# Journal of Chemical Theory and Computation (JCTC)

## Multicenter Bonding in Ditetracyanoethylene Dianion: A Simple Aromatic Picture in Terms of Three-Electron Bonds

### Abstract

The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE]22– is elucidated using high level ab initio Valence Bond (VB) theory coupled with Quantum Monte Carlo (QMC) methods. This dimer is the prototype of the general family of pancake-bonded dimers with large interplanar separations. Quantitative results obtained with a compact wave function in terms of only six VB structures match the reference CCSD(T) bonding energies. Analysis of the VB wave function shows that the weights of the VB structures are not compatible with a covalent bond between the π* orbitals of the fragments. On the other hand, these weights are consistent with a simple picture in terms of two resonating bonding schemes, one displaying a pair of interfragment three-electron σ bonds and the other displaying intrafragment three-electron π bonds. This simple picture explains at once (1) the long interfragment bond length, which is independent of the countercations but typical of three-electron (3-e) CC σ bonds, (2) the interfragment orbital overlaps which are very close to the theoretical optimal overlap of 1/6 for a 3-e σ bond, and (3) the unusual importance of dynamic correlation, which is precisely the main bonding component of 3-e bonds. Moreover, it is shown that the [TCNE]22– system is topologically equivalent to the square C4H42– dianion, a well-established aromatic system. To better understand the role of the cyano substituents, the unsubstituted diethylenic Na+2[C2H4]22– complex is studied and shown to be only metastable and topologically equivalent to a rectangular C4H42– dianion, devoid of aromaticity.

## A New Mean-Field Method Suitable for Strongly Correlated Electrons: Computationally Facile Antisymmetric Products of Nonorthogonal Geminals

### Abstract

We propose an approach to the electronic structure problem based on noninteracting electron pairs that has similar computational cost to conventional methods based on noninteracting electrons. In stark contrast to other approaches, the wave function is an antisymmetric product of nonorthogonal geminals, but the geminals are structured so the projected Schrödinger equation can be solved very efficiently. We focus on an approach where, in each geminal, only one of the orbitals in a reference Slater determinant is occupied. The resulting method gives good results for atoms and small molecules. It also performs well for a prototypical example of strongly correlated electronic systems, the hydrogen atom chain.

## Hirshfeld-E partitioning: AIM charges with an improved trade-off between robustness and accurate electrostatics

### Abstract

For the development of ab-initio derived force fields, atomic charges must be computed from electronic structure computations, such that (i) they accurately describe the molecular electrostatic potential (ESP) and (ii) they are transferable to the force-field application of interest. The Iterative Hirshfeld (Hirshfeld-I or HI) scheme meets both requirements for organic molecules. For inorganic oxide clusters, however, Hirshfeld-I becomes ambiguous because electron densities of nonexistent isolated anions are needed as input. Herein, we propose a simple Extended Hirshfeld (Hirshfeld-E or HE) scheme to overcome this limitation. The performance of the new HE scheme is compared to four popular atoms-in-molecules schemes, using two tests involving a set of 248 silica clusters. These tests show that the new HE scheme provides an improved trade-off between the ESP accuracy and the transferability of the charges. The new scheme is a generalization of the Hirshfeld-I scheme and it is expected that its improvements are to a large extent applicable to molecular systems containing elements from the entire periodic table.

## How Is cis−trans Isomerization Controlled in Dronpa Mutants? A Replica Exchange Molecular Dynamics Study

## Improved Replica Exchange Method for Native-State Protein Sampling

## Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds

### Abstract

A procedure for determining force constants that is independent of the internal redundant coordinate choice is presented. The procedure is based on solving each bond and angle term separately, using the Wilson B matrix. The method only requires a single ab initio frequency calculation at the minimum energy structure and is made available in the software "parafreq". The methodology is validated with a set of small molecules, by showing it can reproduce ab initio frequencies better than other methods such as taking the diagonal terms of the Hessian in internal coordinates or by using standard AMBER force fields. Finally, the utility of the method is demonstrated by parametrizing the dizinc scaffold of bis-dipicolylamine (BDPA) bound to phosphotyrosine, which is then functionalized into promising antitumor drug proteomimetics.

## Ab initio parametrized force field for the flexible metal-organic framework MIL-53(Al)

### Abstract

A force field is proposed for the flexible metal-organic framework MIL-53(Al), which is calibrated using density functional theory calculations on non-periodic clusters. The force field has three main contributions: an electrostatic term based on atomic charges derived with a modified Hirshfeld-I method, a van der Waals (vdW) term with parameters taken from the MM3 model and a valence force field whose parameters were estimated with a new methodology that uses the gradients and Hessian matrix elements retrieved from non-periodic cluster calculations. The new force field, predicts geometries and cell parameters that compare well with the experimental values both for the large and narrow pore phases. The energy profile along the breathing mode of the empty material reveals the existence of two minima, which confirms the intrinsic bistable behaviour of the MIL-53. Even without the stimulus of external guest molecules the material may transform from the large pore (lp) to the narrow pore (np) phase [Liu et al. JACS 2008, 120, 11813]. The relative stability of the two phases critically depends on the vdW parameters and MM3 dispersion interaction has the tendency to overstabilize the np phase.

## Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules

### Abstract

In an earlier work, the authors developed a new method, the mobile block Hessian (MBH) approach, to accurately calculate vibrational modes for partially optimized molecular structures [ J. Chem. Phys. 2007, 126 (22), 224102.]. It is based on the introduction of blocks, consisting of groups of atoms, that can move as rigid bodies. The internal geometry of the blocks need not correspond to an overall optimization state of the total molecular structure. The standard MBH approach considers free blocks with six degrees of freedom. In the extended MBH approach introduced herein, the blocks can be connected by one or two adjoining atoms, which further reduces the number of degrees of freedom. The new approach paves the way for the normal-mode analysis of biomolecules such as proteins. It rests on the hypothesis that low-frequency modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino acid residues. The method is validated for a series of small molecules and further applied to alanine dipeptide as a prototype to describe vibrational interactions between two peptide units; to crambin, a small protein with 46 amino acid residues; and to ICE/caspase-1, which contains 518 amino acid residues.

## Calculating Reaction Rates with Partial Hessians: Validation of the Mobile Block Hessian Approach

### Abstract

In an earlier paper, the authors have developed a new method, the mobile block Hessian (MBH), to accurately calculate vibrational modes for partially optimized molecular structures [J. Chem. Phys. 2007, 126 (22), 224102]. The proposed procedure remedies the artifact of imaginary frequencies, occurring in standard frequency calculations, when parts of the molecular system are optimized at different levels of theory. Frequencies are an essential ingredient in predicting reaction rate coefficients due to their input in the vibrational partition functions. The question arises whether the MBH method is able to describe the chemical reaction kinetics in an accurate way in large molecular systems where a full quantum chemical treatment at a reasonably high level of theory is unfeasible due to computational constraints. In this work, such a validation is tested in depth. The MBH method opens a lot of perspectives in predicting accurate kinetic parameters in chemical reactions where the standard full Hessian procedure fails.