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  • Engineering General  (1,377)
  • Biochemistry  (367)
  • Wiley-Blackwell  (1,744)
  • 2010-2014
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  • 1925-1929
  • 1
    ISSN: 0271-2091
    Keywords: Finite Element ; Quasi-three-dimensional ; Interconnected Aquifer Systmes ; Fluid Mass Balance ; Iterated Frontal Method ; Predictor-Corrector Method ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The quasi-three-dimensional equations controlling the groundwater flow in heterogeneous and interconnected aquifer systems are discretized by finite elements, considering also the aquifer branching. A new method for fluid mass balance evaluation based on the equivalent nodal source (E.N.S.) concept allows one to express the balance in conservative terms, and interpret finite element equations as nodal balance equations. The solution of the system is based on the frontal method. Use of substructures limits the frontal increase in correspondence to the aquifer branching. In the steady state, the frontal method is integrated with an iterative solution technique to eliminate the frontal increase caused by the presence of aquitards. It converges very rapidly, using a forcing technique with an automatic parameter definition. In the unsteady case the same scope is achieved using a predictor-corrector procedure which employs the Crank-Nicolson method in the corrector phase.This very stable procedure permits use of fairly long time-steps and concerns the case of source terms depending on piezometry (problem of interaction between water table and river). This method has been tested with several fairly complex cases.
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  • 2
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    International Journal for Numerical Methods in Fluids 3 (1983), S. 493-506 
    ISSN: 0271-2091
    Keywords: Modified ; Dodge ; Algorithm ; Parabolized ; Navier-Stokes ; Computational Fluid Dynamics ; Low Speed Flow ; Channel Flow ; Zebra Algorithm ; Mass Balancing ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A revised version of Dodge's split-velocity method for numerical calculation of compressible duct flow has been developed. The revision incorporates balancing of mass flow rates on each marching step in order to maintain front-to-back continuity during the calculation. The (chequerboard) zebra algorithm is applied to solution of the three-dimensional continuity equation in conservative form. A second-order A-stable linear multistep method is employed in effecting a marching solution of the parabolized momentum equations. A chequerboard iteration is ued to solve the resulting implicit non-linear systems of finite-difference equations which govern stepwise transition. Qualitive agreement with analytical predictions and experimental results has been obtained for some flows with well-known solutions.
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  • 3
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    International Journal for Numerical Methods in Fluids 3 (1983), S. 529-542 
    ISSN: 0271-2091
    Keywords: Strongly Rotating ; Incompressible ; Free-surface ; Finite-difference ; Coriolis ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The flow of an incompressible fluid in a rapidly rotating right circular cylinder is considered. A source/sink mass distribution at the lateral wall, which is azimuthally uniform and symmetric across the midplane, causes a deviation from wheel flow. The container is only partially full and the inner free surface is allowed to deviate slightly from the vertical. A finite-difference solution of the full axisymmetric, non-linear governing equations was used to obtain the flow field. A special implicit technique for the Coriolis terms which maintains geostrophy was developed and is described. The results obtained for a low Rossby number flow compare quite favourably with the linearized solution. Results are also presented for a case wherein the non-linear terms are important.
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  • 4
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    International Journal for Numerical Methods in Fluids 3 (1983), S. 567-581 
    ISSN: 0271-2091
    Keywords: Advection ; Convection ; Estuary ; Fractional ; Step ; Diffusion ; Dispersion ; Moving ; Co-ordinates Transport ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A successful and economical fractional step algorithm for the convection-dispersion-reaction equation is described. Exact solutions are adopted for the reaction and convection steps, the latter by the introduction of a moving co-ordinate system. The dispersion step uses an optimized finite difference algorithm which specifically accommodates the grid non-uniformity. The excellent performance of the algorithm is confirmed by numerical experiments together with computations of the Fourier response and integrated square error characteristics.
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  • 5
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    International Journal for Numerical Methods in Fluids 3 (1983), S. 583-590 
    ISSN: 0271-2091
    Keywords: QUICK ; Finite Difference ; Free Surface Flow ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The spatially third-order accurate QUICK finite difference technique is applied to the solution of the depth-integrated equations of motion for steady, subcritical, free surface flow in a wide, shallow, rectangular channel with and without an abrupt expansion. The conservative, control-volume discretization of the equations of motion and the use of QUICK in approximating required cell and cell face average quantities is discussed. Results presented show that it is possible to obtain stable solutions for advective free surface flows without resorting to implicit numerical smoothing.
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  • 6
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    International Journal for Numerical Methods in Fluids 4 (1984) 
    ISSN: 0271-2091
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 7
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    International Journal for Numerical Methods in Fluids 3 (1983), S. 591-604 
    ISSN: 0271-2091
    Keywords: Shallow Water Equations ; Finite Element Method ; Wave Equation ; Numerical Noise ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Numerical noise has been a problem with finite element solutions to the shallow water equations. Two methods used to reduce the noise level are evaluated, and these results are compared with published results for equal-order interpolations. The two methods are mixed-interpolation (quadratic interpolation for velocity and linear interpolation for sea level) and a spectral form of the wave equation. Whereas mixed interpolation removes the troublesome sea level mode, it can still have considerable noise in velocity. The spectral wave equation is efficient and does not contain the spurious eigenmodes which contribute to high noise levels.
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  • 8
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 1-12 
    ISSN: 0271-2091
    Keywords: Review ; Finite Elements ; Meteorology ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The application of the finite-element method to the simulation of meterological fluid flow problems is reviewed. Early studies were aimed primarily at demonstrating the viability of the method for one- and two-dimensional flows, whereas more recent studies have been aimed at demonstrating the efficiency and viability of the method for more complex three-dimensional simulations. There has also been a shift towards exploiting such models to better understand and predict the underlying meteorological phenomena, rather than restricting attention to the development of the algorithms.
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  • 9
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    International Journal for Numerical Methods in Fluids 3 (1983), S. 605-622 
    ISSN: 0271-2091
    Keywords: Natural ; Convection ; Stream ; Function ; Finite ; Element ; Formulation ; C1 ; Continuity ; Truncated ; Quintic ; Restricted Variational Principle ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A finite element stream function formulation is presented for the solution to the two-dimensional double-glazing problem. Laminar flow with constant properties is considered and the Boussinesq approximation used. A restricted variational principle is used, in conjunction with a triangular finite element of C1 continuity, to discretize the two coupled governing partial differential equations (4th order in stream function and second order in temperature). The resulting non-linear system of equations is solved in a segregated (decoupled) manner by the Newton-Raphson linearizing technique.Results are produced for the standard test case of an upright square cavity. These are for Rayleigh numbers in the range 103-105, with a Prandtl number of 0.71. Comparisons are made with benchmark results presented at the 1981 International Comparison study in Venice. In the discussion of results, emphasis is placed on the variation of local Nusselt number along the isothermal walls, particularly near the corner. This reveals a noticeable source of error in the evaluation of the maximum Nusselt number by lower order discretization methods.
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  • 10
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 105-105 
    ISSN: 0271-2091
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 11
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 147-158 
    ISSN: 0271-2091
    Keywords: Finite Element ; Incompressible Flow ; Pressure-specification-point ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The discontinuity of a finite-element pressure field that is sometimes present in the neighbourhood of the pressure-specification-point is shown to arise either from round-off, or from mistakes in modelling. The implications of this are considered. In particular it restricts grid refinement near the pressure-specification-point. The analysis can be extended to finite-difference calculations, and to other fields governed by equations similar to Poisson's equation.
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  • 12
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 109-125 
    ISSN: 0271-2091
    Keywords: Finite elements ; Navier-Stokes ; Vorticity-stream function ; Time-dependent ; flows ; Boundary conditions ; Incompressible viscous flows ; Two-dimensional flows ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A new finite element method for solving the time-dependent incompressible Navier-Stokes equations with general boundary conditions is presented. The two second-order partial differential equations for the vorticity and the stream function are factorized, apart from the non-linear advection term, by eliminating the coupling due to the double specification on the stream function at (a part of) the boundary. This is achieved by reducing the no-slip boundary conditions to projection integral conditions for the vorticity field and by evaluating the relevant quantities involved according to an extension of the method of Glowinski and Pironneau for the biharmonic problem. Time integration schemes and iterative algorithms are introduced which require the solution only of banded linear systems of symmetric type. The proposed finite element formulation is compared with its finite difference equivalent by means of a few numerical examples. The results obtained using 4-noded bilinear elements provide an illustration of the superiority of the finite element based spatial discretization.
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  • 13
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    International Journal for Numerical Methods in Fluids 4 (1984) 
    ISSN: 0271-2091
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 14
    ISSN: 0271-2091
    Keywords: Polymer Flows ; Non-Newtonian ; Moving Boundary ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Recent progress in the simulation of polymeric flows of two key problems in the injection moulding process, carried out by a team at Cornell University, is briefly described. For the filling of cooled thin cavities, the fluid is characterized by a power-law viscosity with exponential temperature dependence, and interaction between the transient thermal boundary-layer and the core flow in a domain with moving boundary is essential. The earlier procedure of Hieber and Shen is modified in two aspects: a boundary-integral formulation replaces the finite-element treatment of the pressure, and an ‘energy integral’ approach is used for the transient temperature. The second problem is the steady visco-elastic flow in the juncture region where sudden changes of the geometry and large strain rates occur. The constitutive equation is postulated according to the Leonov model. The main features in the numerical implementation are: integration along a streamline to determine the elastic deformation tensors for a given velocity field, and finite-element treatment (in time-dependent form) of the pressure and fields for given stresses. In an example where the contraction ratio is 7:1, results for nominal Deborah number exceeding 100 show no numerical instability. (However, for this problem, the true Weissenberg number, i.e. the ratio of local first-normal-stress difference to shear stress turns out to be generally O(10).) The predictions also correlate very well with experimental birefringence measurements.
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  • 15
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 303-319 
    ISSN: 0271-2091
    Keywords: Finite Element ; Turbulent Flow ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Although the finite-element (FE) method has been successful in analysing complex laminar flows, a number of difficulties can arise when two-equation turbulence models (e.g. the k-∊ model) are incorporated. This work describes a particular FE discretization of the k-∊ model and reports its performance in recirculating flow. Severe problems encountered in attempts to obtain convergence of the numerical scheme are isolated and analysed, and methods by which the problems can be overcome are suggested.Insight gained in this work has enabled a practical turbulent flow FE code to be constructed which is robust and efficient. This code is the subject of a further paper.
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  • 16
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 321-336 
    ISSN: 0271-2091
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Incorporation of the k-∊ turbulence model into Galerkin finite-element fluid-flow codes (which, unlike upwind finite-difference codes, have no artificial damping) can lead to severe iterative convergence difficulties. This paper introduces an alternative turbulence model (the q-f model) and an associated finite-element discretization method which are designed to overcome these problems. The new model forms the basis of a finite-element fluid-flow code which is robust and efficient. Furthermore, it is demonstrated on a practical example that the code can give good agreement with experiment on fairly coarse meshes.
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  • 17
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 399-419 
    ISSN: 0271-2091
    Keywords: Laminar Boundary Layers ; Finite Element Method ; Finite Difference Method ; Spectral Method Convergence ; Computational Efficiency ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The Dorodnitsyn boundary later formulation is given a finite element interpretation and found to generate very accurate and economical solutions when combined with an implicit, non-iterative marching scheme in the downstream direction. The algorithm is of order (Δ2u, Δx) whether linear or quadratic elements are used across the boundary layer. Solutions are compared with a Dorodnitsyn spectral formulation and a conventional finite difference formulation for three Falkner-Skan pressure gradient cases and the flow over a circular cylinder. With quadratic elements the Dorodnitsyn finite element formulation is approximately five times more efficient than the conventional finite difference formulation.
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  • 18
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 421-439 
    ISSN: 0271-2091
    Keywords: Laminar Flow ; Turbulent Flow ; Compressible Flow ; Separation ; Time-split Method ; Finite Element Method ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The time-split finite element method is extended to compute laminar and turbulent flows with and without separation. The examples considered are the flows past trailing edges of a flat plate and a backward-facing step. Eddy viscosity models are used to represent effects of turbulence. It is found that the time-split method produces results in agreement with previous experimental and computational results. The eddy viscosity models employed are found to give accurate predictions in all regions of flow except downstream of reattachment.
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  • 19
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 441-457 
    ISSN: 0271-2091
    Keywords: Finite Element Method ; Dip Coating ; Newtonian Fluid ; Free Surface ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A finite element simulation of the dip coating process based on a discretization of the continuum with discontinuous pressure elements is presented. The algorithm computes the flow field from natural boundary conditions while an extra condition provided by the existence of free surface is employed to displace the meniscus location towards the actual position. The process is iterative and uses a pseudo-time stepping technique coupled to a cubic spline fitting of the free surface. Numerical predictions exhibit good agreement with experimental data for Newtonian fluids in the case of flat plate dip coating as well as in the case of wire dip coating.
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  • 20
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 459-475 
    ISSN: 0271-2091
    Keywords: Augmented Lagrangian ; Finite Element Method ; Dip Coating ; Non-Newtonian Fluids ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: We apply in this paper the augmented Lagrangian method to the study of various non-Newtonian fluid flow problems, and in particular the dip coating process. We only present in this second part the treatment specific to the non-linearities involved in the constitutive equations, the first part having largely been concerned with the general description of the approximation used.Two rheological models illustrating different rheological behaviours are used to simulate dip coating process: the Carreau-A model for shear-thinning properties of the viscosity and a truncated second-order model for a Newtonian behaviour in viscosity with elastic properties.Numerical predictions show a very good agreement with experimental data for the second-order model. The discrepancy observed in the other case can be explained qualitatively by the elastic properties exhibited by the shear-thinning fluids used: this elasticity is not taken into account in the Carreau-A model.
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  • 21
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 667-683 
    ISSN: 0271-2091
    Keywords: Rotating Flow ; Finite Differences ; Numerical Stability ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A computer program has been developed to predict laminar source-sink flow in a rotating cylindrical cavity. Although the program is based on a standard finite difference technique for recirculating flow, it incorporates two novel features. Step changes in grid size are employed to obtain sufficient resolution in the boundary layers and special treatment is given to the solution of the pressure correction equations, in the ‘SIMPLE’ algorithm, in order to improve the convergence properties of the method. Results are presented both for the flow in an infinite rotating cylindrical annulus and a finite rotating cylindrical cavity, with the inner cylindrical surface acting as a uniform source and the outer cylinder as a sink. These show good agreement with existing analytical solutions and illustrate some of the problems associated with the computation of rapidly rotating flows.
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  • 22
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 685-699 
    ISSN: 0271-2091
    Keywords: Stokes Flows ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A family of simple Stokes flows involving sliding surfaces adjacent to surfaces at rest is considered. Principally, two specific flow configurations are investigated: (i) that arising when parts of the boundary of an infinitely long circular cylinder are rotating about the axis while other parts of the boundary are at rest, and (ii) the flow produced when a cap of a sphere is held at rest while the remainder of the sphere rotates about the symmetry axis. In each case computer plots of streamlines or constant velocity lines are presented to give a general impression of the resulting flow pattern.
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  • 23
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 708-708 
    ISSN: 0271-2091
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 24
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 709-709 
    ISSN: 0271-2091
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 25
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 765-780 
    ISSN: 0271-2091
    Keywords: Diffraction ; Hydrodynamics ; Ocean Engineering ; Underwater Structures ; Wave Forces ; Offshore Structures ; Velocity Potential ; Boundary Elements ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The fluid forces resulting from wave interaction with large submerged structures may be calculated using numerical procedures based on the solution of the associated boundary-value problem. In this paper, the analysis of wave interaction with a fixed submerged object of arbitrary cross-section and infinite length using a two-dimensional boundary value formation based on linear diffraction theory is summarized. Subsequently, the application of the boundary element method to obtain a solution is presented. The numerical considerations are emphasized with particular reference to computational efficiency.Numerical results are presented in the form of dimensionless wave force plots for various structural shapes. In the case of a bottom-seated half cylinder, for which there exists a closed-form solution, comparisons are made between results generated using both boundary element and equivalent finite element approaches. In the case of a submerged cylinder, comparisons are made between boundary element derived values and experimental results. The boundary element results compare well with both the closed-form solution and the experimental values.
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  • 26
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    International Journal for Numerical Methods in Fluids 4 (1984) 
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    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 27
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 931-947 
    ISSN: 0271-2091
    Keywords: Two-layer Flow ; Two-step Scheme ; Selective Lumping Method ; Ishikari Bay ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A finite element method for the analysis of two-layer density flows is presented in this paper. The standard Galerkin method based on linear interpolation functions is used to yield discrete spatial variables. For numerical integration in time, an explicit two-step selective lumping method is used. Here it is applied to a flow analysis of Ishikari Bay, at the mouth of Ishikari River. This case demonstrates a procedure that yields a numerically stable solution.
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  • 28
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 949-969 
    ISSN: 0271-2091
    Keywords: Navier-Stokes ; Discrete Fourier Transform ; Finite Difference ; Short Convolutions ; No-slip Boundary Condition ; Far Field Condition ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A mixed discrete Fourier transform-Finite difference algorithm is developed and used for the calculation of rapidly changing viscous fluid flows past a circular cylinder. The numerical approach has been designed to overcome certain difficulties arising for high Reynolds number simulations. The foremost advantage of the technique lies in its fast calculations of the convolution sums portraying the convective terms of the governing equations. Third-order spatial discretizations and fourth-order time marching are implemented.New schemes are proposed for the boundary conditions at the solid wall and at large distances. The techniques are tested on a case study with other schemes (summarized by Roache1) in order to obtain an optimal choice. Definite indications on the stability and accuracy of boundary condition schemes are achieved. Support for the statement of dominant importance of boundary conditions is also given.A comparison of computational results with experimental data is presented for the case study of the flow past an impulsively started cylinder at Reynolds number 20.The time development of the symmetrical zone of recirculation, which is formed at an early stage of the flow, has been studied for 300 ≤ Re ≤ 9500 by means of the proposed algorithm. Computational results, comparisons with experimental data2 and discussion of upper limits of validity of the procedure will be presented in a companion paper.
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  • 29
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 997-998 
    ISSN: 0271-2091
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 999-999 
    ISSN: 0271-2091
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 31
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 989-996 
    ISSN: 0271-2091
    Keywords: Galerkin ; Spline ; Stability ; Disk ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The perturbation equations which characterize the stability of flow over a rotating infinite disk are derived via strict order of magnitude analysis. These equations contain viscous terms not considered by Stuart,1 curvature and Coriolis terms not considered by Brown,2 and axial velocity terms not considered by Kobayashi et al.3 The strategy for reducing the problem to an algebraic system is Galerkin's method with B-spline discretization. In comparison with the Poiseuille flow solutions of Orszag,4 the method is shown to perform well without placing undue demands on computing capability. Critical values of Reynolds number, wave length, vortex orientation and number of spiral vortices calculated by the present method compare favourably with experimental data of Kobayashi et al.
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  • 32
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    International Journal for Numerical Methods in Fluids 4 (1984), S. 1001-1012 
    ISSN: 0271-2091
    Keywords: Compressible Fluid Flow ; Numerical Analysis ; Pressure Method ; von Kármán Vortex Street ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: In this paper the pressure method for incompressible fluid flow simulation is extended and applied to the numerical simulation of compressible fluid flow. The governing equations, obtained from the physical principles of conservation of momentum, mass and energy, are first studied from a characteristic point of view. Then they are discretized with a semi-implicit finite difference technique in such a fashion that stability is achieved independently of the speed of sound. The resulting algorithm is fast, accurate and particularly efficient in subsonic flow calculations. As an example, the computer simulation of the von Kármán vortex street is described and discussed.
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  • 33
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    Journal of Computational Chemistry 1 (1980), S. 36-45 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The variable-size simplex optimization method is used to reparametrize the I + A and β parameters of an INDO approximation to the perturbed Hartree-Fock calculation of 13C chemical shifts in hydrocarbons. The absolute shifts for 39 nuclei in a set of molecules containing up to four carbons are reproduced within a standard error of 9.9 ppm for an unconstrained optimization and to a standard error of 10.0 ppm for an optimization constrained to yield gross atomic charges in agreement with double-zeta ab initio calculations.
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  • 34
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    Journal of Computational Chemistry 1 (1980), S. 64-68 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A recently developed ab initio pseudopotential molecular orbital approach was applied to the Te42+ ion, a system outside the practical reach of conventional all-electron treatments. Computations were carried out with a minimal STO-4G basis set. Results account reasonably well for the observed optical absorption spectrum and suggest the origin of a hitherto unassigned weak band. Ground-state properties, which included the structure, force field, and vibrational frequencies, were also investigated. Treated as a free, gas-phase ion, tetratellurium (II) yielded a bond length 0.05 Å shorter than the experimental value for the ion in a crystal lattice. Placement of static, point-charge counterions in the Te42+ coordination sphere increased the bond length to a value 0.005 Å longer than derived by experiment. Calculations on neutral, cyclic Te4 provided a theoretical single-bond reference length 0.09 Å longer than that obtained for the ion in a counterion environment. Comparisons between observed and calculated frequencies suggest an assignment of the vibrational spectrum different from the provisional assignment in the literature.
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  • 35
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    Journal of Computational Chemistry 1 (1980), S. 111-117 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A molecular mechanical force field for fluorinated ethylenes and propylenes is described. The field computes geometries, dipole moments, and energy differences between isomers and rotamers. Component analysis indicates that “classical” strains alone (skeletal, nonbonded, electrostatic) cannot account for energy relationships. The discussion is supplemented by a semiempirical quantum chemical comparison of cis- and trans-FCH=CHF and of gauche- and anti-FCH2CH2F.
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  • 36
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    Journal of Computational Chemistry 1 (1980), S. 99-109 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2-methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI-CARB, a version of MMI with changes in some of the equilibrium C—O bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the C—C—O—H torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for C—C and C—O bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.
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  • 37
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    Journal of Computational Chemistry 1 (1980), S. 281-284 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Calculations at the STO-3G and 4-31G levels have been carried out on propylamine and ethylmethylamine, using geometries determined by molecular mechanics by allowing complete molecular relaxation in all degrees of freedom except for torsion about the central bond, and at 30° increments for the latter. It was found that a butanelike potential exists in each case. From 0° (cis) to 360° in order, the 4-31G values for the energy extrema are 5.92, 0.12, 3.88, 0.00, 3.94, and 0.51 kcal/mole for propylamine (with the nitrogen lone pair gauche to carbon), and 7.06, 1.45, 3.44, 0.0, 2.87, and 1.44 kcal/mole for ethylmethylamine.
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  • 38
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    Journal of Computational Chemistry 2 (1981), S. 188-199 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with the STO-3G basis set have been performed to investigate the structural, energetic, and electronic properties of mixed water-uracil dimers formed at the six hydrogen-bonding sites in the uracil molecular plane. Hydrogen-bond formation at three of the carbonyl oxygen sites leads to cyclic structures in which a water molecule bridges N1—H and O2, N3—H and O2, and N3—H and O4. Open structures form at O4, N1—H, and N3—H. The two most stable structures, with energies of 9.9 and 9.7 kcal/mole, respectively, are the open structure at N1—H and the cyclic one at N1—H and O2. These two are easily interconverted, and may be regarded as corresponding to just one “wobble” dimer. At 1 kcal/mole higher in energy is another “wobble” dimer consisting of an open structure at N3—H and a cyclic structure at N3—H and O4. The third cyclic structure at N3—H and O2 collapses to the “wobble” dimer at N3—H and O4. The two “wobble” dimers are significantly more stable than the open dimer formed at O4, which has a stabilization energy of 5.4 kcal/mole. Uracil is a stronger proton donor to water through N1—H than N3—H, owing to a more favorable molecular dipole moment alignment when association occurs through H1. Hydration of uracil by additional water molecules has also been investigated. Dimer stabilization energies and hydrogen-bond energies are nearly additive in most 2:1 water:uracil structures. There are three stable “wobble” trimers, which have stabilization energies that vary from 7 to 9 kcal/mole per water molecule. Hydrogen-bond strengths are slightly enhanced in 3:1 water:uracil structures, but the cooperative effect in hydrogen bonding is still relatively small. The single stable water-uracil tetramer is a “wobble” tetramer, with two water molecules which are relatively free to move between adjacent hydrogen-bonding sites, and a stabilization energy of approximately 8 kcal/mole per water molecule. Within the rigid dimer approximation, successive hydration of uracil is limited to the addition of one, two, or three water molecules.
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  • 39
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    Journal of Computational Chemistry 1 (1980), S. 373-385 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations with full geometry optimization have been carried out on the planar cCc, cTc, tTc, tCt, tTt, and cCt conformers of β-hydroxyacrolein using the 4-21G basis set, and on the cCc and cCt conformers using the 4-31G basis set. The hydrogen-bonded cCc conformer is the most stable and the cCt conformer the least stable, with the other conformers following the above sequence. β-Hydroxy substitution has scarcely any influence on the geometry of the trans-acrolein structure, whereas the geometry of the cis-acrolein structure shows significant changes which depend on whether the O—H group is cis or trans with respect to the CHO group about the C=C bond. The ΔET values for cis → trans isomerization about the C—C bond in cCt and cTc support the hypothesis that these changes in geometry are the result of a destabilizing interaction in cCt and a stabilizing interaction in cTc. The geometry of the hydrogen-bonded structure cCc sets it apart from all the other conformers: it has by far the longest C=C, the longest C=O, the longest O—H, the shortest C—C, and the shortest C—O. Its formation from cCt involves a lengthening of C=C, C=O, and O—H and a shortening of C—C and C—O, indicating a delocalization of charge within the ring. 4-21G calculations have also been made for a distorted cCt structure that has the same bond lengths and angles as the equilibrium cCc structure, and the distortion energy, cCt (equm. geom.) → cCt (distorted geom.), is found to be +13.1 kJ mole-1. Taking the energy of this distorted cCt structure as the baseline, the hydrogen-bonding energy in cCc is found to be  - 80.3 kJ mole-1.
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    Journal of Computational Chemistry 2 (1981) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 41
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    Journal of Computational Chemistry 2 (1981), S. 392-401 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The all-valence-electron CNDO/2 calculations were performed for the three isomeric nitrophenols. Using the newly derived σ-core charges and subsequently revising the valence-state ionization potentials and one-center two-electron repulsion integrals, Pariser-Parr-Pople (PPP) CI calculations were performed on the title compounds following the Nishimoto-Forster scheme. A better agreement between theory and experiment has been observed in spectral assignments compared to the conventional PPP approach. Information from the CNDO/2 calculations was used to obtain useful electronic structural parameters and to get a quantitative insight into the chemical reactivity of these molecules. All the results were compared with the basic compounds, phenol and nitrobenzene. The electronic spectra of these isomers were recorded in both polar and nonpolar solvents.
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  • 42
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    Journal of Computational Chemistry 2 (1981), S. 416-421 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with the STO-3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water-water interactions and nonadditivity effects are also significant.
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  • 43
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    Journal of Computational Chemistry 2 (1981), S. 460-469 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational behavior of the C-terminal neurotensin pentapeptide, Arg-Pro-Tyr-Ile-Leu OH [NT(9-13)], was investigated using empirical energy calculations. A special aim was to display the specific contribution of each residue to induce conformations able to interact with biological receptors. Restrictions were then introduced in intramolecular interactions involving the Arg side chain and the terminal COOH group. The stablest conformations include in the order of decreasing stability: a distorted helical form for the C-terminal tetrapeptide, a (Pro2-Tyr3) β turn I, an α helix, an extended form, and a (Tyr2-Ile3) β turn III, which are energetically rather close (ΔE 〈 3 kcal/mol). The NT(9-13) peptide appears then as a rather flexible molcule with a noteworthy ability of adaptation to a substrate. Extended forms would be in agreement with a zipper model of interactions with receptors, whereas folded forms involving helices and β, γ turns would support a lock and key model. The specific contribution of side chains, specially those of Tyr and Arg residues as well as the key position of the Pro residue emerge clearly from this study.
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  • 44
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The triplet-triplet absorption spectrum of naphthalene (3B1g ← 3B2u; 3Ag ← 3B2u) was calculated using an ab initio method with a STO-3G basis set and moderately large configuration interaction. Eight bands were found in the region 18,000-45,000 cm-1 and compared with those of the experimental spectrum. The strongest band observed at about 44,000 cm-1 was assigned to a 3Ag ← 3B2u tansition. The excited triplet and singlet ground-state electronic charge distributions are compared.
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  • 45
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    Journal of Computational Chemistry 3 (1982), S. 28-36 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The topological resonance energy (TRE) model was introduced independently by the Zagreb Group (in 1975) and by Aihara (in 1976). Several practical obstacles arise in the computation of TRE. Ways to surmount them are pointed out. Descriptions of algorithms, optimizations, and the efficient computer program are presented. Possible numerical instability is discussed.
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    Journal of Computational Chemistry 3 (1982), S. 62-68 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF molecular orbital calculations have been performed to ascertain the conformational preferences of protonated, neutral, and deprotonated amidine [HC(=NH)NH2], using the 3-21G split valence basis set. The states of eight stable species, eight transition states, and four higher-order saddle points have been determined by complete geometry optimization utilizing analytic energy gradient techniques. Protonation at the amidine =NH is preferred over the -NH2 site by 37.1 kcal/mol. Neutral amidine has rotational barriers of 9.6 and 11.7 kcal/mol for the HN=CN cis and trans isomers, respectively, while all the stable HC(NH2)2+ and HC(NH)2- species possess torsional barriers larger than 23 kcal/mol. There is, however, essentially free C - N single-bond rotation in HC(=NH)NH3+, the calculated barriers being 0.7 and 1.8 kcal/mol for the cis and trans HN=CN isomers, respectively.
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  • 47
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    Journal of Computational Chemistry 3 (1982), S. 89-94 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformation of the cyclic pentapeptide malformin A has been deduced by systematically generating possible models for the molecule, and minimizing the conformation energy of each. Only one of the low-energy solutions is fully consistent with the reported CD and NMR spectra, and this is the proposed model. The disulfide ring linking adjacent cystine residues is highly strained, as has been predicted from the S—S vibration frequency. The conformation of the backbone, but not that of the disulfide ring, is similar to a model previously proposed.
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  • 48
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    Journal of Computational Chemistry 2 (1981), S. 422-432 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with the STO-3G basis set have been performed to investigate substituent effects on the structures and stabilization energies of water:4-R-pyrimidine complexes, with R including CH3, NH2, OH, F, C2H3, CHO, and CN. Except for the cyclic water:4-aminopyrimidine complex hydrogen bonded at N3, these complexes have open structures stabilized by a nearly linear hydrogen bond formed through a nitrogen lone pair of electrons. When hydrogen bonding occurs at N3, the complexes may have planar or perpendicular conformations depending on the substituent, but when hydrogen bonding occurs at N1, the perpendicular is generally slightly preferred, and there is essentially free rotation of the 4-R-pyrimidine. Primary substituent effects alter the electronic environment at the nitrogens, and tend to make N3 a poorer site for hydrogen bonding than N1, primarily because of a stronger π electron-withdrawing effect at N3. However, the relative stabilities of complexes hydrogen bonded at N1 and N3 are also influenced by secondary substituent effects, which may be significant in stabilizing complexes bonded at N3. Substitutent effects on the structures and stabilization energies of the water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyridine complexes. Configuration interaction calculations indicate that although absorption of energy by the pyrimidine ring destabilizes the water:4-R-pyrimidine complexes, these may still remain bound in the excited n → π* state. This is in contrast to the fate of open water:2-R-pyridine and water:4-R-pyridine complexes, which dissociate in this state.
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  • 49
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    Journal of Computational Chemistry 3 (1982) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Closed-shell SCF calculations on the ground states and direct SCF calculations on the ionized doublet states were carried out for a series of ten-electron hydrides. The correlation of ionization potentials with the degree of protonation and the nuclear charge has been studied for hole states derived from excitation out of both the core and valence molecular orbitals. Calculated proton affinities of the ground states and hole states derived from a given symmetry orbital show a similar trend to that of the ionization potentials.
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    Journal of Computational Chemistry 3 (1982), S. 40-46 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several deficiencies and potential sources of error in the torsion angle driving method, the approach employed most frequently for the simulation of conformational interconversions, have been studied. A general explanation of the observed effects is given in terms of the energy surface and of the effects brought about by “side valleys.” Several examples of molecular mechanics calculations of conformational interconversions, among them the cyclohexane ring inversion, illustrate the problems.
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    Journal of Computational Chemistry 3 (1982), S. 75-88 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article develops computer programs for computer generation of nuclear spin species and nuclear spin statistical weights of rovibronic levels. The programs developed here generate nuclear spin species and statistical weights from the group structures known as generalized character cycle indices (GCCIs) which are computed easily from the character table of the PI group of the molecule under consideration. Procedures are illustrated with examples.
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    Journal of Computational Chemistry 3 (1982), S. 112-116 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital calculations are reported for the H2SSH· and H2SCl· radicals and for the H2SClH+· radical cation. The two neutral species are found to be very weakly bound van der Waals' complexes, whereas the H2SClH+· radical cation is bound by 11.9 kcal mol-1 at MP2/4-31G. The importance of charge in σ* radicals is discussed.
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    Journal of Computational Chemistry 3 (1982), S. 117-124 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A blend of Haselgrove's method and the biased selection method for evaluating multidimensional integrals was tested. The results were mixed. The error estimate varied from being proportional to 1/N when N was less than ca. 60,000 to being proportional to 1/√N when N was greater than 60,000. Also, for N greater than 60,000, the error estimate was one-half the error estimate given by biased selection alone. These numbers should be compared with the 10,000 points used to find an optimum set of Haselgrove's parameters. It is reasonable to expect that if 100,000 points were used in the optimization of Haselgrove's parameters that the above results would be found with 60,000 replaced by 600,000.
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    Journal of Computational Chemistry 3 (1982), S. 135-139 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is well known that if the formation of hydrocarbons during Fischer-Tropsch synthesis occurs via the condensation polymerization mechanism, there is little hope for selectivity enhancement in the desired range of products. Recent data on low surface area model catalysts, where readsorption is unlikely, have shown that at low conversions, the product distribution obeys the condensation polymerization mechanism and the distribution of products is shifted to lower-molecular-weight hydrocarbons. We have used a computer simulation of the growth of hydrocarbon chains to obtain a picture of the catalyst surface under synthesis conditions. Such an approach could prove useful in distinguishing between various theoretical models. We have applied the simulation to compare the changes in selectivity when readsorption occurs and when it does not. The dynamic behavior of the reacting system which is obtained from the computer results has shown that selectivity to lower-molecular-weight hydrocarbons is a stronger function of the extent of reaction than the incorporation of readsorption into the chain growth mechanism.
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  • 56
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: MNDO has been extended to sulfur, but without inclusion of 3d AOs. Calculations are reported for heats of formation, geometries, dipole moments, and ionization energies of a variety of sulfur-containing molecules. The average discrepancy between calculated and observed heats of formation is larger than for compounds of other elements, a difference probably due, at least partly, to the lower accuracy of the thermochemical data for sulfur compounds. The calculated dipole moments agree well with experiment as do the calculated ionization energies, except for those corresponding to ionization from sulfur “lone-pair” orbitals which are too high by ca. 1 eV, probably as a result of the neglect in NDDO of interactions between inner and valence shell orbitals. As in the case of other third-period elements, the calculated heats of formation of compounds of sulfur in its higher valence states (SIV, SVI) were too positive by large amounts, due presumably to the neglect of 3d AOs.
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  • 57
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    Journal of Computational Chemistry 4 (1983), S. 127-135 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A relativistic effective core potential (REP) has been generated for the uranium atom and used in self-consistent-field calculations of the A states of UH, UF, and their ions. Energy curves were calculated at the base configuration level which ensures the dissociating atoms are described by Hartree-Fock wavefunctions. The electronic bonding of these molecules is found to be similar to that of comparable alkaline-earth hydrides and fluorides. The uranium 6p, 6d, and 5f orbitals retain their atomic character but the orbitals extend into the bonding region and are distorted by overlap repulsion and electrostatic effects. Nonetheless, the atomic energetic coupling determines that low energy states will have the maximum spin multiplicity and maximum orbital angular momentum projection consonant with the charge-transfer bonding.
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  • 58
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    Journal of Computational Chemistry 3 (1982), S. 229-233 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Fifty-one structures have been calculated by the MINDO/3 method to evaluate the errors introduced by branching and by the presence of the heteroatom. The structures are evaluated by comparisons which reveal that the calculated ΔHf values reflect a bias because of the presence of the heteroatom. With two carbons or more in a chain attached to a heteroatom group, a linear relationship exists which makes possible the calculation of reasonably accurate ΔHf values for unbranched alcohols, primary or secondary amines, ethers, thioethers, thiols, and alkyl chlorides. Branching errors do not seem to be linearly related among the systems. Some errors in calculations of geometries are also discussed.
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  • 59
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    Journal of Computational Chemistry 3 (1982), S. 234-250 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical HF/6-31G* (Hartree-Fock, 6-31G* basis set) and MP2/6-31G* (second-order Møller-Plesset, 6-31G* basis set) vibrational frequencies based on complete quadratic force fields have been obtained for a set of 36 one- and two-heavy-atom molecules comprising first-row elements for which experimental spectroscopic data are available. Frequencies calculated at the HF/6-31G* level are an average of 12.6% higher than experimental values. Partial treatment of electron correlation via the perturbation method of Møller and Plesset, terminated at second order, leads to a significant reduction in this error, although theoretical MP2/6-31G* frequencies are still larger than the experimental quantities by 7.3%. Part of the difference may be traced to the restriction of quadratic force fields, as comparison with experimental harmonic frequencies shows deviations of only 9.5% and 4.7% for the two levels, respectively. The calculated frequencies are used in conjunction with the corresponding theoretical equilibrium structures to obtain absolute molecular entropies, which may in turn be used to yield entropies of reaction. These latter quantities are generally in good accord with entropies derived using experimental structures and frequencies.
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  • 60
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    Journal of Computational Chemistry 3 (1982), S. 265-268 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicit functional forms for both the two-electron Coulomb integral, (aa∣bb), and the one-center core-orbital integrals, ZA-1 (aa∣ZA), are derived which permit the penetration integrals to be fully derived and calculated. With these forms the 3Σu+ of the H2 molecule is unstable. These forms are generalized so that they are suitable for optimizing semiempirical predictions of experimental one-electron properties.
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  • 61
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    Journal of Computational Chemistry 3 (1982), S. 277-282 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A simple but efficient coupled iteration procedure is proposed for searching saddle points and extrema along the line of constrained minimum energy paths by (analytical) calculation of the derivatives, i.e., the reduced forces and reduced force constants. The advantage of the method is shown with analytical potentials as well as a calculation of HCH—HNC rearrangement, as working examples.
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  • 62
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Ab initio calculations using the unscaled 4-31G basis set have been carried out on the cc, tc, and tt conformers of carbonic acid and the bicarbonate ion, with full geometry optimization assuming the structures to be planar. The complete harmonic force field is reported for the (most stable) tt conformer and for the bicarbonate ion, also selected quadratic force constants for the cc and tc conformers. The changes in certain bond lengths and stretching force constants in the cc → tc, tc → tt, and cc → tt conformer conversion reactions are indicative of intramolecular hydrogen bonding, C=O…H—O and H—O…H—O, which is examined in greater detail by partitioning the overall conformer conversion energy into distortion and bonding energy components. The fundamental vibration frequencies for the tt conformer and the bicarbonate ion are calculated from the force constant matrices, and hence, using a scaling factor based on a comparison of calculated and experimental values for the bicarbonate ion and trans-formic acid, a value is predicted for the zero-point energy of the tt conformer. A new estimate of ΔH˚ for the hydration reaction, H2O + CO2 → H2CO3, at 298 K in the gas phase; is made from thermochemical data, +20.2 ± 3.4 kJ mol-1, which, together with estimates of (H298˚ - H0˚) and the zero-point energy for H2CO3, gives +8.1 ± 7.0 kJ mol-1 for ΔET(expt). ΔET calculated from the 4-31G basis set data is -29.1 kJ mol-1. Comparison of the experimental value, the Hartree-Fock limit value, and values calculated with a variety of basis sets for the bond separation reaction, CO2 + CH4 → 2H2CO, suggests that the differences, ΔET(expt) minus ΔET(SCF), are due mainly to basis set limitations and not substantial correlation energy contributions.
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    Journal of Computational Chemistry 3 (1982), S. 344-353 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures of fluorobenzene, 1,3-difluorobenzene, 1,3,5-trifluorobenzene, 1,2,3-trifluorobenzene, pentafluorobenzene, and hexafluorobenzene have been determined by the ab initio gradient method with a 4-21 basis set. Approximate corrections have been developed to yield re and r0 structures so that comparison can be made with the available experimental information. The C—F bond distance decreases in a uniform manner with increasing fluorination of the ring, either on adjacent or on meta sites. The ring structure also shows systematic deformation, with a decrease of about 0.01 Å in the C—C bond length adjacent to the point of substitution and an increase of about 2.5˚ in the ring angle at the substitution site in those cases where the requirement of ring closure permits.
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  • 64
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    Journal of Computational Chemistry 3 (1982), S. 372-380 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Spin-orbit and dispersion energy contributions to the energy curves of XeF are examined. A rapid variation in the spin-orbit coupling with internuclear separation is found for both the ground and excited states. This result can explain the experimentally observed ordering of the ionic excited states when the spin-orbit perturbation couples 2σ and 2π energy curves obtained by both all-electron and effective core potential (ECP) calculations at the first-order configuration interaction (FOCI) level of accuracy. Damped dispersion energy contributions to the ground-state energy curve are shown to be comparable to the charge transfer contribution. The energy curve for XeF is in reasonable agreement with experimental results and a calculation of the analogous XeCl curve confirms the qualitative correctness of the calculation. The energy curves and transition moments were then applied to two problems related to the efficiency of the XeF laser. Photodissociation of the X state provides a means of removing a bottlenecked vibrational level but a calculation of the radiative transition probability between the X and A states finds the cross section is too small to yield rates competitive with collisional deactivation. The bottlenecked state may also be removed by electron dissociative attachment but the calculated energy curves for the X states of XeF and XeF- do not cross at a low energy indicating a small cross section.
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  • 65
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    Journal of Computational Chemistry 4 (1983), S. 58-67 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A low-cost microcomputer and package of assembly language routines has been developed to emulate the structure and performance of a large analog computer. The advantages of the analog computer, as implemented in this scheme, include (1) a significant reduction in the programming effort involved in modeling complex dynamic systems and (2) the control of the simulation and model parameters in a completely interactive and flexible manner. The symbolic nomenclature and schematic representations involving devices, such as integrators, comparators, multipliers, and function generators, offers a powerful alternative to the more conventional numerical methods, that is, to provide very simply the solutions to large systems of differential equations. This approach invariably leads the user to a more thorough understanding of the dynamic character of the system. The technique is illustrated using a chemical kinetics example involving the simulation of laser-induced fluorescence. The results of this work have provided an assessment of a systematic error that occurs when using induced resonance fluorescence to measure OH concentrations in the troposphere of the earth.
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    Journal of Computational Chemistry 4 (1983), S. 110-113 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A rapid method is described for calculating the number of bonds on the shortest path between each two pairs of atoms of a molecule.
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    Journal of Computational Chemistry 4 (1983), S. 48-52 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effect of basis functions on molecular one-electron property expectation values calculated by approximate methods is examined using weighted and unweighted least-squares Gaussian-type orbital function expansions of Slater-type orbital functions.
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    Journal of Computational Chemistry 4 (1983), S. 73-83 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Structures XY⋅3XY⋅2XY3 of symmetry C2v (of which propane is an example) are examined and the rearrangement due to the internal rotation of the end groups XY3 studied. The isomerization graph is constructed, various forms of which are displayed and the symmetry of which has been determined. The order of the group is 72. There are nine prime (irreducible) representations (4A + E + 4G) with the following partitioning of the elements into classes: 1, 42, 62, 9, 122, 18. When the mechanism for rearrangement is generalized to include enantiomers, a duplex graph is produced with the order of the group 144 which is isomorphic to the group S2(S3,S2) (generalized wreath product of the symmetric group S2 and S3). The corresponding graph has been constructed and displayed in one of more symmetrical forms. Isomorphism of groups of order 144 is discussed and a procedure is outlined in which correspondence between distinctive combinatorial objects is established by inducing permutations of m elements from available permutations of n elements. The scheme is based on selection of suitable graph invariants in one system and their labeling as m objects which form the basis for representation of the symmetry for the other system.
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    Journal of Computational Chemistry 4 (1983), S. 114-122 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM2 molecular mechanics force field, as modified for halogens, is able to predict the structures, dipole moments, and energies of the isomers of benzene hexachloride. For benzene tetrachloride and naphthalene tetrachloride the field exaggerates the stability of conformers with axial chlorine, but gives satisfactory results if the field is modified to allow for interaction between electronegative substituents and the π electrons.
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    Journal of Computational Chemistry 4 (1983), S. 124-124 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983), S. 333-336 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The nearest-neighbor exclusion model for intercalation was studied using an energetical approach. It was shown that creation of the intercalation site in the exclusion model corresponds to the same energetical destabilization of the structure as in the standard model of intercalation. The stability of the intercalation complex formed in the case of the exclusion model is lower by 68 kcal/mol as compared with the standard model, but geometrical structures of both complexes are very similar. The electrostatic molecular potential method was also used to further characterize the intercalation site formed within both models of intercalation.
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    Journal of Computational Chemistry 4 (1983), S. 181-186 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Gaussian basis sets, consisting of 15 s-type, 11 p-type, and 6 d-type functions, for the fourth-row main group elements, In-Xe, are presented. In order to compare these basis sets with larger ones, calculations have been performed in I2 and TeO2.
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    Journal of Computational Chemistry 4 (1983), S. 241-251 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: STO-3G minimal basis sets for first- and second-row transition metals have been formulated and applied to the calculation of equilibrium geometries for a variety of inorganic systems, metal carbonyls, and organometallic compounds. While the overall level of agreement with experiment is not as good as that previously noted for main-group compounds, most trends and many subtle features in geometries are reproduced.
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    Journal of Computational Chemistry 4 (1983) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983), S. 267-275 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure has been devised to determine the automorphism partition and the automorphism group for nondirected graphs. The general approach is to reveal the permutational symmetry by means of its systematic destruction. Symmetry decomposition pathways are created by numerically weighting specific series of vertices. Each pathway leads to a discrete ordered vector. Each pair of pathways that match reveals an element of the automorphism group. Results are presented for two molecular graphs. Further potential applications of this approach to problems of isomorphism, canonical labeling, and structural indexing are discussed.
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    Journal of Computational Chemistry 4 (1983), S. 276-282 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A scheme is presented that enables photographic representation of the (two-dimensional) surfaces of (three-dimensional) molecular orbitals and electron density functions. The algorithm has been implemented by a program which is completely general and computationally efficient.
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    Journal of Computational Chemistry 5 (1984), S. 225-229 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Changes of electronic charge distribution following the lowest singlet n-π* transitions of benzaldehyde, benzamide, benzoic acid, the phthalaldehydes, pyridine, and the diazines have been examined using the CNDO-S/CI method. A Singlet n-π* transition is found as a general rule to direct electronic charges to the para position of the atom in the ring that carries the lone pair or to which the substituent carrying the lone pair is attached.
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    Journal of Computational Chemistry 5 (1984), S. 217-224 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MINDO/3 calculations were performed on the potential energy profile involved in the equilibrium \documentclass{article}\pagestyle{empty}\begin{document}$$ \begin{array}{l} {\rm crotonic acid \rightleftharpoons isocrotonic acid \rightleftharpoons but-3-enoic acid} \\ {\rm (III)\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(II)\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(I)} \\ {\rm } \,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\to {\rm propene + CO}_{\rm 2} \\ \end{array} $$\end{document}Optimized structures of stable molecules and transition states have been determined; thermodynamic stabilities of pure acids and barriers indicated that the equilibrium can be set up from any acids. It was argued that direct decarboxylation is only conceivable from (I), since in this process a 1, 5-hydrogen shift is involved, whereas a higher barrier process of 1, 3-hydrogen shift is required in direct decarboxylations from other acids. Direct interconversion of (I) and (III) was found to be unfavorable due to a high barrier involved.
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    Journal of Computational Chemistry 5 (1984), S. 261-262 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 5 (1984), S. 252-260 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Formulas are given for convergence-accelerated lattice sums over all intermolecular Coulomb, London, and repulsive interactions. Their implementation in the consistent force field is described. Optimum values of convergence constant and summation limit are found for r-12, r-9, and r-1 interaction terms. Energy minimization in all degrees of freedom, also intramolecular, for crystals of Ar, KCl, and C2H6 is reported.
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    Journal of Computational Chemistry 5 (1984), S. 248-251 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The equilibrium between three pairs of 1,4- and 1,6-dialkylcyclooctatetraenes was investigated with the two quantum mechanical algorithms, IBMOL and PCILO. PCILO computations reproduce the trend of stability within each pair of isomers obtained earlier by Allinger with molecular mechanics calculations, while IBMOL computations do not. These results not only can be explained in the light of, but also are a confirmation of Allinger's conclusions that the conformational stability is governed by the magnitude of the van der Waals' attraction between the two alkyl groups: The dispersion energy, which is essentially an electron correlation effect, is not accounted for by a method like IBMOL that, albeit ab initio, is based on the Hartree-Fock independent particle model, while it is fairly well reproduced by a method like PCILO that, albeit semiempirical, is based on a configuration interaction approach. Simulation of the full configuration interaction (CI) correction through a suitable dispersion term brings IBMOL results to a good agreement with the molecular mechanics ones.
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    Journal of Computational Chemistry 5 (1984), S. 263-271 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: The effect of correlation energy on the relative stability of different structures and dissociation products of complex lithium beryllohydrides has been investigated. The adequacy of the method employed (third-order Möller-Plesset perturbation theory) and the basis set dependence have been assessed. Trends of the correlation energy according to the molecular structure have been discussed, and the validity of an additive scheme based on electron pair contributions has been tested.
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    Journal of Computational Chemistry 5 (1984), S. 280-287 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program is described which evaluates the second-order Møller-Plesset energy using the integral list formed by HONDO 5. In this program use may be made of full molecular symmetry for most common point groups, even if they contain two-dimensional representations. The algorithm for the integral transformation may also be applied to other methods beyond Hartree-Fock. Some numerical results and timings are presented.
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    Journal of Computational Chemistry 5 (1984), S. 299-306 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanical calculations for hetero-substituted hydrocarbons present certain difficulties that are not encountered in dealing with hydrocarbons. Ways are proposed to overcome such difficulties, sometimes by two-step or iterative computation. The following topics are considered: fitting the force field by using data from studies in solution; ways to estimate atomic charges or, alternatively, bond moments; ways to account for field effects upon atomic charges and bond moments.
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  • 85
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    Journal of Computational Chemistry 4 (1983), S. 461-469 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energy calculations are presented for the head-to-head dimerized β helices for Gramicidin A transmembrane channel structures. The calculations take into account both left- and right-handed β helices, and various side-chain conformations. The energetics of the dimerization is studied by considering various docking geometries. It is concluded from these vacuum-energy calculations that the lowest energy conformation for the channel dimer is that comprised of left-handed β helices.
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  • 86
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    Journal of Computational Chemistry 5 (1984), S. 197-199 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Group equivalents which are useful for converting energies derived from ab initio calculations into enthalpies of formation have been obtained. They allow ΔHf to be estimated from 6-31G* energies with an uncertainty on the order of ±2 kcal/mol.
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  • 87
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    Journal of Computational Chemistry 5 (1984), S. 207-215 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effect of different exponents, Slater, Burns, Clementi, and Best Limited Molecular Orbital (BLMO) on the approximate one-electron property expectation values from minimum basis-set calculations is reported for Roothaan-Hartree-Fock (RHF), neglect of diatomic differential overlap (NDDO), and maximum overlap method (MOM) calculations on FH, CO, and LiH.
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  • 88
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    Journal of Computational Chemistry 5 (1984), S. 241-247 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Previous investigators have shown that statistical mechanical averages for configuration-dependent physical properties of long unperturbed polyoxyethylene chains are sensitive to the gauche-trans energy difference for rotation about C—C bonds. Agreement between theory and experiment could be obtained only by significant adjustment of this energy away from values predicted by semiempirical conformational energy computations. The present work examines the success of MM2 in evaluating conformational properties of long unperturbed polyoxyethylene chains. Calculations are performed which identify the rotational isomers, and their energies, for the indicated bonds in CH3OCH2CH2O—CH2—CH2—OCH2CH2OCH3. These energies are used to assign statistical weights utilized in the configuration partition function for a rotational isomeric state chain with symmetric threefold interdependent rotations. The customary generator matrix scheme is employed to evaluate the mean-square unperturbed end-to-end distance, mean-square unperturbed dipole moment, and their temperature coefficients. Contrary to computational schemes employed previously, MM2 is found to provide an estimate of the gauche-trans energy difference for rotation about C—C which is in harmony with the known dimensions and dipole moments of the unperturbed polymer. MM2 also provides good estimates for most of the other parameters required in the rotational isomeric state treatment. A notable exception is provided by the gauche-trans energy difference for rotation about the C—O bond. This energy difference is overestimated by MM2.
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  • 89
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    Journal of Computational Chemistry 5 (1984), S. 290-290 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 90
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A modified version (MM2′) of the Allinger's 1977 force field is checked against cycloheptane and cyclooctane. Cycloheptane is characterized by two pseudorotating itineraries, chair/twist-chair and boat/twist-boat, separated by a barrier of 8.5 kcal mol-1. The activation energy in the C/TC pseudorotation is estimated to be 0.96 kcal mol-1, while B and TB transform into each other freely at an energy level 3.8 kcal mol-1 above the global energy minimum (TC). With cyclooctane the lowest energy is calculated for the boat-chair form which participates in a pseudorotational process with TBC through a saddle point lying 3.5 kcal mol-1 above BC. The chair/chair and boat/boat families contain only one local minimum, crown and BB, respectively, on the MM2′ surface. The results are presented as an illustration for quick coverage of torsional energy surface by two-bond driver calculation with the block-diagonal Newton-Raphson minimization, followed by the force search of stationary points by full-matrix Newton-Raphson optimization.
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  • 91
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    Journal of Computational Chemistry 5 (1984), S. 343-348 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical calculations by the combined empirical force-field (EFF)-extended Hückel molecular orbital (EHMO) approach confirm that octalene and benzo-|c|-octalene present π-bond fixation with a common single bond between the cyclooctatetraene and cyclooctatriene fragments, whereas the structure of dibenzo-|c, j|-octalene is characterized by a central double bond. The dynamic behavior of these compounds is discussed and the interconversion energy barriers are calculated; the inversion of the cyclooctatriene ring is faster than that of the cyclooctatetraene ring in octalene, but it is slower in benzo-|c|-octalene.
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  • 92
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    Journal of Computational Chemistry 5 (1984), S. 358-362 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MNDO has been parametrized for iodine. Since d atomic orbitals (AOS) are not included, the calculations are restricted to II. Heats of formation, molecular geometries, ionization energies, and dipole moments are reproduced with useful accuracy.
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  • 93
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    Journal of Computational Chemistry 5 (1984), S. 381-386 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The nitrogen protonation energies of the imino bases HN=CHR, where R is H, CH3, NH2, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split-valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree-Fock 4-31G quality. Consistent relative protonation energies can be obtained at the Hartree-Fock level with smaller basis sets. Extending the split-valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree-Fock nitrogen protonation energies of the imino bases HN=CHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases O=CHR.
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  • 94
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    Journal of Computational Chemistry 5 (1984), S. 182-185 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The principles of a new method, the method of zero determinants, are described which can be used for the determination of the number of exponentials in accurate, multiexponential decay curves, as well as for the smoothing of multiexponential experimental data. It is based on the idea that the determinant of an overdetermined data matrix for accurate data is zero. The method is not limited by mathematical approximations, and thus uncovers the decay curve hidden in the data set.
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  • 95
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    Journal of Computational Chemistry 5 (1984), S. 411-426 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The π-bond order-bond length relationship is reintroduced to the literature and extended to heteronuclear bonds by presenting graphs derived solely by theoretical methods. π-bond order and overlap population results for carbon-carbon, carbon-nitrogen, and carbon-oxygen bonds obtained from ab initio STO-3G calculations using theoretically-optimized geometries are reported for a series of pteridines and for a wide range of small organic molecules. The order-length correlation graphs are used in predicting the “intrinsic” single bond lengths for sp2 - sp2 and sp - sp hybridized C—C, C—N, and C—O bonds, and in evaluating the relative importance of hybridization, π-electron delocalization and bond polarization effects in causing bond shortening in conjugated and hyperconjugated molecules. The calculated value of the π-bond order for a given bond in a molecule is shown to be relatively insensitive to moderate geometry changes: Hence, a use for the correlation graphs in geometry prediction is suggested. Some results for the extended 4-21G basis set are also presented.
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  • 96
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures and conformational energies of several conformations of propanoic acid, 2-methylpropanoic acid, and butanoic acid were determined by geometrically unconstrained ab initio gradient geometry refinement on the 4-21G level. The O=C—C—C torsional potentials of propanoic acid and butanoic acid are found to be practically identical. There are energy minima at 0° and 120°, and maxima in the 60° region and at 180°. In 2-methylpropanoic acid there are energy minima at H—C—C=O dihedral angles of 0° and 120°, and maxima at 60° and 180°. The exact positions of the maxima and minima of the H—C—C=O torsional potential of 2-methylpropanoic acid are found to be predictable from propanoic acid rotational-potential parameters. Some conformationally dependent, local geometry trends are discussed.
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  • 97
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    Journal of Computational Chemistry 5 (1984), S. 457-465 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Fortran-77 computer program has been written which calculates the rotation-torsion profile of a vibronic transition using an asymmetric top/free internal rotor Hamiltonian. The program is applicable to any molecule that is composed of a frame portion of C2v symmetry a free rotor portion of C3v symmetry. Rotation-torsion bands of A-, B-, and C-type contours may be calculated within an assumed Boltzmann distribution of rotation-torsion level populations or within a specified non-Boltzmann distribution of torsional level populations.
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  • 98
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    Journal of Computational Chemistry 5 (1984) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 99
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    Journal of Computational Chemistry 5 (1984), S. 500-505 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The organization of a computer code to compute transition moments between states described in different orbital basis sets (a nonorthogonal transition moment) is described. The code is organized to minimize redundant work and allow efficient threshold checking. Three sample calculations are presented.
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  • 100
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    Journal of Computational Chemistry 5 (1984), S. 486-499 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A set of procedures and guidelines are presented for the estimation of bond length, bond angle, and torsional potential constants for molecular mechanics force fields. The force field constants are ultimately derived by “subtracting” nonbonded molecular mechanics energies from corresponding molecular orbital energies using a model compound containing the chemical structure to be parameterized. Case study examples of bond length, bond angle, and torsional rotation force field parameterizations are presented. A general discussion of molecular mechanics force field parameterization strategy is included for reference and completeness. Finally, a curve-fitting program to generate force field parameters from raw data is given in Appendix I.
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