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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 973-980 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We reconsider the potential energy surface of the He–LiH system recently examined by Gianturco and co-workers [F. A. Gianturco et al., Chem. Phys. 215, 227 (1997)]. We compute the He–LiH interaction energy at the CCSD(T) level using large correlation consistent atomic basis sets supplemented with bond functions. To capture the severe anisotropy of the He–LiH potential, we interpolate our ab initio points in the angular direction with cubic splines, then expand the splines in terms of Legendre polynomials. The resulting smooth potential surface differs substantially from that of Gianturco et al.; in particular, our attractive He–LiH well is more than twice as deep as that of Gianturco et al., with a He–LiH binding energy of De=176.7 cm−1. © 1999 American Institute of Physics.
    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 99 (1993), S. 2942-2963 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have investigated the effect of potential energy saddles on the evolution of chaos in small (three- to seven-atom) inert gas clusters by comparing the local Kolmogorov entropy (K entropy) accumulated near a saddle with that accumulated in a potential well. We find that saddles which are relatively flat along the isomerization coordinate are most effective at reducing the local K entropy in the saddle region, indicating that these saddles tend to regularize the dynamics close to the saddle point. In three- and four-atom clusters, we also find that flat saddles decouple some or all of the cluster's vibrational modes from one another; this leads to approximately quasiperiodic behavior in some degrees of freedom near the saddle regions of these clusters.
    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 96 (1992), S. 1376-1390 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have calculated the Kolmogorov entropy for three- and seven-particle clusters bound by Lennard-Jones potentials and for three-particle clusters bound by Morse potentials of various ranges. We have used two quite different methods, one of which is new, which give consistent results. We find that all of these systems are classically chaotic over a wide range of energies surrounding the estimated quantum-mechanical zero point energies. Furthermore, for the three-particle clusters, we can rationalize the variation in the degree of chaos with total energy in terms of the local structure of the clusters' potential energy surface.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    The European physical journal 26 (1993), S. 391-393 
    ISSN: 1434-6079
    Keywords: 36.40.+d ; 05.45.+b
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We have computed the local Kolmogorov entropy of molecular dynamics trajectory segments near the potential energy saddles of model Ar3 and Ar5 clusters. In the case of Ar3 clusters bound with a Lennard-Jones potential, the local Kolmogorov entropy of the cluster is significantly smaller in the saddle region than in other areas of the potential surface. This behavior indicates an increase in the degree of nearly quasiperiodic motion near the Ar3 saddle due to the partial decoupling of the cluster's vibrational modes there. Lennard-Jones Ar5 clusters do not exhibit similar behavior, but Ar5 clusters bound with a short-range Morse potential do. This suggests that the “regularizing” effect of saddle regions is strongly dependent on the shape of the energy surface near the saddle. From these observations, we can determine which features of the saddle are most important in this respect; the flatness of the saddle region seems to be one such feature.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 63-76 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Matrix elements for the first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for stretching, linear, nonlinear, and out-of-plane bending and torsional motion. Derivatives of the energy with respect to the Cartesian coordinates are calculated with the chain rule. Derivatives of the energy with respect to the internal coordinates are straightforward, but the calculation of the derivatives of the internal coordinates with respect to the Cartesian coordinates can be simplified by the following two steps outlined in this article. First, the number of terms in the analytical functions can be reduced or will vanish when the derivatives of the bond length, bond angle, and torsion angle are reported in a local coordinate system in which one bond lies on an axis and an adjacent bond lies in the plane of two axes or is projected onto perpendicular planes for linear and out-of-plane bending motion. Second, a simple rotation transforms these derivatives to the appropriate orientation in the space-fixed molecular coordinate system. Functions of the internal coordinates are invariant with respect to translation and rotation. The translational invariance and the symmetry of the second derivatives for a system with L atoms are used to select L-1- and L(L-1)/2-independent first and second derivatives, respectively, of which approximately half of the latter vanish in the local coordinate system. The rotational invariance permits the transformation of the simplified derivatives in the local coordinate system to any orientation in space. The approach outlined in this article simplifies the formulas by expressing them in a local coordinate system, identifies the most convenient independent elements to compute, from which the dependent ones are calculated, and defines a transformation to the space-fixed molecular coordinate system.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The results of a study of the binding to DNA of substituted cis-Pt(II) diammines, (cis-DP) are presented. Computer modeling of a series of cis-Pt(NH2R)2+2 - where R = H, CH3, cyclopropyl, cyclobutyl, and cyclopentyl - to N7(G) atoms of two adjacent intrastrand guanine bases in a square planar complex in a pentamer duplex of DNA were performed. The stability of the complexes is studied by calculating the relative conformational energy of the cis-DP-DNA complexes with molecular mechanics (MM) and the intrinsic binding energy, which is the relative binding energy for ligand replacement in the presence of the substituents R with quantum mechanics. In the model, the receptor site geometry and the conformation of the DNA is changed little in the accommodation of the series of monosubstituted diammines. These diammines bind to one family of DNA conformations, denoted as IC in a previous study, and this suggests that a common conformational feature in the DNA may exist to explain the smooth trend in activity. The slight increase in van der Waals energy resulting from an increasing number of atoms in the substituents is countered by a larger decrease in the ligand replacement energy as the substituent increases in size. This overall decrease in relative energy is consistent with the slight decrease in activity as the substituent size increases.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of cis-Pt(II) diammine (cis-DP) to double-stranded DNA was studied with several kinked conformations that can accommodate the formation of a square planar complex. Molecular mechanics (MM) calculations were performed to optimize the molecular fit. These results were combined with quantum mechanical (QM) calculations to ascertain the relative energetics of ligand binding through water vs direct binding of the phosphate to the ammine and platinum, and to guide the selection of DNA conformations to model complex formation. Based on QM and MM calculations, models are proposed that may be characterized by several general features. A structure involving hydrogen bonding between each ammine and distinct adjacent phosphate groups, referred to as closed conformation (CC), has already been reported. This is also found in the crystal structure of small dimers. We report alternative conformations that may be important in platination of duplex DNA. They are characterized by an intermediate conformation (IC), involving hydrogen bonding between one ammine and phosphate group, and an open conformation (OC), without ammine phosphate hydrogen bonding. The IC and OC can be stabilized by water bridges in the space between the ammine and the phosphate groups. Sugar puckers alternate from the type C(2′)-endo or C(1′)-exo (S), to the type C(3′)-endo or C(2′)-exo (N), with intermediate types near O(1′)-endo (O). In general, the sugar puckers alternate from S to N to S through the platinated region (3′-TpG*pG*p-5′), with the complexed strand exhibiting, (3′)-S*-N*-S-(5′) alternation, while the complementary strand shows either (3′)-S*-N*-S(5′) or (3′)-S*-N*-O-(5′) alternation. In both the OC and IC, a hydrogen bond is found between the ammine and O4(T) on thymine (T) at the (3′) end, adjacent to the complex site. There is a continuous range of backbone conformations through the platinated region which relate the OC to the IC. The models presented suggest that the dynamics of the binding of the cis-Pt(II)-diammines to adjacent N7(G) in double-stranded DNA may encompass several conformational possibilities, and that water bridges may play a roll in supporting open and intermediate conformations. Proton-proton distances are reported to assist in the experimental determination of conformations.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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