Computational Chemistry: Reviews of Current Trends

The following sections are included:

• PREFACE

• CONTENTS

In this review we discuss the fundamental issues underlying first-principles quantum transport theory in molecular- and atomic-scale systems, making emphasis on the actual numerical implementation of them. For this purpose we focus on the ab initio method named Gaussian Embedded Cluster Method, recently developed by the authors, which is based on the popular quantum chemistry code GAUSSIAN98/03. Various examples that illustrate the applicability and reliability of this method in the study and interpretation of a large range of experiments in the field of molecular electronics are also presented.

The ultimate goal of nanosciences is to develop tools for spatial and chemical control of single molecules. A number of experimental techniques have emerged in recent years which allow for mechanical manipulations of single molecules including single molecule fluorescence, optical and magnetic tweezers, atomic force spectroscopy. Proper understanding of experimental results requires adequate theory. In this paper we present an overview of recent advances and trends in applications of computer simulations aimed at understanding of atomic force microscope (AFM) experiments. Special attention is devoted to those variants of classical molecular dynamics (MD) simulations, such as steered MD or biased MD, which are particularly helpful in interpretation of experimental data obtained for single biopolymer molecules. A short meta-review (review of recent reviews) of advances in the MD technology is also presented.

Molecular dynamics simulations using ab initio force fields and signal processing techniques are combined to analyze the dynamic properties of a minimum unit of a field programmable random molecular array also called nanocell. We analyze stretching, angular, and torsional internal modes at several temperatures of operation and their correlations as well as the possibility of signal modulation and processing at terahertz frequencies. The proposed scenario is another alternative for molecular electronics, which is being developed at very low frequencies of operation using the electronic states of molecules, clusters and other nanoscopic systems.

Formulation and pilot numerical implementation of linear response theories (LRT) for excited state potential energy surfaces (PES) are presented, which are based on a class of state specific (SS) multi-reference coupled electron-pair approximation (CEPA)-like methods (SS-MRCEPA). These theories, termed as MRCEPA-LRT, are suited for the excited states whose ground state either have intruders at some region of the PES, or displays real or weakly avoided crossings. Genesis of the SS-MRCEPA approximations is traced from the parent full-blown state specific multi-reference coupled cluster theory (SS-MRCC), and its efficacy to provide accurate PES for the ground state in an intruder-free manner is emphasized. Two CEPA versions are discussed, and the MRCEPA-LRT emerge as the LRT based on the two SS-MRCEPA. They provide size-intensive energies in the sense that they yield excitation energies for the fragments in the limit of noninteracting fragments, just like in the single-reference CCLRT. The set of MRCEPA-LRT developed in this article bears close structural resemblance to our LRT based on the SS-MRCC method (MR-CCLRT), just as the SS-MRCEPA does to the parent SS-MRCC method. Pilot applications to the PES of some low-lying excited states of the P4 model and Li₂ molecule, whose ground states possess quasi-degeneracy or face intruders indicate very satisfactory performance, comparing quite favorably with the results of the full-blown MR-CCLRT, despite the neglect of a host of complicated terms.

A procedure for calculating magnetic exchange coupling constants in rare earth (RE)-transition metal (TM) dimers is presented. In a first step RE-TM transfer (hopping) integrals between orbitals carrying unpaired (magnetic) electrons on RE and TM are determined from a MO-calculation utilising the concept of orbital exchange pathway and effective Hamiltonian theory. In a second step, many-electron wave-functions for ground or excited electronic states on RE and TM are constructed in which spin-orbit coupling (which dominates for the RE) is fully (variationally) taken into account. Finally, the data from steps 1 and 2 are combined to obtain numerical values for kinetic exchange integrals (within Anderson's superexchange theory) utilising a non-Heisenberg (orbital dependent) exchange operator. The MO's corresponding to the d(Mn) and f(Yb) magnetic orbitals have been used to also calculate ferromagnetic contributions to the exchange coupling. The model is applied to Yb³⁺-Mn²⁺ dimers with corner, edge and face shared octahedra and Cl− and Br− ligands. For that purpose we utilise a spectroscopically adjusted (to spectra of single nucleous octahedral Mn²⁺, Cr³⁺ and Yb³⁺ complexes) parameterisation of the Extended Huckel theory. The expediency of the approach is discussed based on a comparison between calculated and experimental (available from inelastic neutron scattering experiments) anisotropic exchange parameters in Br₃Cr³⁺-µ(Br₃) Yb³⁺Br₃ dimers. Ferromagnetic exchange parameters for the ground state and the lowest emitting excited state increase from corner to edge to face Mn-Cl-Yb sharing thus varying in the same way as the efficiency of the up-conversion found for such species. This lends support for an exchange mechanism for this phenomenon postulated previously.

The dihydrogen bonds (DHBs) are considered. The examples of such interactions existing in crystal structures are presented. These interactions are compared with conventional hydrogen bonds. The comparison shows that DHBs are often similar in nature to O-H…O and other typical H-bonds. One can observe for DHBs the elongation of the proton donating bond due to complexation and the correlations between geometrical, energetic and topological parameters. There are different types of DHBs, such as those with π-electron delocalization, similar to resonance assisted hydrogen bonds (RAHBs). The insight into the nature of DHBs shows that in principle the interaction energy decomposition scheme for them is similar to that one for conventional H-bonds showing that the electrostatic energy term is the most important attractive term. The case of σ-bonds as the proton acceptors is also considered. The relationships derived from the bond valence model are in agreement with the experimental neutron diffraction results as well as with ab initio and DFT calculations. The spin-spin coupling constants for dihydrogen bonded systems are analyzed.

The following sections are included:

• INDEX

• CONTENT INDEX