Application of time-dependent density-functional theory to the 3Σu− first excited state of H2

Eremoxylarins D-J, Antibacterial Eremophilane Sesquiterpenes Discovered from an Endolichenic Strain of Xylaria hypoxylon

An endolichenic strain of the Ascomycetaceous Xylaria hypoxylon, cultivated alone or in coculture with another endolichenic fungus Dendrothyrium variisporum, produced seven new bioactive eremophilane sesquiterpenes eremoxylarins D-J (1-7). The isolated compounds disclosed a high similarity with the eremophilane core of the bioactive integric acid, and structures were elucidated by 1D and 2D NMR spectra and electronic circular dichroism (ECD) analyses. Eremoxylarins D, F, G, and I showed a selective activity against Gram-positive bacteria such as methicillin-resistant Staphylococcus aureus with minimum inhibitory concentration (MIC) values between 0.39 and 12.5 μg/mL. Eremoxylarin I, the most antibacterial active sesquiterpene, was also active against HCoV-229E at a concentration nontoxic to the hepatoma Huh-7 cell line with an 50% inhibitory concentration (IC₅₀) of 18.1 μM and a 50% cytotoxic concentration (CC₅₀) of 46.6 μM.

Excitation energies from thermally assisted-occupation density functional theory: Theory and computational implementation

The time-dependent density functional theory (TDDFT) has been broadly used to investigate the excited-state properties of various molecular systems. However, the current TDDFT heavily relies on outcomes from the corresponding ground-state DFT calculations, which may be prone to errors due to the lack of proper treatment in the non-dynamical correlation effects. Recently, thermally assisted-occupation DFT (TAO-DFT) [J.-D. Chai, J. Chem. Phys. 136, 154104 (2012)], a DFT with fractional orbital occupations, was proposed, explicitly incorporating the non-dynamical correlation effects in the ground-state calculations with low computational complexity. In this work, we develop TDTAO-DFT, which is a TD, linear-response theory for excited states within the framework of TAO-DFT. With tests on the excited states of H₂, the first triplet excited state (1³Σ_u ⁺) was described well, with non-imaginary excitation energies. TDTAO-DFT also yields zero singlet-triplet gap in the dissociation limit for the ground singlet (1¹Σ_g ⁺) and the first triplet state (1³Σ_u ⁺). In addition, as compared to traditional TDDFT, the overall excited-state potential energy surfaces obtained from TDTAO-DFT are generally improved and better agree with results from the equation-of-motion coupled-cluster singles and doubles.

Single-photon emitters in hexagonal boron nitride: a review of progress

This report summarizes progress made in understanding properties such as zero-phonon-line energies, emission and absorption polarizations, electron-phonon couplings, strain tuning and hyperfine coupling of single photon emitters in hexagonal boron nitride. The primary aims of this research are to discover the chemical nature of the emitting centres and to facilitate deployment in device applications. Critical analyses of the experimental literature and data interpretation, as well as theoretical approaches used to predict properties, are made. In particular, computational and theoretical limitations and challenges are discussed, with a range of suggestions made to overcome these limitations, striving to achieve realistic predictions concerning the nature of emitting centers. A symbiotic relationship is required in which calculations focus on properties that can easily be measured, whilst experiments deliver results in a form facilitating mass-produced calculations.

Molecular quantum cellular automata cell design trade-offs: latching vs. power dissipation

The use of molecules to enact quantum cellular automata (QCA) cells has been proposed as a new way for performing electronic logic operations at sub-nm dimensions. A key question that arises concerns whether chemical or physical processes are to be exploited. The use of chemical reactions allows the state of a switch element to be latched in molecular form, making the output of a cell independent of its inputs, but costs energy to do the reaction. Alternatively, if purely electronic polarization is manipulated then no internal latching occurs, but no power is dissipated provided the fields from the inputs change slowly compared to the molecular response times. How these scenarios pan out is discussed by considering calculated properties of the 1,4-diallylbutane cation, a species often used as a paradigm for molecular electronic switching. Utilized are results from different calculation approaches that depict the ion either as a charge-localized mixed-valence compound functioning as a bistable switch, or else as an extremely polarizable molecule with a delocalized electronic structure. Practical schemes for using molecular cells in QCA and other devices emerge.

Putting David Craig’s Legacy to Work in Nanotechnology and Biotechnology

David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.

Electric field effects on aromatic and aliphatic hydrocarbons: a density-functional study

The influence of a uniform static external electric field on some aliphatic and aromatic molecular species is studied within the density functional theory (DFT) employing the 6-311++G(2d,2p) basis set with B3LYP exchange-correlation prescription. The electric field perturbs the molecular geometry but drastically alters the dipole moments and engenders, to a varying degree, the molecular vibrational Stark effect, i.e., shifts in the infrared (IR) vibrational frequencies accompanied by spectral intensity redistribution. For polar molecules, significant negative ("red") and positive ("blue") frequency shifts are observed for field orientations both parallel and antiparallel to their permanent dipole moments. Further, a selective reordering of frontier orbitals is observed to be brought about by moderately intense fields. In particular, molecules having a lowest unoccupied molecular orbital (LUMO) with predominant pi character possess a threshold field beyond which energy gap between the highest occupied molecular orbital (HOMO) and LUMO diminishes rapidly. A time-dependent (TD) DFT analysis reveals that an increase in the applied field strength by and large increases the excitation energies corresponding to significant electronic transitions among frontier MOs with a concomitant decrease in their oscillator strengths.

Nonadiabatic couplings from time-dependent density functional theory: Formulation in the Casida formalism and practical scheme within modified linear response

We present an efficient method to compute nonadiabatic couplings (NACs) between the electronically ground and excited states of molecules, within the framework of time-dependent density functional theory (TDDFT) in frequency domain. Based on the comparison of dynamic polarizability formulated both in the many-body wave function form and the Casida formalism, a rigorous expression is established for NACs, which is similar to the calculation of oscillator strength in the Casida formalism. The adiabatic local density approximation (ALDA) gives results in reasonable accuracy as long as the conical intersection (ci) is not approached too closely, while its performance quickly degrades near the ci point. This behavior is consistent with the real-time TDDFT calculation. Through the use of modified linear response theory together with the ground-state-component separation scheme, the performance of ALDA can be greatly improved, not only in the vicinity of ci but also for Rydberg transitions and charge-transfer excitations. Several calculation examples, including the quantization of NACs from the Jahn-Teller effect in the H3 system, have been given to show that TDDFT can efficiently give NACs with an accuracy comparable to that of wave-function-based methods.

The Green's Function Density Functional Tight-Binding (gDFTB) Method for Molecular Electronic Conduction

A review is presented of the nonequilibrium Green's function (NEGF) method "gDFTB" for evaluating elastic and inelastic conduction through single molecules employing the density functional tight-binding (DFTB) electronic structure method. This focuses on the possible advantages that DFTB implementations of NEGF have over conventional methods based on density functional theory, including not only the ability to treat large irregular metal-molecule junctions with high nonequilibrium thermal distributions but perhaps also the ability to treat dispersive forces, bond breakage, and open-shell systems and to avoid large band lineup errors. New results are presented indicating that DFTB provides a useful depiction of simple gold-thiol interactions. Symmetry is implemented in DFTB, and the advantages it brings in terms of large savings of computational resources with significant increase in numerical stability are described. The power of DFTB is then harnessed to allow the use of gDFTB as a real-time tool to discover the nature of the forces that control inelastic charge transport through molecules and the role of molecular symmetry in determining both elastic and inelastic transport. Future directions for the development of the method are discussed.

Photoinduced Intramolecular Charge Transfer Reaction in (E)-3-(4-Methylamino-phenyl)-acrylic Acid Methyl Ester: A Fluorescence Study in Combination with TDDFT Calculation

A donor-acceptor substituted aromatic system (E)-3-(4-Methylamino-phenyl)-acrylic acid methyl ester (MAPAME) has been synthesized, and its photophysical behavior obtained spectroscopically has been compared with the theoretical results. The observed dual fluorescence from MAPAME has been assigned to emission from locally excited and twisted intramolecular charge transfer states. The donor and acceptor angular dependency on the ground and excited states potential energy surfaces have been calculated both in vacuo and in acetonitrile solvent using time dependent density functional theory (TDDFT) and TDDFT polarized continuum model (TDDFT-PCM), respectively. Calculation predicts that a stabilized twisted excited state is responsible for red shifted charge transfer emission.

Single molecule conductivity: The role of junction-orbital degeneracy in the artificially high currents predicted by ab initio approaches

A priori evaluations, using Hartree-Fock self-consistent-field (SCF) theory or density-functional theory (DFT), of the current passing between two electrodes through a single bridging molecule result in predicted conductivities that may be up to one to two orders of magnitude larger than observed ones. We demonstrate that this is, in part, often due to the improper application of the computational methods. Conductivity is shown to arise from tunneling between junction states of the electrodes through the molecule; these states are inherently either quasi two-fold or four-fold degenerate and always comprise the (highest occupied molecular orbital) HOMO band at the Fermi energy of the system. Frequently, in previous cluster based molecular conduction calculations, closed-shell SCF or Kohn-Sham DFT methods have been applied to systems that we demonstrate to be intrinsically open shell in nature. Such calculations are shown to induce artificial HOMO-LUMO (LUMO-lowest unoccupied molecular orbital) band splittings that Landauer-based formalisms for steady-state conduction interpret as arising from extremely rapid through-molecule tunneling at the Fermi energy, hence, overestimating the low-voltage conductivity. It is demonstrated that these shortcomings can be eliminated, dramatically reducing calculated current magnitudes, through the alternate use of electronic-structure calculations based on the spin-restricted open-shell formalism and related multiconfigurational SCF of DFT approaches. Further, we demonstrate that most anomalies arising in DFT implementations arise through the use of hybrid density functionals such as B3LYP. While the enhanced band-gap properties of these functionals have made them the defacto standard in molecular conductivity calculations, we demonstrate that it also makes them particularly susceptible to open-shell anomalies.

Potential-energy surfaces for excited states in extended systems

With a simple and physically intuitive method, first-principles calculations of potential-energy surfaces are performed for excited states in a number of illustrative systems, including dimers (H(2) and NaCl) and gas-surface systems [Cl-Na(100) and Cl(2)-Na(100)]. It is based on density-functional theory and is a generalization of the Delta self-consistent field (DeltaSCF) method, where electron-hole pairs are introduced in order to model excited states, corresponding to internal electron transfers in the considered system. The desired excitations are identified by analysis of calculated electron orbitals, local densities of states, and charge densities. For extended systems, where reliable first-principles methods to account for electronically excited states have so far been scarce, our method is very promising. Calculated results, such as the chemiluminescence of halogen molecules impinging on a alkali-metal surface, and the vertical (5 sigma-->2 pi(*)) excitation within the adsorbed CO molecule on the Pd(111) surface, are in working agreement with those of other studies and experiments.

The Appropriateness of Density-Functional Theory for the Calculation of Molecular Electronics Properties

As molecular electronics advances, efficient and reliable computation procedures are required for the simulation of the atomic structures of actual devices, as well as for the prediction of their electronic properties. Density-functional theory (DFT) has had widespread success throughout chemistry and solid-state physics, and it offers the possibility of fulfilling these roles. In its modern form it is an empirically parameterized approach that cannot be extended toward exact solutions in a prescribed way, ab initio. Thus, it is essential that the weaknesses of the method be identified and likely shortcomings anticipated in advance. We consider four known systematic failures of modern DFT: dispersion, charge transfer, extended pi conjugation, and bond cleavage. Their ramifications for molecular electronics applications are outlined and we suggest that great care is required when using modern DFT to partition charge flow across electrode-molecule junctions, screen applied electric fields, position molecular orbitals with respect to electrode Fermi energies, and in evaluating the distance dependence of through-molecule conductivity. The causes of these difficulties are traced to errors inherent in the types of density functionals in common use, associated with their inability to treat very long-range electron correlation effects. Heuristic enhancements of modern DFT designed to eliminate individual problems are outlined, as are three new schemes that each represent significant departures from modern DFT implementations designed to provide a priori improvements in at least one and possible all problem areas. Finally, fully semiempirical schemes based on both Hartree-Fock and Kohn-Sham theory are described that, in the short term, offer the means to avoid the inherent problems of modern DFT and, in the long term, offer competitive accuracy at dramatically reduced computational costs.

Time-dependent density functional theory (TDDFT) study of the excited charge-transfer state formation of a series of aromatic donor-acceptor systems

Singlet excitation energy calculations for a series of acceptor para-substituted N,N-dimethyl-anilines that are dual (4-(N,N-dimethylamino)benzonitrile, 4DMAB-CN, 4-(N,N-dimethylamino)benzaldhyde, 4DMAB-CHO, 1-methyl-7-cyano-2,3,4,5-tetrahydro-1H-1-benzazepine, NMC7) and nondual (4-aminobenzonitrile, 4AB-CN, 3-(N,N-dimethylamino)benzonitrile, 3DMAB-CN, and 4-nitro(N,N-dimethyl) aniline, 4DMAB-NO(2)) fluorescent have been performed using time-dependent density functional theory (TDDFT). The B3LYP and MPW1PW91 functionals with a 6-311+G(2d,p) (Bg) basis set have been used to compute excitation energies. Ground-state geometries were optimized using density functional theory (DFT) with both B3LYP and MPW1PW91 functionals combined with a 6-31G(d) basis set. For most of the molecules presented in this study, potential energy surfaces have been computed according to the coordinates related to the three following mechanisms proposed in the literature: twisting, wagging, and planar intramolecular charge transfer (ICT). Comparison of the three models for the different molecules leads to the conclusion that only the twisting ICT model is able to explain the low frequency, strongly solvent-dependent energy band present in the fluorescence spectra. According to this model, the 4AB-CN molecule is calculated to be nondual fluorescent in agreement with the experimental spectra. The single band observed in the fluorescence spectra of TMAB-CN (4-(N,N-dimethylamino)-3,5-(dimethyl)benzonitrile) is due to a large stabilization of the charge-transfer excited state along the twisting coordinate. The nondual fluorescence of the 4DMAB-NO(2) molecule is explained by the same mechanism. In the case of 3DMAB-CN, the single observed emission, which is solvent-dependent, has been assigned to the lowest charge-transfer excited state. The dual fluorescence of 4DMAB-CN and 4DMAB-CHO is explained within the twisting ICT model by a double mechanism (already proposed by Serrano et al.: Serrano-Andrés, L.; Merchán, M.; Roos, B. J.; Lindh, R. J. Am. Chem. Soc. 1995, 117, 3189) that involves the presence of two low-lying states close enough in energy. The observation of dual fluorescence in NMC7, that has been one of the origins of the planar ICT model put forward by Zachariasse et al. (Zachariasse, K.; van der Haar, T.; Hebecker, A.; Leinhos, U.; Kühnle, W. Pure Appl. Chem. 1993, 65, 1745), could be fully understood by a double mechanism within the twisting ICT model. Within the set of investigated molecules, our calculations confirm that the twisting ICT model is the only mechanism acceptable to explain the dual and nondual fluorescence phenomenon. Our calculations are in complete agreement with experimental data.