Nicholas A. Besley

Q-Chem 2.0: A High-Performance Ab Initio Electronic Structure Program Package

Q‐Chem 2.0 is a new release of an electronic structure program package, capable of performing first principles calculations on the ground and excited states of molecules using both density functional theory and wave function‐based methods. A review of the technical features contained within Q‐Chem 2.0 is presented. This article contains brief descriptive discussions of the key physical features of all new algorithms and theoretical models, together with sample calculations that illustrate their performance.

Direct transformation of graphene to fullerene

Although fullerenes can be efficiently generated from graphite in high yield, the route to the formation of these symmetrical and aesthetically pleasing carbon cages from a flat graphene sheet remains a mystery. The most widely accepted mechanisms postulate that the graphene structure dissociates to very small clusters of carbon atoms such as C(2), which subsequently coalesce to form fullerene cages through a series of intermediates. In this Article, aberration-corrected transmission electron microscopy directly visualizes, in real time, a process of fullerene formation from a graphene sheet. Quantum chemical modelling explains four critical steps in a top-down mechanism of fullerene formation: (i) loss of carbon atoms at the edge of graphene, leading to (ii) the formation of pentagons, which (iii) triggers the curving of graphene into a bowl-shaped structure and which (iv) subsequently zips up its open edges to form a closed fullerene structure.

Self-Consistent Field Calculations of Excited States Using the Maximum Overlap Method (MOM) †

We present a simple algorithm, which we call the maximum overlap method (MOM), for finding excited-state solutions to self-consistent field (SCF) equations. Instead of using the aufbau principle, the algorithm maximizes the overlap between the occupied orbitals on successive SCF iterations. This prevents variational collapse to the ground state and guides the SCF process toward the nearest, rather than the lowest energy, solution. The resulting excited-state solutions can be treated in the same way as the ground-state solution and, in particular, derivatives of excited-state energies can be computed using ground-state code. We assess the performance of our method by applying it to a variety of excited-state problems including the calculation of excitation energies, charge-transfer states, and excited-state properties.

Self-consistent-field calculations of core excited states

The accuracy of core excitation energies and core electron binding energies computed within a Delta self-consistent-field framework is assessed. The variational collapse of the core excited state is prevented by maintaining a singly occupied core orbital using an overlap criterion called the maximum overlap method. When applied to a wide range of small organic molecules, the resulting core excitation energies are not systematically underestimated as observed in time-dependent density functional theory and agree well with experiment. The accuracy of this approach for core excited states is illustrated by the calculation of the pre-edge features in x-ray absorption spectra of plastocyanin, which shows that accurate results can be achieved with Delta self-consistent-field calculations when used in conjunction with uncontracted basis functions.

X-ray and Electron Spectroscopy of Water

Here we present an overview of recent developments of X-ray and electron spectroscopy to probe water at different temperatures. Photon-induced ionization followed by detection of electrons from either the O 1s level or the valence band is the basis of photoelectron spectroscopy. Excitation between the O 1s and the unoccupied states or occupied states is utilized in X-ray absorption and X-ray emission spectroscopies. These techniques probe the electronic structure of the liquid phase and show sensitivity to the local hydrogen-bonding structure. Both experimental aspects related to the measurements and theoretical simulations to assist in the interpretation are discussed in detail. Different model systems are presented such as the different bulk phases of ice and various adsorbed monolayer structures on metal surfaces.

Computation of the amide I band of polypeptides and proteins using a partial Hessian approach

A partial Hessian approximation for the computation of the amide I band of polypeptides and proteins is introduced. This approximation exploits the nature of the amide I band, which is largely localized on the carbonyl groups of the backbone amide residues. For a set of model peptides, harmonic frequencies computed from the Hessian comprising only derivatives of the energy with respect to the displacement of the carbon, oxygen, and nitrogen atoms of the backbone amide groups introduce mean absolute errors of 15 and 10 cm(-1) from the full Hessian values at the Hartree-Fock/STO-3G and density functional theory EDF16-31G(*) levels of theory, respectively. Limiting the partial Hessian to include only derivatives with respect to the displacement of the backbone carbon and oxygen atoms yields corresponding errors of 24 and 22 cm(-1). Both approximations reproduce the full Hessian band profiles well with only a small shift to lower wave number. Computationally, the partial Hessian approximation is used in the solution of the coupled perturbed Hartree-Fock/Kohn-Sham equations and the evaluation of the second derivatives of the electron repulsion integrals. The resulting computational savings are substantial and grow with the size of the polypeptide. At the HF/STO-3G level, the partial Hessian calculation for a polypeptide comprising five tryptophan residues takes approximately 10%-15% of the time for the full Hessian calculation. Using the partial Hessian method, the amide I bands of the constituent secondary structure elements of the protein agitoxin 2 (PDB code 1AGT) are calculated, and the amide I band of the full protein estimated.

Structure and bonding in ionized water clusters.

The structure and bonding in ionized water clusters, (H2O)(n)(+) (n = 3–9), has been studied using the basin hopping search algorithm in combination with quantum chemical calculations. Initially candidate low energy isomers were generated using basin hopping in conjunction with density functional theory. Subsequently, the structures and energies were refined using second order Møller–Plesset perturbation theory and coupled cluster theory, respectively. The lowest energy isomers are found to involve proton transfer to give H(3)O(+) and a OH radical, which are more stable than isomers containing the hemibonded hydrazine-like fragment (H(2)O–OH(2)), with the calculated infrared spectra consistent with experimental data. For (H(2)O)(9)(+) the observation of a new structural motif comprising proton transfer to form H(3)O(+) and OH, but with the OH radical involved in hemibonding to another water molecule is discussed.

Structural optimization of molecular clusters with density functional theory combined with basin hopping

Identifying the energy minima of molecular clusters is a challenging problem. Traditionally, search algorithms such as simulated annealing, genetic algorithms, or basin hopping are usually used in conjunction with empirical force fields. We have implemented a basin hopping search algorithm combined with density functional theory to enable the optimization of molecular clusters without the need for empirical force fields. This approach can be applied to systems where empirical potentials are not available or may not be sufficiently accurate. We illustrate the effectiveness of the method with studies on water, methanol, and water + methanol clusters as well as protonated water and methanol clusters at the B3LYP+D/6-31+G* level of theory. A new lowest energy structure for H(+)(H(2)O)(7) is predicted at the B3LYP+D/6-31+G* level. In all of the protonated mixed water and methanol clusters, we find that H(+) prefers to combine with methanol rather than water in the lowest-energy structures.

Theoretical study of the structures and stabilities of iron clusters

Abstract An empirical many-body potential energy function, derived previously by fitting data for two allotropes of iron (bcc and fcc), has been applied to the study of the structures and relative stabilities of iron clusters with up to 671 atoms. For small clusters, growth is predicted to occur via the fusion of tetrahedral units, leading eventually to icosahedral clusters. A subset of larger clusters, with high symmetries and shell structures (so called Geometric Shell Magic Number Clusters) was studied and the stability order icosahedral > rhombic dodecahedral (bcc) > decahedral > cuboctahedral (fcc) established in the nuclearity range studied, though crossover of stability between icosahedral and (bulk-like) bcc structures is predicted to occur at around 2000 atoms.

Di-8-ANEPPS Emission Spectra in Phospholipid/Cholesterol Membranes: A Theoretical Study

We have investigated the effects of explicit molecular interactions and the membrane dipole potential on the absorption and emission spectra of a widely used fluorescent probe, di-8-ANEPPS, in a dipalmitoylphosphatidylcholine (DPPC) and a mixed DPPC/cholesterol membrane bilayer. Ground-state and excited-state geometries were calculated with the complete active space self-consistent field (CASSCF) method. Interactions with up to 260 atoms of the membrane bilayer were explicitly incorporated using a decoupled quantum mechanics/molecular mechanics (QM/MM) approach, utilizing recent advances in time-dependent density functional theory (TDDFT). We find that no specific molecular interactions affect the fluorescence of di-8-ANEPPS; rather, the magnitude of the membrane dipole potential is key to the shifts observed in both of the two lowest excited states.