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  • 1
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 109 (1987), S. 2245-2250 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 117 (2002), S. 1441-1449 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have investigated the performance of the new optimized exchange functional (OPTX) developed by Handy and Cohen [Mol. Phys. 99, 403 (2001)] for predicting geometries, heats of reaction, and barrier heights for twelve organic reactions (six closed-shell and six radical). OPTX has been used in conjunction with, among others, the well-known Lee–Yang–Parr (LYP) correlational functional to form two new functionals, OLYP and O3LYP. These are similar to the well-established BLYP and B3LYP functionals, respectively, with OPTX replacing the standard Becke exchange functional, B88. Our results strongly support claims made by their developers that OLYP is superior to BLYP, and essentially renders it obsolete. The computed OLYP heats of reaction, barrier heights, and even molecular geometries (with larger basis sets), are comparable with, if not better than, the corresponding B3LYP values. The O3LYP functional is overall better than B3LYP, albeit not by much. Both OLYP and O3LYP are among the best functionals currently available; the performance of OLYP in particular is noteworthy given that this functional includes no exact exchange. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 6566-6572 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present an improved version of our recent algorithm [B. Paizs, G. Fogarasi, and P. Pulay, J. Chem. Phys. 109, 6571 (1998)] for optimizing the geometries of large molecules. The approximate Cholesky factorization technique has been generalized to the case of redundant coordinates, and an alternative approach involving use of the B†B matrix in the iterative coordinate back transformation is described. The generalized full Cholesky factors of B†B are very sparse and the corresponding force and geometry transformations are fast and numerically stable, permitting us to apply this technique for internal coordinate geometry optimization of molecules containing thousands of atoms. As an example we present optimization data on alpha-helical alanine polypeptides, and various globular proteins. Results for the alanine polypeptides indicates that internal coordinate optimization is clearly superior to the first-order Cartesian optimization techniques generally used in force field calculations. The largest system investigated is alpha-helical Ac-(Ala)999-NH2 containing 9999 atoms, which was successfully optimized using less than a megaword of memory. Optimization of various globular proteins shows that our procedure can easily deal with highly redundant (including full primitive) coordinate sets. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 2063-2079 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Twelve organic reactions (six closed shell and six radical) were studied using semiempirical, traditional ab initio and density functional methodologies. Full geometry optimizations of all species, both minima and transition states, were performed, and calculated geometries and barrier heights compared with experimental data. Our results demonstrate that although currently available density functionals tend to underestimate barrier heights, especially for radical reactions—in some cases reactions with low barriers are predicted to be essentially barrier free—they provide a significant improvement over standard methods. The adiabatic connection method recently proposed by Becke [J. Chem. Phys. 98, 5648 (1993)], in which a portion of the exact Hartree–Fock exchange is mixed in to the density functional, looks very promising. © 1994 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 8894-8902 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Full density functional geometry optimizations on hydrogen peroxide and heptane/dimethyl pentane using six different numerical grids are presented. The grids vary in quality and gradients are calculated (1) assuming a fixed grid and no weight derivatives, and (2) with full allowance for a "moving'' atom-centered grid and inclusion of the weight derivatives. The results clearly demonstrate that accurate energies and geometries can be obtained with around 3500 points per atom for medium-sized systems (up to say 30 atoms) without the necessity of including the weight derivatives. The latter only begin to influence the results for grids which are of insufficient quality to guarantee reliable values in any case.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 4986-4991 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using a Z-matrix-like approach for generating new Cartesian coordinates from a new geometry defined in terms of delocalized internal coordinates, we eliminate the costly O(N3) iterative back-transformation required in standard geometry optimizations using delocalized (or natural/redundant) internals, replacing it with a procedure which is only O(N). By replacing the gradient transformation with an iterative solution of a set of linear equations, we also reduce this step from O(N3) to roughly O(N2). This allows a very efficient method for geometry optimization of large molecules in internal coordinates. Several optimizations on systems containing up to 500 atoms are presented, comparing the performance of the new algorithm with its predecessor, and demonstrating the practical utility and efficiency of our approach. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 11100-11107 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using redundant inverse-power distance coordinates we present a series of optimizations on randomly generated argon clusters containing 12, 24, and 48 argon atoms. Our results clearly show that inverse distance coordinates perform significantly better for optimizing the geometries of atomic clusters than either Cartesian or natural/delocalized internal coordinates. The potential utility of these coordinates for global optimization is discussed. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 192-212 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Following on from the earlier work of Pulay and Fogarasi [J. Chem. Phys. 96, 2856 (1992)] we present an alternative definition of natural internal coordinates. This set of delocalized internal coordinates can be generated for any molecular topology, no matter how complicated, and is fully nonredundant. Using an appropriate Schmidt-orthogonalization procedure, all standard bond length, bond angle, and dihedral angle constraints can be imposed within our internal coordinate scheme. Combinatorial constraints (in which sums or differences of stretches, bends, and torsions remain constant) can also be imposed. Optimizations on some fairly large systems (50–100 atoms) show that delocalized internal coordinates are far superior to Cartesians even with reliable Hessian information available at the starting geometry. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 97 (1997), S. 59-66 
    ISSN: 1432-2234
    Keywords: Key words: DFT ; Dynamics ; Barrier height ; Isomerization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. We present the results of a comprehensive study on the inner-hydrogen migration in free base porphyrin, using density functional theory with the hybrid B3-LYP exchange-correlation functional, and both the 6-31G(d ) and a triple-zeta double-polarization (TZ2P) basis set. The latter computations, involving 726 contracted functions, are the largest calculations on this system to date. Full geometry optimization was carried out for the cis and trans minima, the transition state for trans-cis isomerization, and the symmetric stationary point for the synchronous trans-trans isomerization. All stationary points were characterized by vibrational analysis. Our results strongly support the conclusion, reached by earlier workers, that trans-trans hydrogen transfer occurs in a two-step process via a cis intermediate. With the TZ2P basis and including zero-point effects for the -h 2 isotopomer, the trans-cis barrier height is 13.1 kcal/mol, the cis-trans energy difference is 8.1 kcal/mol and the reverse cis-trans barrier height is 5.0 kcal/mol. The trans-cis barrier height agrees well with the value of Braun et al. (J Am Chem Soc (1996) 118: 7231) obtained from NMR line shapes and a modified Bell tunneling model, but our cis-trans energy difference is higher, and the reverse barrier is lower, than the values of Braun et al. Tunneling precludes the existence of -h 2 cis-porphyrin as an observable species, but the -d 2 and, especially, -t 2 isotopomers might be observable at low temperatures if the reverse barrier is higher than our calculated value. We predict the theoretical vibrational spectrum of cis-porphyrin and suggest that IR active modes at 566 cm−1 and 2333 cm−1 in the -d 2 isotopomer may be used to detect the presence of the cis intermediate.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 68 (1985), S. 221-229 
    ISSN: 1432-2234
    Keywords: Valency ; Bond order ; Atomic charge ; Orbital population ; Mulliken analysis ; Löwdin analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Alternative definitions of bond order, valency, gross orbital populations and total atomic charge for SCF wavefunctions are compared. It is found that there are sound theoretical and numerical reasons for preferring definitions based on the Löwdin density matrix.
    Type of Medium: Electronic Resource
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