the intermediate time scale of the ps range such errors, as known from our previous work, are somewhat larger, but still more or less negligibly. Thus we also report results from an investigation of the very short time (in the range 0-0.4 ps) behaviour of the |D1〉 state compared with that of an expansion of the exact solution in powers of time t. This expansion is reliable for about 0.12 ps for special cases as shown in the previous paper. However, the accuracy of the exactly known value of the norm and the expectation value of the Hamiltonian finally indicates up to what time a given expansion is valid, as also shown in the preceding paper. The comparison of the expectation values of the operators representing the relevant physical observables, formed with the third order wave function and with the corresponding results of |D1〉 simulations has shown, that our expansion is valid up to a time of roughly 0.10-0.15 ps. Within this time the second and third order corrections turned out to be not very important. This is due to the fact that our first order state contains already some terms of the expansion, summed up to inifinite order. Further we found good agreement of the results obtained with our expansion and those from the corresponding |D1〉 simulations within the time of about 0.10 ps. At later times, the factors with explicit powers of t in second and third order become dominant, making the expansion meaningless. Possibilities for the use of such expansions for larger times are described. Alltogether we have shown (together with previous work on medium times), that the |D1〉 state, although of approximative nature, is very close to an exact solution of the Davydov model on time scales from some femtoseconds up to nanoseconds. Especially the very small time region is of importance, because in this time a possible soliton formation from the initial excitation would start.
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  • 10
    ISSN: 0948-5023
    Keywords: Serine protease mechanism ; Force field calculation ; Substrate specifity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Acylenzyme intermediates, produced by transfer of the acyl portions of selected natural substrates onto the catalytic serine hydroxyl of the serine protease chymotrypsin, were modeled with the AMBER force field. The obtained structures were used to calculate interaction and deformation energies. A set of 32 geometry variables were extracted out of each structure. They describe deformation effects specific for each substrate. It is shown by statistical analyses, that the interaction and deformation energies correspond to measured substrate reactivities. The extracted geometry variables are able to reproduce this dependency through multivariante statistical methods. These analyses suggest that there exist specific deformations of both the substrate and the enzyme portion, which are related to substrate reactivity. The geometry changes observed for high specific substrates are interpreted in terms of mechanistical requirements of the enzymatic reaction. The obtained model validates the hypothesis of induced strain as possible source of substrate specifity of chymotrypsin.
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