Conformations density function theory

Detection of the dA N1 and dC N3 adducts may not in one sense be particularly important for DNA based on their central position within the helical conformation and hydrogen bonding network.37,38 Still, the deoxynucleoside studies helped to focus attention on the reversibility of alkylation by QM and provided insight into the reactions of duplex DNA described below in Section 9.3. Reaction at the deoxynucleoside level also provided an essential system for developing a theoretical treatment of QM reaction.50-52 Computations based on density functional theory well rationalized the published results on d A and correctly anticipated the results on dG and dC reviewed above and described in more detail in Chapter 2 (Freccero). 

Figure 2.14. Density functional theory calculated (BP/DNP) IR spectral profiles of the N—O bond stretching region for the i71-Af 1Cu(NO)2 12I2 complex in the attracto and repulso conformation (after [75]).

In recent years, density-functional theory has emerged as the computational quantum chemistry method of choice for biological problems of medium size range (up to a few hundreds of atoms) in applications that do not require extensive conformational sampling. The field continues to advance in the accuracy of new functionals, the improvement of algorithms and the functionality and computational performance of software [81]. 

The crystal structures of raer-[lr(en)(enl I )C13]C1 1120 and mer-[Ir(en)(en )Cl3] show that the coordination geometry of Ir is almost identical in the two complexes, with the only difference being in the conformation of the unidentate en and enH+ groups.122 Density functional theory and ab initio calculations have been performed on the two complexes and the calculated confirmations agree well with the X-ray diffraction values.123 The enH+ ligand is stabilized via intramolecular N—H - - Cl hydrogen bonds. 

A recent ab initio quantum mechanical study (Han et al, 1998) used B3LYP/6-31G density functional theory to examine the relative stabilities of eight conformers of AAMA with four explicit water... 

St.-Amant, A., W. D. Cornell, P. Kollman, and T. A. Halgren. 1995. Calculation of Molecular Geometries, Relative Conformation Energies, Dipole Moments, and Molecular Electrostatic Potential Fitted Charges of Small Organic Molecules of Biochemical Interest by Density Functional Theory. J. Comp. Chem. 16, 1483. 

Lelj, F., C. Adamo, and V. Barone. 1994. Role of Hartree-Fock exchange in density functional theory. Some aspects of the conformational potential energy surface of glycine in the gas phase. Chem. Phys. Lett. 230, 189. 

Group 2 complexes are formally electron deficient and conformationally floppy only small energies (often only 1-2 kcal mol-1) are required to alter their geometries by large amounts (e.g., bond angles by 20° or more). In such cases, the inclusion of electron-correlation effects becomes critical to an accurate description of the molecules structures. Both HF/MP2 and density functional theory (DFT) methods have been applied to organoalkaline earth compounds. DFT approaches, which implicitly incorporate electron correlation in a computationally efficient form, are generally the more widely used. Molecular orbital calculations that successfully reproduce bent... 

Molecular-level studies of mechanisms of proton and water transport in PEMs require quantum mechanical calculations these mechanisms determine the conductance of water-filled nanosized pathways in PEMs. Also at molecular to nanoscopic scale, elementary steps of molecular adsorption, surface diffusion, charge transfer, recombination, and desorption proceed on the surfaces of nanoscale catalyst particles these fundamental processes control the electrocatalytic activity of the accessible catalyst surface. Studies of stable conformations of supported nanoparticles as well as of the processes on their surface require density functional theory (DFT) calculations, molecular... 

Figure 11.31 Conformational equilibria of pyridine-2,6-dicarboxamides, as calculated using density functional theory (B3LYP/6-311-L G //B3LYP/6-31G ), favors a syn-syn conformation.

The conformations of various cyclic phosphate derivatives of 2-deoxyribose (e.g., compound 6, Section 10.09.3.2) have been studied using density functional theory (DFT) methods <2005JOC7107>. 

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