Dmitrij Rappoport

Property-optimized Gaussian basis sets for molecular response calculations

With recent advances in electronic structure methods, first-principles calculations of electronic response properties, such as linear and nonlinear polarizabilities, have become possible for molecules with more than 100 atoms. Basis set incompleteness is typically the main source of error in such calculations since traditional diffuse augmented basis sets are too costly to use or suffer from near linear dependence. To address this problem, we construct the first comprehensive set of property-optimized augmented basis sets for elements H-Rn except lanthanides. The new basis sets build on the Karlsruhe segmented contracted basis sets of split-valence to quadruple-zeta valence quality and add a small number of moderately diffuse basis functions. The exponents are determined variationally by maximization of atomic Hartree-Fock polarizabilities using analytical derivative methods. The performance of the resulting basis sets is assessed using a set of 313 molecular static Hartree-Fock polarizabilities. The mean absolute basis set errors are 3.6%, 1.1%, and 0.3% for property-optimized basis sets of split-valence, triple-zeta, and quadruple-zeta valence quality, respectively. Density functional and second-order Møller-Plesset polarizabilities show similar basis set convergence. We demonstrate the efficiency of our basis sets by computing static polarizabilities of icosahedral fullerenes up to C(720) using hybrid density functional theory.

III – Density Functional Methods for Excited States: Equilibrium Structure and Electronic Spectra

This chapter discusses density functional methods for excited states. Density functional theory (DFT) is nowadays one of the most popular methods for ground state electronic structure calculations in quantum chemistry and solid state physics. A number of commercial programs are available, and DFT calculations of ground state energies, structures, and many other properties are routinely performed by nonexperts in (bio-)chemistry, physics, and materials sciences. The chapter focuses on the use of time-dependent density functional theory (TDDFT). Algorithms to compute spectra and excited state properties are also reviewed. The chapter describes the steps necessary in a TDDFT excited state calculation and some timing for typical applications are presented. Further the chapter also summarizes the performance of TDDFT excitation energies, transition moments, and excited state properties. Specific applications are surveyed that included compounds such as aromatic systems and fullerenes, porphyrins and related compounds, transition metal compounds, metal and semiconductor clusters, organic polymers, and biologically relevant systems.

Analytical time-dependent density functional derivative methods within the RI-J approximation, an approach to excited states of large molecules

Time-dependent density functional theory (TDDFT) is now well established as an efficient method for molecular excited state treatments. In this work, we introduce the resolution of the identity approximation for the Coulomb energy (RI-J) to excited state gradient calculations. In combination with nonhybrid functionals, the RI-J approximation leads to speed ups in total timings of an order of magnitude compared to the conventional method; this is demonstrated for oligothiophenes with up to 40 monomeric units and adamantane clusters. We assess the accuracy of the computed adiabatic excitation energies, excited state structures, and vibrational frequencies on a set of 36 excited states. The error introduced by the RI-J approximation is found to be negligible compared to deficiencies of standard basis sets and functionals. Auxiliary basis sets optimized for ground states are suitable for excited state calculations with small modifications. In conclusion, the RI-J approximation significantly extends the scope of applications of analytical TDDFT derivative methods in photophysics and photochemistry.

Lagrangian approach to molecular vibrational Raman intensities using time-dependent hybrid density functional theory

The authors propose a new route to vibrational Raman intensities based on analytical derivatives of a fully variational polarizability Lagrangian. The Lagrangian is constructed to recover the negative frequency-dependent polarizability of time-dependent Hartree-Fock or adiabatic (hybrid) density functional theory at its stationary point. By virtue of the variational principle, first-order polarizability derivatives can be computed without using derivative molecular orbital coefficients. As a result, the intensities of all Raman-active modes within the double harmonic approximation are obtained at approximately the same cost as the frequency-dependent polarizability itself. This corresponds to a reduction of the scaling of computational expense by one power of the system size compared to a force constant calculation and to previous implementations. Since the Raman intensity calculation is independent of the harmonic force constant calculation more, computationally demanding density functionals or basis sets may be used to compute the polarizability gradient without much affecting the total time required to compute a Raman spectrum. As illustrated for fullerene C60, the present approach considerably extends the domain of molecular vibrational Raman calculations at the (hybrid) density functional level. The accuracy of absolute and relative Raman intensities of benzene obtained using the PBE0 hybrid functional is assessed by comparison with experiment.

The Binding of Benzoarylsulfonamide Ligands to Human Carbonic Anhydrase is Insensitive to Formal Fluorination of the Ligand.

Its the water that matters. Pairs of benzo- and perfluorobenzoarylsulfonamide ligands bind to human carbonic anhydrase with a conserved binding geometry, an enthalpy-driven binding, and indistinguishable binding affinities (see picture). These data support the pervasive theory that the lock-and-key model disregards an important component of binding: the water, which fills the binding pocket of the protein and surrounds the ligand.

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

Conformationally-locked metallomacrocycles—prototypes for a novel type of axial chirality

A series of ditopic ligands incorporating two 2,2′:6′,2″-terpyridine (tpy) metal-binding domains linked to a central naphthalenediyl core by ethyleneoxy chains of various lengths have been prepared and their iron(II) complexes prepared. The major thermodynamic products of complexation are ferracycles of [1 + 1], [2 + 2] or [3 + 3] stoichiometry. In the case of the [1 + 1] complexes, the linker between the two tpy domains is spatially restricted and the cations exhibit chirality associated with the conformation about the central N–Fe–N bonds. The dynamic processes by which the enantiomeric forms interconvert are investigated in the presence of chiral anions by NMR and circular dichroism spectroscopy making use of the Pfeiffer effect. We have shown that ditopic bis(2,2′:6′,2″-terpyridine) ligands give rise to conformationally restricted complexes with iron(II) centres. The absolute configuration of the cations in the diastereomeric ion pairs obtained through the Pfeiffer effect has been calculated using TDDFT methods.

Characterizing the metal-SAM interface in tunneling junctions.

This paper investigates the influence of the interface between a gold or silver metal electrode and an n-alkyl SAM (supported on that electrode) on the rate of charge transport across junctions with structure Met(Au or Ag)(TS)/A(CH2)nH//Ga2O3/EGaIn by comparing measurements of current density, J(V), for Met/AR = Au/thiolate (Au/SR), Ag/thiolate (Ag/SR), Ag/carboxylate (Ag/O2CR), and Au/acetylene (Au/C≡CR), where R is an n-alkyl group. Values of J0 and β (from the Simmons equation) were indistinguishable for these four interfaces. Since the anchoring groups, A, have large differences in their physical and electronic properties, the observation that they are indistinguishable in their influence on the injection current, J0 (V = 0.5) indicates that these four Met/A interfaces do not contribute to the shape of the tunneling barrier in a way that influences J(V).

Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

Introducing Ionic and/or Hydrogen Bonds into the SAM//Ga 2 O 3 Top- Interface of Ag TS /S(CH 2 ) n T//Ga 2 O 3 /EGaIn Junctions

Junctions with the structure Ag(TS)/S(CH2)nT//Ga2O3/EGaIn (where S(CH2)nT is a self-assembled monolayer, SAM, of n-alkanethiolate bearing a terminal functional group T) make it possible to examine the response of rates of charge transport by tunneling to changes in the strength of the interaction between T and Ga2O3. Introducing a series of Lewis acidic/basic functional groups (T = -OH, -SH, -CO2H, -CONH2, and -PO3H) at the terminus of the SAM gave values for the tunneling current density, J(V) in A/cm(2), that were indistinguishable (i.e., differed by less than a factor of 3) from the values observed with n-alkanethiolates of equivalent length. The insensitivity of the rate of tunneling to changes in the terminal functional group implies that replacing weak van der Waals contact interactions with stronger hydrogen- or ionic bonds at the T//Ga2O3 interface does not change the shape (i.e., the height or width) of the tunneling barrier enough to affect rates of charge transport. A comparison of the injection current, J0, for T = -CO2H, and T = -CH2CH3--two groups having similar extended lengths (in Å, or in numbers of non-hydrogen atoms)--suggests that both groups make indistinguishable contributions to the height of the tunneling barrier.