Hamiltonian matrix and reduced density matrix construction with nonlinear wave functions

An efficient procedure to compute Hamiltonian matrix elements and reduced one- and two-particle density matrices for electronic wave functions using a new graphical-based nonlinear expansion form is presented. This method is based on spin eigenfunctions using the graphical unitary group approach (GUGA), and the wave function is expanded in a basis of product functions (each of which is equivalent to some linear combination of all of the configuration state functions), allowing application to closed- and open-shell systems and to ground and excited electronic states. In general, the effort required to construct an individual Hamiltonian matrix element between two product basis functions H(MN) = M|H|N scales as theta (beta n4) for a wave function expanded in n molecular orbitals. The prefactor beta itself scales between N0 and N2, for N electrons, depending on the complexity of the underlying Shavitt graph. Timings with our initial implementation of this method are very promising. Wave function expansions that are orders of magnitude larger than can be treated with traditional CI methods require only modest effort with our new method.     

Properties of the generalized master equation: Green's functions and probability density functions in the path representation

The Green's function for the master equation and the generalized master equation in path representation is an infinite sum over the length of path probability density functions (PDFs). In this paper, the properties of path PDFs are studied both qualitatively and quantitatively. The results are used in building efficient approximations for Green's function in 1D, and are relevant in modeling and in data analysis.     

Evaluation of the second-order reduced density matrix for correlated electronic wave functions

Formulas are presented for the evaluation of the second-order reduced density matrix for correlated wave functions, including wave functions constructed from pairwise nonorthogonal orbitals. Numerical results are provided for the correlation holes and conditional nuclear spin densities for the water molecule.     

Experimental determination of adsorption energies, adsorption isotherms, probability density functions, and lateral molecular interactions on CXHY/CaO systems

Reversed-flow gas chromatography (RF-GC) is extended to the measurements of the probability density function for the adsorption energies as well as the differential energies of adsorption due to lateral interactions of molecules adsorbed on different heterogeneous solid surfaces. All these calculations are based on a non-linear adsorption isotherm model as it is well accepted that the linear one is inadequate for substances such as these used in this work. Thus, some new important physicochemical parameters have been obtained for the characterization of the heterogeneous systems studied. The adsorbent used in this study was calcium oxide. The adsorption of many significant hydrocarbons was investigated. With these systematic experiments under conditions which are similar to the atmospheric ones, an extrapolation of the results obtained to "real" atmospheres with a high degree of confidence is possible.     

Energy transfer between polyatomic molecules II: Energy transfer quantities and probability density functions in benzene, toluene, p-xylene, and azulene collisions

Collisional energy transfer, CET, is of major importance in chemical, photochemical, and photophysical processes in the gas phase. In Paper I of this series (J. Phys. Chem. B 2005, 109, 8310) we have reported on the mechanism and quantities of CET between an excited benzene and cold benzene and Ar bath. In the present work, we report on CET between excited toluene, p-xylene, and azulene with cold benzene and Ar and on CET of excited benzene with cold toluene, p-xylene, and azulene. We compare our results with those of Paper I and report average vibrational, rotational, and translational energy quantities, , transferred in a single collision. We discuss the effect of internal rotation on CET and the identity of the gateway modes in CET and the relative role of vibrational, rotational, and translational energies in the CET process, all that as a function of temperature and excitation energy. Energy transfer probability density functions, P(E,E'), for the various systems are reported and the shape of the curves for various systems and initial conditions is discussed. The major findings for polyatomic-polyatomic collisions are: CET takes place mainly via vibration-to-vibration energy transfer assisted by overall rotations. Internal free rotors in the excited molecule hinder energy exchange while in the bath molecule they do not. Energy transfer at low temperatures and high temperatures is more efficient than that at intermediate temperatures. Low-frequency modes are the gateway modes for energy transfer. Vibrational temperatures affect energy transfer. The CET probability density function, P(E,E'), is convex at low temperatures and can be concave at high temperatures. A mechanism that explains the high values of and the convex shape of P(E,E') is that in addition to short impulsive collisions there are chattering collisions where energy is transferred in a sequence of short encounters during the lifetime of the collision complex. This also leads to the observed supercollision tail at the down wing of P(E,E'). Polyatomic-Ar collisions show mechanistic similarities to polyatomic-polyatomic collisions, but there are also many dissimilarities: internal rotations do not inhibit energy transfer, P(E,E') is concave at all temperatures, and there is no contribution of chattering collisions.     

Approximate density matrices and wigner distribution functions from density,kinetic energy density,and idempotency constraints

The Wigner distribution function and the corresponding density matrix are calculated using a form for the distribution function suggested by maximization of the entropy. Wigner functions and density matrices are determined by imposing conditions of idempotency on the density matrix. Exchange energies and Compton profiles calculated from density matrices obtained by imposing the idempotency constraints are compared with the results of calculations using the Hartree–Fock density matrix and a Gaussian approximation for the density matrix for H and the noble gases He through Xe. Compton profiles from Wigner functions with idempotency constraints show improvements over the Gaussian approximation for the lighter atoms, but do not show significant changes for the heavier atoms. Exchange energies from density matrices with idempotency constraints show improvements over the Gaussian approximation except for the heavier atoms Kr and Xe.     

Energy transfer between polyatomic molecules. 3. Energy transfer quantities and probability density functions in self-collisions of benzene, toluene, p-xylene and azulene

This paper is the third and last in a series of papers that deal with collisional energy transfer, CET, between aromatic polyatomic molecules. Paper 1 of this series (J. Phys. Chem. B 2005, 109, 8310) reports on the mechanism and quantities of CET between an excited benzene and cold benzene and Ar bath. Paper 2 in the series (J. Phys. Chem., in press) discusses CET between excited toluene, p-xylene and azulene with cold benzene and Ar and CET between excited benzene colliding with cold toluene, p-xylene and azulene. The present work reports on CET in self-collisions of benzene, toluene, p-xylene and azulene. Two modes of excitation are considered, identical excitation energies and identical vibrational temperatures for all four molecules. It compares the present results with those of papers 1 and 2 and reports new findings on average vibrational, rotational, and translational energy, , transferred in a single collision. CET takes place mainly via vibration to vibration energy transfer. The effect of internal rotors on CET is discussed and CET quantities are reported as a function of temperature and excitation energy. It is found that the temperature dependence of CET quantities is unexpected, resembling a parabolic function. The density of vibrational states is reported and its effect on CET is discussed. Energy transfer probability density functions, P(E,E'), for various collision pairs are reported and it is shown that the shape of the curves is convex at low temperatures and can be concave at high temperatures. There is a large supercollision tail at the down wing of P(E,E'). The mechanisms of CET are short, impulsive collisions and long-lived chattering collisions where energy is transferred in a sequence of short internal encounters during the lifetime of the collision complex. The collision complex lifetimes as a function of temperature are reported. It is shown that dynamical effects control CET. A comparison is made with experimental results and it is shown that good agreement is obtained.     

Energy transfer between polyatomic molecules. 1. Gateway modes, energy transfer quantities and energy transfer probability density functions in benzene-benzene and Ar-benzene collisions

We report collisional energy transfer, CET, quantities for polyatomic-polyatomic collisions and use excited benzene collisions with cold benzene bath, B-B, as our sample system and compare our results with the CET of excited benzene with Ar bath. We find that the gateway mode for both systems is the out-of-plane modes and that in B-B CET, vibration to vibration, V-V, is the dominant channel. Rotations play a mechanistic role in the CET but the net rotational energy transfer is small compared to V-V. The shape of the down side of the energy transfer probability density function, P(E,E'), is convex for B-B collisions and it becomes less so as the temperature increases. In Ar-B collisions, P(E,E') is concave and it becomes less so as the temperature decreases. We report average vibrational, rotational, and translational energy transferred, , as function of temperature for various initial conditions.     

Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models

To generate reduced point charge models of proteins, we developed an original approach to hierarchically locate extrema in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions. A charge fitting program was used to assign charge values to the so-obtained reduced representations. In continuation to a previous work, the Amber99 force field was selected. To easily generate reduced point charge models for protein structures, a library of amino acid templates was designed. Applications to four small peptides, a set of 53 protein structures, and four KcsA ion channel models, are presented. Electrostatic potential and solvation free energy values generated by the reduced models are compared with the corresponding values obtained using the original set of atomic charges. Results are in closer agreement with the original all-atom electrostatic properties than those obtained with a previous reduced model that was directly built from the smoothed MEP functions [Leherte and Vercauteren in J Chem Theory Comput 5:3279–3298, 2009].     

Marginal electron density and density-difference functions

Summary For visual analysis of the density reorganization and distortion, the one-dimensional cut (x, y ₀,z ₀) and the two-dimensional cut (x, y, z ₀) of the three-dimensional electron density difference function (x, y, z) are frequently employed. However, these cut functions do not satisfy any sum rules in contrast to the original difference function (x, y, z). To avoid this difficulty, the use of the marginal electron density functions _x (x) and _xy (x, y) and their difference functions _x (x) and _xy (x, y) is proposed. The marginal densities are condensation of the three-dimensional density onto a particular plane or line of our interest, and they satisfy the sum rule (i.e., the conservation of the number of electrons) exactly. Some basic properties of the marginal electron density are clarified for typical diatomic molecular orbitals. An illustrative application is given for the bonding and antibonding processes in the H₂ system.     

Some properties of reduced density matrices,correlated and uncorrelated,for pure and mixed states

Some results pertaining to the form of Γ⁽¹⁾ usually assumed in density functional theory, the properties of natural states of mixed states, their variational characterization, and a representation of pure states through reproducing kernels are given.     

A simultaneous probability density for the intracule and extracule coordinates

We introduce the intex density X(R,u), which combines both the intracular and extracular coordinates to yield a simultaneous probability density for the position of the center-of-mass radius (R) and relative separation (u) of electron pairs. One of the principle applications of the intex density is to investigate the origin of the recently observed secondary Coulomb hole. The Hartree-Fock (HF) intex densities for the helium atom and heliumlike ions are symmetric functions that may be used to prove the isomorphism 2I(2R)=E(R), where I(u) is the intracule density and E(R) is the extracule density. This is not true of the densities that we have constructed from explicitly correlated wave functions. The difference between these asymmetric functions and their symmetric HF counterparts produces a topologically rich intex correlation hole. From the intex hole distributions (X(exact)(R,u)-X(HF)(R,u)), we conclude that the probability of observing an electron pair with a very large interelectronic separation increases with the inclusion of correlation only when their center-of-mass radius is close to half of their separation.     

Density functional resonance theory: complex density functions, convergence, orbital energies, and functionals

Aspects of density functional resonance theory (DFRT) [D. L. Whitenack and A. Wasserman, Phys. Rev. Lett. 107, 163002 (2011)], a recently developed complex-scaled version of ground-state density functional theory (DFT), are studied in detail. The asymptotic behavior of the complex density function is related to the complex resonance energy and system's threshold energy, and the function's local oscillatory behavior is connected with preferential directions of electron decay. Practical considerations for implementation of the theory are addressed including sensitivity to the complex-scaling parameter, θ. In Kohn-Sham DFRT, it is shown that almost all θ-dependence in the calculated energies and lifetimes can be extinguished via use of a proper basis set or fine grid. The highest occupied Kohn-Sham orbital energy and lifetime are related to physical affinity and width, and the threshold energy of the Kohn-Sham system is shown to be equal to the threshold energy of the interacting system shifted by a well-defined functional. Finally, various complex-scaling conditions are derived which relate the functionals of ground-state DFT to those of DFRT via proper scaling factors and a non-Hermitian coupling-constant system.     

On the inner and outer radial density functions

Starting from the two-electron radial density D ₂(r ₁,r ₂), a generalized partitioning of the one-electron radial density function D(r) into two component densities D _a (r) and D _b (r) is discussed for many-electron systems. The literature partitioning (Koga and Matsuyama Theor Chem Acc 115:59, 2006) of D(r) into the inner D _<(r) and outer D _>(r) radial densities is shown to minimize the average variance of the two component density functions D _a (r) and D _b (r). It is also found that the average radial separation halved, , constitutes a lower bound to the standard deviation σ of D(r).     

Surface area, density and porosity measurements using the magnetic suspension balance

Summary The advantage of gravimetry in the determination of surface area is discussed in comparison with the volumetric method. The magnetic suspension balance is described and new developments are presented. As an example of the application of gravimetric measurements the determination of apparent density and specific surface area before and after oxidation of a Poco graphite are described.

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Oberflächen-, Poren- und Dichtebestimmungen mit der magnetischen Schwebewaage

     

Computation of dipole, quadrupole, and octupole surfaces from the variational two-electron reduced density matrix method

Recent advances in the direct determination of the two-electron reduced density matrix (2-RDM) by imposing known N-representability conditions have mostly focused on the accuracy of molecular potential energy surfaces where multireference effects are significant. While the norm of the 2-RDM's deviation from full configuration interaction has been computed, few properties have been carefully investigated as a function of molecular geometry. Here the dipole, quadrupole, and octupole moments are computed for a range of molecular geometries. The addition of Erdahl's T2 condition [Int. J. Quantum Chem. 13, 697 (1978)] to the D, Q, and G conditions produces dipole and multipole moments that agree with full configuration interaction in a double-zeta basis set at all internuclear distances.     

The evaluation of electronic extracule and intracule densities and related probability functions in terms of Gaussian basis functions

The evaluation of the basic two-electron integrals involved in the calculation of extracule and intracule densities is described. Expressions are given for the evaluation of the related spherically averaged, longitudinal, and transverse probability functions from wave functions constructed from Gaussian basis sets. All results are expressed in closed analytical forms which are suited to efficient coding. Given that certain pair densities can be related to experimental scattering cross sections, the formulae reported herein will facilitate further comparison between experiment and theory and lead to a more comprehensive understanding of the electronic structures of molecules.     

Correlated holes and their relationships with reduced density matrices and cumulants

This paper describes a matrix formulation for the correlated hole theory within the framework of the domain-averaged model in many electron systems (atoms, molecules, condensed matter, etc.). General relationships between this quantity and one-particle reduced density matrices for any independent particle or correlated state functions are presented. This formulation turns out to be suitable for computational purposes due to the straightforward introduction of cumulants of two-particle reduced density matrices within the quantum field structure. Numerical calculations in selected simple molecular systems have been performed in order to determine preliminary correlated values for such a quantity.     

Inner and outer radial density functions in many-electron atoms

When any two electrons are considered simultaneously, the radial density function D(r) in many-electron atoms is shown to be rigorously separated into inner D _<(r) and outer D _>(r) radial densities. Accordingly, radial properties such as the electron–nucleus attraction energy V _en and the diamagnetic susceptibility χ _d are the sum of the inner and outer contributions. The electron–electron repulsion energy V _ee has an approximate relation with the minus first moment of the outer density D _>(r). For the 102 atoms He through Lr in their ground states, different characteristics of local maxima in the radial densities D _<(r), D _>(r), and D(r) are reported based on the numerical Hartree-Fock wave functions. Relative contributions of the inner and outer components to V _en and are also discussed for these atoms.