Donor-acceptor molecules, computational

The effects of cooperativity can also extend to other properties such as quadrupole coupling constants. These quantities were computed for the D and nuclei in linear clusters of (HCN), with n varying up to 6, at the SCF level with a 6-31+G basis set. The calculated values are listed in Table 5.5 where d refers to the proton donor molecule on one end of the chain, a to the acceptor on the other end, and d-a to a combined donor-acceptor molecule in the middle of each chain. 

Since the first use of catalyzed hydrogen transfer, speculations about, and studies on, the mechanism(s) involved have been extensively published. Especially in recent years, several investigations have been conducted to elucidate the reaction pathways, and with better analytical methods and computational chemistry the catalytic cycles of many systems have now been clarified. The mechanism of transfer hydrogenations depends on the metal used and on the substrate. Here, attention is focused on the mechanisms of hydrogen transfer reactions with the most frequently used catalysts. Two main mechanisms can be distinguished (i) a direct transfer mechanism by which a hydride is transferred directly from the donor to the acceptor molecule and (ii) an indirect mechanism by which the hydride is transferred from the donor to the acceptor molecule via a metal hydride intermediate (Scheme 20.3). 

As points of reference, we will take two well-established hydrogen-bond donor/ acceptors, H2O and NH3. Their computed gas-phase Vs,max and Vs,mm are in Table 5, along with the same data for all of the molecules that have been discussed hydroxylamine (5), dimethylhydroxylamine (6), acetoxime (7), acetohydroxamic acid (8), and the isomeric pairs of oximes examined in the last section. Finally, we included an additional hydroxamic acid, 11, to see the effects of the strongly electron-withdrawing cyano group. 

The elucidation of the structure, dynamics and self assembly of biopolymers has been the subject of many experimental, theoretical and computational studies over the last several decades. [1, 2] More recently, powerful singlemolecule (SM) techniques have emerged which make it possible to explore those questions with an unprecedented level of detail. [3-55] SM fluorescence resonance energy transfer (FRET), [56-60] in particular, has been established as a unique probe of conformational structure and dynamics. [26-55] In those SM-FRET experiments, one measures the efficiency of energy transfer between a donor dye molecule and an acceptor dye molecule, which label specific sites of a macromolecule. The rate constant for FRET from donor to acceptor is assumed to be given by the Forster theory, namely [59,61-64]... 

Because of their sensitivity to small redistributions of electron density, the computation of the intensities of vibrational modes has proven to be more demanding than the frequencies. Table 3.5 reports calculations of the intensities at the SCF and correlated levels. The intensity of the internal vibration of the proton-acceptor molecule is changed only little by the perturbation, but that of the donor undergoes a large increase by a factor of three or four. The latter intensification is characteristic of H-bonds and will be seen repeatedly. 

Quantum chemical computations of H complexes heats formation in case of interaction of large organic molecules lead to high errors. A more perspective way is the use of well known relations of physical organic chemistry for this purpose. These equations allow to predict the heats of hydrogen-bonded or donor-acceptor complexes formation on the basis of donor (base) and acceptor (acid) empirical parameters. There are Drago and Weyland s equation [71]... 

At Astex, the initial partitioning of fragments into cocktails is achieved using a computational procedure that minimizes chemical similarity [43]. Fragments are described as feature vectors, which encode such properties as the number of donors/ acceptors/non-hydrogen atoms, number of five- and six-membered rings and their substitution patterns. The chemical dissimilarity between two molecules, d(i, j), is then calculated as the distance between the two vectors. 

Table 29.1 Binding energies (—A , in kcal/mol) computed for various acceptor molecules, all with CH4 as proton donor data corrected by counterpoise procedure...

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