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  • Articles  (1,076)
  • American Institute of Physics  (622)
  • American Institute of Physics (AIP)
  • Cambridge University Press
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  • 11
    Electronic Resource
    Electronic Resource
    Geometry optimization of large biomolecules in redundant internal coordinates (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 6566-6572 
    Details
    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
    URL: http://dx.doi.org/10.1063/1.1308551
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  • 12
    Electronic Resource
    Electronic Resource
    Geometry optimization in delocalized internal coordinates: An efficient quadratically scaling algorithm for large molecules (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 4986-4991 
    Details
    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
    URL: http://dx.doi.org/10.1063/1.478397
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  • 13
    Electronic Resource
    Electronic Resource
    The generation and use of delocalized internal coordinates in geometry optimization (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 192-212 
    Details
    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
    URL: http://dx.doi.org/10.1063/1.471864
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  • 14
    Electronic Resource
    Electronic Resource
    A resonance enhanced multiphoton ionization study of the CS2 molecule: The 4p Rydberg states (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 2436-2444 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The resonance enhanced multiphoton ionization (REMPI) spectrum of jet-cooled CS2 has been recorded in the one-photon wavelength range 460–500 nm, corresponding to the three photon excitation energy range 60 000–65 000 cm−1. A previous assignment of one photon forbidden transitions in this region to 3d Rydberg states is shown to be incorrect and reassigned to the 4pπ 1,3Δu states. In fact all the observed states in this region can be assigned to 4p Rydberg states; the 4pσ 1,3Πu states at 62 768 and 62 083 cm−1, respectively, and the 4pπ 1,3Δu states at 64 214 and 63 698 cm−1, respectively. Another band at 64 374 cm−1 may be due to a three photon excitation to the 4pπ 1Σ+u Rydberg state. Our resolution is sufficient to resolve band shapes enabling symmetry assignments when coupled with their polarization behavior. The fact that the origin bands are not degraded and that Δν=0 sequence bands are strongly excited whereas Δν≠0 transitions are either absent or very weak implies that the upper states have a linear geometry similar to that of the ground state. A comparison of singlet–triplet splittings suggests the 4pπ Δu states have stronger Hund's case (c) character than the 4pσ Πu state. While CS+2 was generally the predominant ion formed, resonance ionization through the 1Δu←X 1Σ+g origin band led to an unusual predominance of S+ and CS+ ions. This is explained by multiphoton fragmentation of CS+2 via an accidental one-photon resonance from the X 2Π1/2 (v=0) ionic ground state. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469666
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  • 15
    Electronic Resource
    Electronic Resource
    A two-color (1+1′)+1 multiphoton ionization study of CS2 in the 61 000–65 600 cm−1 energy region (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 4847-4854 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The (1+1′)+1 resonance enhanced multiphoton ionization (REMPI) spectrum of jet-cooled CS2 has been recorded in the 61 000–65 600 cm−1 excitation energy range. Four prominent band groups are observed that can be assigned to Δν2=−1 and Δν2=1 sequences of the two-photon electronically forbidden 4p 1,3Δu←X˜ 1Σ+g transitions. Weak bands to higher energy appear to be associated with the 310, 230 and 110210 bands and corresponding sequence bands. The results show that the upper states are not 3d Rydberg states as has been previously supposed, and are consistent with a recent reinvestigation of the corresponding (3+1) REMPI spectrum. Further experimental information is obtained on the anomalous vibrational band structure of transitions to the 3Δu state. The 201 and 212 bands of the 4p 1Πu←X˜ 1Σ+g transition are also observed, but are much weaker, suggesting that vibronic interactions are less important in this state compared to the 4p 1,3Δu states. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470620
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  • 16
    Electronic Resource
    Electronic Resource
    Disorder induced enhancement of the third order optical nonlinearity in a conjugated polymer (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 2295-2301 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We report on the relationship between material disorder and nonlinear optical response for a conjugated polymer. Inverse Raman scattering, the technique used here, is sensitive to the transition cross sections of both the purely electronic (Sv=01↔Sv=00) and vibronic (Sv=01↔Sv=10) transitions accessed, and both of these quantities are related to the extent of disorder in the polymer backbone. We have verified these morphology dependencies using crystalline and amorphous samples of the polydiacetylene poly(4BCMU). The magnitude of the nonlinear response per backbone repeat unit in the amorphous material is comparable to that of the crystalline form because of the large potential well displacement between the ground and excited electronic states characteristic of the disordered material. This increased potential well displacement compensates for the nonlinear response lost to the reduced macroscopic polymer alignment associated with the two-dimensionally isotropic spin cast film. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468717
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  • 17
    Electronic Resource
    Electronic Resource
    A study of some organic reactions using density functional theory (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 2063-2079 
    Details
    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
    URL: http://dx.doi.org/10.1063/1.468728
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  • 18
    Electronic Resource
    Electronic Resource
    First observation of the v=3 level of the B 1Σ+ Rydberg state of CO (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 3956-3961 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new diffuse vuv band of 12C16O at 92 800 cm−1 has been observed in absorption and assigned to the B–X(3–0) transition. The assignment is based on the excellent agreement found between the observed band and a calculated spectrum of the B–X(3–0) transition, where a previously optimized two channel close-coupling model of the B 1Σ+–D' 1Σ+ Rydberg–valence predissociation interaction has been used to calculate the B(v=3) state molecular constants, J dependent predissociation widths and the J dependent B–X(3–0) vibronic transition moments. The relative absorption cross-section for this transition has also been calculated. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468523
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  • 19
    Electronic Resource
    Electronic Resource
    Hyperfine and Zeeman quantum beats in the B 2Π1/2 state of NO (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 3968-3976 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Quantum beat signals have been observed in v=0, 1, 2, and 3 of the B 2Π1/2 state of NO for the first time and are used to carry out Doppler free spectroscopy in these levels. Beat signals are observed at zero magnetic field in all four vibrational levels between different hyperfine components for J=3/2 and J=5/2, and are analyzed to derive accurate hyperfine constants and quadrupole coupling parameters. Although from their magnetic tuning rates the beats between the different hyperfine levels can be assigned to particular F'↔F separations, the energy ordering of the F levels and the parity assignment remain to be determined. Independently of this exact assignment a small variation in the hyperfine parameters with vibrational state is observed which is irregular in v=3 indicating the presence of an interaction with another electronic state. When a small magnetic field is applied much more intense beat signals are observed which occur between the Zeeman split components of a single hyperfine level. The B 2Π1/2 state is nominally nonmagnetic in the Hund's case (a) limit and so the effective g values vary rapidly with J due to spin–orbit uncoupling. The relative intensities of these beat signals and their variation with both magnetic field and vibrational level is accurately predicted using the known spectroscopic constants and a fitted value of gr. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468525
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  • 20
    Electronic Resource
    Electronic Resource
    The effect of grid quality and weight derivatives in density functional calculations (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 8894-8902 
    Details
    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
    URL: http://dx.doi.org/10.1063/1.468081
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