Deborah L. Crittenden

A Systematic CCSD(T) Study of Long-Range and Noncovalent Interactions between Benzene and a Series of First- and Second-Row Hydrides and Rare Gas Atoms

Binding energies, potential energy curves, and equilibrium intermonomer distances describing the interaction between benzene and a series of first- and second-row hydrides and rare gas atoms are calculated using coupled-cluster theory with single, double, and perturbative triple excitations (CCSD(T)) in conjunction with a large augmented quadruple-zeta basis set (aug-cc-pVQZ). These benchmark results are accurate to within one eighth of 1 kcal/mol and, as such, provide a reliable foundation for the development and testing of more approximate methods for calculating long-range and noncovalent interactions.

Intracule functional models. II. Analytically integrable kernels

We present, within the framework of intracule functional theory (IFT), a class of kernels whose correlation integrals can be found in closed form. This approach affords three major advantages over other kernels that we have considered previously; ease of implementation, computational efficiency, and numerical stability. We show that even the simplest member of the class yields reasonable estimates of the correlation energies of 18 atomic and 56 molecular systems and we conclude that this kernel class will prove useful in the development of future IFT models.

Intracule functional models. IV. Basis set effects

We have calculated position and dot intracules for a series of atomic and molecular systems, starting from an unrestricted Hartree-Fock wave function, expanded using the STO-3G, 6-31G, 6-311G, 6-311++G, 6-311++G(d,p), 6-311++G(3d,3p), and 6-311++G(3df,3pd) basis sets as well as the nonpolarized part of Dunnings cc-pV5Z basis. We find that the basis set effects on the intracules are small and that correlation energies from the dot intracule ansatz are remarkably insensitive to the basis set quality. Mean absolute errors in correlation energies across the G1 data set agree to within 2 mE(h) for all basis sets tested.

Intracule functional models. Part III. The dot intracule and its Fourier transform.

The dot intracule D(x) of a system gives the Wigner quasi-probability of finding two of its electrons with u.v = x, where u and v are the interelectronic distance vectors in position and momentum space, respectively. In this paper, we discuss D(x) and show that its Fourier transform d(k) can be obtained in closed form for any system whose wavefunction is expanded in a Gaussian basis set. We then invoke Parsevals theorem to transform our intracule-based correlation energy method into a d(k)-based model that requires, at most, a one-dimensional quadrature.

Computation and interpretation of molecular Omega intracules

The Omega intracule is a three-dimensional function that describes the relative positions, momenta, and directions of motion of pairs of electrons in a system. In this paper, we describe the computation of the Omega intracule for a molecular system whose electronic wave function is expanded in a Gaussian basis set. This is followed by implementation details and numerical tests. Finally, we use the Omega intracules of a number of small systems to illustrate the power of this function to extract simple physical insights from complicated wave functions.

Multifunctional and Stable Monolayers on Carbon: A Simple and Reliable Method for Backfilling Sparse Layers Grafted from Protected Aryldiazonium Ions

A new strategy for preparation of robust multifunctional low nanometer thickness monolayers on carbon substrates is presented. Beginning with protected aryldiazonium salts, sparse monolayers of ethynyl-, amino-, and carboxy-terminated tethers are covalently anchored to the surface. The layers are then backfilled with a second modifier via the nucleophilic addition of an amine derivative to the surface. Through use of electroactive moieties coupled to the tethers, and an electroactive amine for backfilling, electrochemical measurements reveal that backfilling approximately doubles the surface concentration of the monolayer. Cyclic voltammetry of solution-based redox probes at the modified surfaces is consistent with the expected blocking properties at various stages of surface preparation. Fractional surface coverages of the layers are estimated using electrochemically determined surface concentrations of modifiers and computationally derived modifier footprints. Assuming free rotation of the coupled ferrocenyl or nitrophenyl groups leads to physically unreasonable fractional surface coverages, indicating that these larger modifiers must be rotationally restricted. Using a conformationally constrained model produces lower bound estimates of the total fractional surface coverage close to 0.4, with tether-only coverages close to 0.2. The backfilled tether layers constitute practical platforms for controlled construction of complex interfaces with many potential applications including sensing, molecular electronics, and catalysis.

Cyclopropenium Cations Break the Rules of Attraction to Form Closely Bound Dimers.

The crystal structures of tris(ethylmethylamino)-cyclopropenium chloride and tris(diethylamino)-cyclopropenium iodide reveal the presence of closely bound dicationic dimers formed from two closed-shell monomer units. The distances between the C3 centroids of the staggered monomers are at the short end of those normally found in π-stacked neutral arenes, let alone charged aromatic rings. Computational analysis reveals that short-range interactions are dominated by strong dispersion forces, enabling metastable dicationic dimers to form without covalent intermolecular bonding. Surrounding counterions then provide a background source of charge balance, imparting strong thermodynamic stability to the system. Additionally, these counterions form a weak but attractive electrostatic bridge between the monomer units, contributing to the surprisingly short observed intermolecular C3-C3 centroid distance.

The PyPES library of high quality semi-global potential energy surfaces

In this article, we present a Python‐based library of high quality semi‐global potential energy surfaces for 50 polyatomic molecules with up to six atoms. We anticipate that these surfaces will find widespread application in the testing of new potential energy surface construction algorithms and nuclear ro‐vibrational structure theories. To this end, we provide the ability to generate the energy derivatives required for Taylor series expansions to sixth order about any point on the potential energy surface in a range of common coordinate systems, including curvilinear internal, Cartesian, and normal mode coordinates. The PyPES package, along with FORTRAN, C, MATLAB and Mathematica wrappers, is available at http://sourceforge.net/projects/pypes-lib.

PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

Abstract The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order). Program summary Program title: PyVCI Catalogue identifier: AFAC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AFAC_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: MIT License No. of lines in distributed program, including test data, etc.: 401703 No. of bytes in distributed program, including test data, etc.: 7091446 Distribution format: tar.gz Programming language: Python, C. Computer: PC. Operating system: Linux, MacOSX, Windows. RAM: Varies widely Classification: 16.3. External routines: Numpy, Scipy, Cython Nature of problem: The simulation of accurate molecular vibrational spectra is a significant and long-standing problem in computational chemistry. There are two major challenges: constructing an accurate ab initio potential energy surface and solving the nuclear vibrational problem. Both scale poorly with respect to molecular size, requiring large amounts of CPU time and memory. Solution method: We have implemented a straightforward numerical differentiation algorithm to construct quartic force fields in normal mode coordinates using second derivatives of the energy with respect to nuclear displacement obtained from ab initio quantum chemical calculations, for nuclear vibrational structure algorithm development and testing purposes. We have also provided an interface to the PyPES library of high quality semi-global potential energy surfaces, which enable quantitative prediction of molecular vibrational spectra. To solve the nuclear vibrational problem, we use a vibrational configuration interaction algorithm in a harmonic oscillator basis. Unusual features: One of the unusual features of our code is its flexibility, with multiple ways of generating or supplying force field data, dynamic memory allocation, adjustable screening thresholds, and explicit user control over terms in the VCI wave-function (maximum excitation level and extent of mode-coupling). We employ sparse matrix linear algebra libraries to reduce the memory required for VCI matrix storage and diagonalization, and provide for parallel VCI matrix construction to reduce required wall times. Additional comments: User Manual and examples (tutes) included Running time: Varies widely

Balancing accuracy and efficiency in selecting vibrational configuration interaction basis states using vibrational perturbation theory

This work describes the benchmarking of a vibrational configuration interaction (VCI) algorithm that combines the favourable computational scaling of VPT2 with the algorithmic robustness of VCI, in which VCI basis states are selected according to the magnitude of their contribution to the VPT2 energy, for the ground state and fundamental excited states. Particularly novel aspects of this work include: expanding the potential to 6th order in normal mode coordinates, using a double-iterative procedure in which configuration selection and VCI wavefunction updates are performed iteratively (micro-iterations) over a range of screening threshold values (macro-iterations), and characterisation of computational resource requirements as a function of molecular size. Computational costs may be further reduced by a priori truncation of the VCI wavefunction according to maximum extent of mode coupling, along with discarding negligible force constants and VCI matrix elements, and formulating the wavefunction in a harm...