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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    The chemical educator 3 (1998), S. 1-17 
    ISSN: 1430-4171
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Molecular vibration plays an important role in chemistry, both in chemical reactions and in the characterization and measurement of molecular structure and bonding. Normal modes provide the conceptual framework for understanding molecular vibrations. For example, the analysis of infrared spectra, an important tool for chemists, relies heavily on the concept of normal modes; yet, undergraduate students, even chemistry majors, seldom gain a thorough understanding of normal modes through the traditional chemistry curriculum. In fact, the most commonly used physical chemistry textbooks give only a cursory introduction to this concept, leaving out the substantive development. This occurs presumably because normal modes emerge from a multistepped mathematical analysis of the molecular dynamics. While the mathematical skill needed for each step typically has been covered in an introductory calculus course, the full development is a lengthy process and skipped in the texts. Thus, students have little opportunity to develop a sound conceptual understanding of ‘vibrational modes’ and ‘fundamental vibrational frequencies,’ even though they inevitably encounter these terms in their future work.
    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 86 (1987), S. 3711-3719 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Experimental diffraction peaks and resonance splittings are analyzed with a close coupling scattering calculation to give a consistent He–graphite interaction potential. The interaction is modeled as a sum of effective He–C pair interactions. Previous, more approximate, estimates of bound state matrix elements of the potential were 30% larger than present estimates. The corrugation of the equipotential surface is estimated to be a little smaller than previous "hard wall'' estimates. The results are compared with recent ab initio potentials.
    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. 9978-9985 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An improved way of estimating the local tangent in the nudged elastic band method for finding minimum energy paths is presented. In systems where the force along the minimum energy path is large compared to the restoring force perpendicular to the path and when many images of the system are included in the elastic band, kinks can develop and prevent the band from converging to the minimum energy path. We show how the kinks arise and present an improved way of estimating the local tangent which solves the problem. The task of finding an accurate energy and configuration for the saddle point is also discussed and examples given where a complementary method, the dimer method, is used to efficiently converge to the saddle point. Both methods only require the first derivative of the energy and can, therefore, easily be applied in plane wave based density-functional theory calculations. Examples are given from studies of the exchange diffusion mechanism in a Si crystal, Al addimer formation on the Al(100) surface, and dissociative adsorption of CH4 on an Ir(111) surface. © 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 115 (2001), S. 9644-9656 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A method for systematically finding the optimal orientation and location of a hyperplanar dividing surface during a transition state theory calculation of a transition rate is presented. The optimization can be carried out during a reversible work evaluation of the free energy barrier. An application to Al adatom diffusion on an Al(100) surface is described. There, the method can converge to give the free energy barrier for the optimal mechanism, a concerted displacement, even when the calculation is initially set up for the less optimal hop mechanism. This illustrates that the method can reveal the optimal mechanism of a transition even when the calculation is started with an incorrect guess. © 2001 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 111 (1999), S. 10664-10669 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have developed a new method for finding and representing dividing surfaces which can, for example, be used to identify "atoms" in molecules or condensed phases based on Bader's definition. Given the total electron density of the system, the dividing surface is taken to be the zero-flux surface, i.e., the surface on which the normal component of the gradient vanishes. Our method for finding this surface involves creating an "elastic sheet" represented by a swarm of fictitious particles which interact with each other so as to give a nearly uniform distribution of points on the sheet. Two kinds of forces act on the particles: (1) the component of the gradient of the density normal to the elastic sheet, and (2) an interparticle force which only acts in the local tangent plane of the sheet. Starting with a spherical surface and applying an optimization algorithm that minimizes the forces leads to convergence of the particles to the zero-flux surface. The elastic sheet tends to round off regions where the zero-flux surface has sharp cusps or points, but this appears not to be a serious problem in cases we have studied. The elastic sheet method is robust and can converge in situations where currently used methods fail. We demonstrate the method with a study of water clusters and a Si interstitial in a Si crystal. © 1999 American Institute of Physics.
    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 101 (1994), S. 8964-8971 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A theoretical basis is presented for reversible work evaluation of transition rates within the framework of transition state theory. The method involves computing statistical averages of forces without having to evaluate transition state partition functions or densities, and therefore eliminates the need for a harmonic reference system. The method can be applied to systems of high dimensionality which is particularly important in calculations on quantum systems, where each quantum particle may be represented by several images in a Feynman path integral chain. The relationship between this method and the fixed centroid method of Gillan and centroid density theories is established. The various methods are compared on a model quantum system consisting of an Eckart barrier coupled to a harmonic oscillator.
    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 111 (1999), S. 7010-7022 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The problem of determining which activated (and slow) transitions can occur from a given initial state at a finite temperature is addressed. In the harmonic approximation to transition state theory this problem reduces to finding the set of low lying saddle points at the boundary of the potential energy basin associated with the initial state, as well as the relevant vibrational frequencies. Also, when full transition state theory calculations are carried out, it can be useful to know the location of the saddle points on the potential energy surface. A method for finding saddle points without knowledge of the final state of the transition is described. The method only makes use of first derivatives of the potential energy and is, therefore, applicable in situations where second derivatives are too costly or too tedious to evaluate, for example, in plane wave based density functional theory calculations. It is also designed to scale efficiently with the dimensionality of the system and can be applied to very large systems when empirical or semiempirical methods are used to obtain the atomic forces. The method can be started from the potential minimum representing the initial state, or from an initial guess closer to the saddle point. An application to Al adatom diffusion on an Al(100) surface described by an embedded atom method potential is presented. A large number of saddle points were found for adatom diffusion and dimer/vacancy formation. A surprisingly low energy four atom exchange process was found as well as processes indicative of local hex reconstruction of the surface layer. © 1999 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 102 (1995), S. 1796-1805 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We simulate the compression of a two-component Lennard-Jones liquid at a variety of constant temperatures using a molecular dynamics algorithm in an isobaric–isothermal ensemble. The viscosity of the liquid increases with pressure, undergoing a broadened transition into a structurally arrested, amorphous state. This transition, like the more familiar one induced by cooling, is correlated with a significant increase in icosahedral ordering. In fact, the structure of the final state, as measured by an analysis of the bonding, is essentially the same in the glassy, frozen state whether produced by squeezing or by cooling under pressure. We have computed an effective hard-sphere packing fraction at the transition, defining the transition pressure or temperature by a cutoff in the diffusion constant, analogous to the traditional laboratory definition of the glass transition by an arbitrary, low cutoff in viscosity. The packing fraction at this transition point is not constant, but is consistently higher for runs compressed at higher temperature. We show that this is because the transition point defined by a constant cutoff in the diffusion constant is not the same as the point of structural arrest, at which further changes in pressure induce no further structural changes, but that the two alternate descriptions may be reconciled by using a thermally activated cutoff for the diffusion constant. This enables estimation of the characteristic activation energy for diffusion at the point of structural arrest. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physical Chemistry 51 (2000), S. 623-653 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract The study of adsorption, diffusion, island formation, and interlayer transport of atoms on a growing surface has been an active field in the past decade, because of both experimental and theoretical advances. Experiments can give detailed images of patterns formed on growing surfaces. An important challenge to the theoretical studies is the identification of dynamical processes controlling the pattern formation and overall surface morphology. This can be achieved by accurate modeling of the atomic interactions, a thorough search for active atomic-scale processes, and simulation of the growth on the experimental timescale to allow for detailed comparison with the experimental measurements. An overview of some of the theoretical methodology used in these studies and results obtained for one of the most extensively studied systems, Pt(111), is given here. A remarkable richness of phenomena has emerged from these studies, where apparently small effects can shift the balance between competing molecular processes and thereby change the morphology of a growing surface. The article concludes with a discussion of possible future directions in this research area.
    Type of Medium: Electronic Resource
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  • 10
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    Unknown
    Chapel Hill, N.C. : Periodicals Archive Online (PAO)
    Social Forces. 27:1/4 (1948/1949) 452 
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