DFTB/PCM Applied to Ground and Excited State Potential Energy Surfaces

Robust and Efficient Implicit Solvation Model for Fast Semiempirical Methods

We present a robust and efficient method to implicitly account for solvation effects in modern semiempirical quantum mechanics and force fields. A computationally efficient yet accurate solvation model based on the analytical linearized Poisson-Boltzmann (ALPB) model is parameterized for the extended tight binding (xTB) and density functional tight binding (DFTB) methods as well as for the recently proposed GFN-FF general force field. The proposed methods perform well over a broad range of systems and applications, from conformational energies over transition-metal complexes to large supramolecular association reactions of charged species. For hydration free energies of small molecules, GFN1-xTB(ALPB) is reaching the accuracy of sophisticated explicitly solvated approaches, with a mean absolute deviation of only 1.4 kcal/mol compared to the experiment. Logarithmic octanol-water partition coefficients (log K_ow) are computed with a mean absolute deviation of about 0.65 using GFN2-xTB(ALPB) compared to experimental values indicating a consistent description of differential solvent effects. Overall, more than twenty solvents for each of the six semiempirical methods are parameterized and tested. They are readily available in the xtb and dftb+ programs for diverse computational applications.

Perspective on Simplified Quantum Chemistry Methods for Excited States and Response Properties

We review recent developments in the framework of simplified quantum chemistry for excited state and optical response properties (sTD-DFT) and present future challenges for new method developments to improve accuracy and extend the range of application. In recent years, the scope of sTD-DFT was extended to molecular response calculations of the polarizability, optical rotation, first hyperpolarizability, two-photon absorption (2PA), and excited-state absorption for large systems with hundreds to thousands of atoms. The recently introduced spin-flip simplified time-dependent density functional theory (SF-sTD-DFT) variant enables an ultrafast treatment for diradicals and related strongly correlated systems. A few drawbacks were also identified, specifically for the computation of 2PA cross sections. We propose solutions to this problem and how to generally improve the accuracy of simplified schemes. New possible simplified schemes are also introduced for strongly correlated systems, e.g., with a second-order perturbative correlation correction. Interpretation tools that can extract chemical structure-property relationships from excited state or response calculations are also discussed. In particular, the recently introduced method-agnostic RespA approach based on natural response orbitals (NROs) as the key concept is employed.

Recent developments in the general atomic and molecular electronic structure system

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.

Density-functional tight-binding: basic concepts and applications to molecules and clusters

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.

Time-Dependent Long-Range-Corrected Density-Functional Tight-Binding Method Combined with the Polarizable Continuum Model

In this study, excited-state free energies and geometries were efficiently evaluated using a linear-response time-dependent long-range-corrected density-functional tight-binding method integrated with the polarizable continuum model (TD-LC-DFTB2/PCM). Although the LC-DFTB method required the evaluation of the exchange-type term, which was moderately computationally expensive, a single evaluation of the excited-state gradient for a system consisting of more than 1000 atoms in a vacuum was completed within 30 min using one CPU core. Benchmark calculations were conducted for 3-hydroxyflavone, which exhibits dual emission: the absorption and enol-form emission wavelengths calculated by TD-LC-DFTB2/PCM agreed well with those predicted based on the density functional theory using a long-range corrected functional; however, there was a large error in the predicted keto-form emission wavelength. Further benchmark calculations for more than 20 molecules indicated that the conventional TD-DFTB method underestimated the absorption and 0-0 transition energies compared with those which were measured experimentally, whereas the TD-LC-DFTB2 method systematically overestimated these metrics. Nevertheless, the agreement of the results of the TD-LC-DFTB2 method with those obtained by the CAM-B3LYP method demonstrates the potential of the TD-LC-DFTB2/PCM method. Moreover, changing the range separation parameter to 0.15 minimized this deviation.

Catalytic Mechanism of Amyloid-β Peptide Degradation by Insulin Degrading Enzyme: Insights from Quantum Mechanics and Molecular Mechanics Style Møller-Plesset Second Order Perturbation Theory Calculation

Insulin degrading enzyme (IDE), a metalloprotease that degrades amyloid-β (Aβ) peptides and insulin, is associated with Alzheimer's disease and diabetes. The mechanism of IDE catalyzed degrading of Aβ peptides, which is of fundamental importance in the design of therapeutic methods for Alzheimer's disease, has not been fully understood. In this work, combined quantum mechanics and molecular mechanics (QM/MM) style Møller-Plesset second order perturbation theory (MP2) geometry optimization calculations are performed to investigate the catalytic mechanism of the Aβ40 Phe19-Phe20 peptide bond cleavage by human IDE. The analyses using QM/MM MP2 optimization suggest that a neutral water molecule is at the active site of the enzyme-substrate (ES) complex. The water molecule is in hydrogen bonding with the nearby anionic Glu111 of IDE but not directly bound to the catalytic Zn ion. This is confirmed by QM/MM DFTB3 molecular dynamics simulation. Our studies also reveal that the hydrolysis of the Aβ40 Phe19-Phe20 peptide bond by IDE consists of four key steps. The neutral water is first activated by moving toward and binding to the Zn ion. A gem-diol intermediate is then formed by the activated neutral water molecule attacking the C atom of the Phe19-Phe20 peptide bond. The next is the protonation of the N atom of Phe19-Phe20 peptide bond to form an intermediate with an elongated C-N bond. The final step is the breaking of the Phe19-Phe20 C-N bond. The final step is the rate-determining step with a calculated Gibbs free energy of activation of 17.34 kcal/mol, in good agreement with the experimental value 16.7 kcal/mol. This mechanism provides the basis for the design of biochemical methods to modulate the activity of IDE in humans.

Role of solute-solvent hydrogen bonds on the ground state and the excited state proton transfer in 3-hydroxyflavone. A systematic spectrophotometric study

A detailed account on the photophysics of 3-hydroxyflavone (3HF) in 27 organic solvents is reported. Dual fluorescence of neutral 3HF was observed in protic, polar, and weakly polar solvents, endowed with sufficiently high hydrogen bond accepting and/or donating capabilities. Ground-state solvent-induced 3HF deprotonation was reported in 14 cases. 3HF anion photophysics was investigated, and the deprotonation constant Kdep calculated. Previously reported models (based on solute-solvent intermolecular hydrogen bonds) to explain solvent effects on Excited-State Intramolecular Proton Transfer (ESIPT) and on solvent-induced deprotonation have been re-examined and improved in order to rationalize the observed photophysical behaviour in all the studied solvents. Hydrogen bond donor acidity and hydrogen bond acceptor basicity are shown to be key parameters. The results are discussed in the framework of the use of 3HF as an environment-sensitive fluorescent sensor in several research fields, and as a model system in the study of ESIPT reactions. Solvent effects on 3HF reactivity are also discussed, as the role of the surrounding media on the chemistry of flavonols is an emerging topic in natural product research.

Time-Dependent Extension of the Long-Range Corrected Density Functional Based Tight-Binding Method

We present a consistent linear response formulation of the density functional based tight-binding method for long-range corrected exchange-correlation functionals (LC-DFTB). Besides a detailed account of derivation and implementation of the method, we also test the new scheme on a variety of systems considered to be problematic for conventional local/semilocal time-dependent density functional theory (TD-DFT). To this class belong the optical properties of polyacenes and nucleobases, as well as charge transfer excited states in molecular dimers. We find that the approximate LC-DFTB method exhibits the same general trends and similar accuracy as range-separated DFT methods at significantly reduced computational cost. The scheme should be especially useful in the determination of the electronic excited states of very large molecules, for which conventional TD-DFT is supposed to fail due to a multitude of artificial low energy states.

Prediction of pKa Values for Druglike Molecules Using Semiempirical Quantum Chemical Methods

Rapid yet accurate pK_a prediction for druglike molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pK_a values of 53 amine groups in 48 druglike compounds. The approach uses an isodesmic reaction where the pK_a value is computed relative to a chemically related reference compound for which the pK_a value has been measured experimentally or estimated using a standard empirical approach. The AM1- and PM3-based methods perform best with RMSE values of 1.4-1.6 pH units that have uncertainties of ±0.2-0.3 pH units, which make them statistically equivalent. However, for all but PM3/SMD and AM1/SMD the RMSEs are dominated by a single outlier, cefadroxil, caused by proton transfer in the zwitterionic protonation state. If this outlier is removed, the RMSE values for PM3/COSMO and AM1/COSMO drop to 1.0 ± 0.2 and 1.1 ± 0.3, whereas PM3/SMD and AM1/SMD remain at 1.5 ± 0.3 and 1.6 ± 0.3/0.4 pH units, making the COSMO-based predictions statistically better than the SMD-based predictions. For pK_a calculations where a zwitterionic state is not involved or proton transfer in a zwitterionic state is not observed, PM3/COSMO or AM1/COSMO is the best pK_a prediction method; otherwise PM3/SMD or AM1/SMD should be used. Thus, fast and relatively accurate pK_a prediction for 100-1000s of druglike amines is feasible with the current setup and relatively modest computational resources.

The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model

The electronic gap in proteins is analyzed in detail, and it is shown that FMO-DFTB/PCM is efficient and accurate in describing the molecular structure of proteins in solution.

Synthesis and characterization of copolycarbonates having azobenzene units in the main chain as an active group for optical logic gate devices

These copolymers, suitable as optical logical gate, show a reversible photoisomerization, also in solid state. An unexpected fluorescence emission was observed and rationalized by means of an in silico TD-DFT approach.