Mechanism of hydrogen bond assisted cis-trans isomerization in the excited state of 2-naphthol

Stationary points on the ground and first two excited state potential energy surfaces of 2-naphthol and the hydrogen bonded complex 2-naphtholNH(3) have been located using an approximate method (time dependent density functional based tight-binding) based on time dependent density functional theory (TDDFT). For the obtained extrema, single point calculations at the full TDDFT level (PW916-311+G(**)) were performed for validation purposes. The energetical ordering of the cis and trans forms of 2-naphthol in the different electronic states is found to be in good agreement with available experimental data. Interestingly, also the optical spectrum is correctly predicted by TDDFT in contrast to calculations on unsubstituted acenes in the literature. Besides the stationary points, also the minimum energy paths connecting them are calculated using an adaptive nudged elastic band approach in order to estimate isomerization barriers. While the increase of barrier height going from the ground to the first excited state is already documented, the authors find as a new result a significant barrier reduction upon hydrogen bond formation in the S(2). The observed effect can contribute to the explanation of recent experiments on infrared laser induced cis-trans isomerization in 2-naphthol.     

Time-dependent density functional theory gradients in the Amsterdam density functional package: geometry optimizations of spin-flip excitations

An implementation of time-dependent density functional theory (TDDFT) energy gradients into the Amsterdam density functional theory program package (ADF) is described. The special challenges presented by Slater-type orbitals in quantum chemical calculation are outlined with particular emphasis on details that are important for TDDFT gradients. Equations for the gradients of spin-flip TDDFT excitation energies are derived. Example calculations utilizing the new implementation are presented. The results of standard calculations agree well with previous results. It is shown that starting from a triplet reference, spin-flip TDDFT can successfully optimize the geometry of the four lowest singlet states of CH₂ and three other isovalent species. Spin-flip TDDFT is used to calculate the potential energy curve of the breaking of the C?CC bond of ethane. The curve obtained is superior to that from a restricted density functional theory calculation, while at the same time the problems with spin contamination exhibited by unrestricted density functional theory calculations are avoided.     

Highly efficient implementation of pseudospectral time‐dependent density‐functional theory for the calculation of excitation energies of large molecules

We have developed and implemented pseudospectral time‐dependent density‐functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm–Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time‐dependent density‐functional theory with full linear response (PS‐FLR‐TDDFT) and within the Tamm–Dancoff approximation (PS‐TDA‐TDDFT) for G2 set molecules using B3LYP/6‐31G*^* show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS‐FLR‐TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS‐FLR‐TDDFT and best estimations demonstrate that the accuracy of both PS‐FLR‐TDDFT and PS‐TDA‐TDDFT. Calculations for a set of medium‐sized molecules, including C_n fullerenes and nanotubes, using the B3LYP functional and 6‐31G^** basis set show PS‐TDA‐TDDFT provides 19‐ to 34‐fold speedups for C_n fullerenes with 450–1470 basis functions, 11‐ to 32‐fold speedups for nanotubes with 660–3180 basis functions, and 9‐ to 16‐fold speedups for organic molecules with 540–1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46‐residue crambin protein, fullerenes up to C₅₄₀ and nanotubes up to 14×(6,6), using the B3LYP functional and 6‐31G^** basis set with up to 8100 basis functions show that PS‐FLR‐TDDFT CPU time scales as N^2.05 with the number of basis functions. © 2016 Wiley Periodicals, Inc.     

QM/MM calculation of solvent effects on absorption spectra of guanine

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

A first principles calculations and experimental study of the ground- and excited-state properties of ladder oligo(p-aniline)s

The molecular structure of three ladder oligo(p-aniline)s, 5,11-diethyl-6,12-dimethylindolo[3,2-b]carbazole (DIMER 2P), 14-ethyl-5,8-dihydro-diindolo[3,2-b:2',3'-h]carbazole (TRIMER 2P), and 5,8,14-triethyl-diindolo[3,2-b:2',3'-h]carbazole (TRIMER 3P) were investigated by first principles calculations at the Hartree-Fock (HF6-31G*) and density functional theory (DFTB3LYP6-31G*) levels. It is found that the agreement between theoretical and x-ray geometrical parameters is good and rather similar for both theoretical methods. The nature and the energy of the first two singlet-singlet electronic transitions have been obtained by Zerner intermediate neglect of differential overlap/spectroscopy semiempirical calculations performed on the HF6-31G* and DFTB3LYP6-31G* optimized geometries, as well as time-dependent density functional theory (TDDFT) calculations performed on the DFTB3LYP6-31G* optimized structures. For all the compounds and for all the theoretical approaches, it is observed that the S(1)<--S(0) electronic transition (pipi*) is weakly allowed and polarized along the short axis (y) of the molecule. On the other hand, the S(2)<--S(0) electronic transition of each oligomer possesses a much larger oscillator strength and is polarized along the long (x) molecular axis. It is found that TDDFT calculations provide the best overall agreement between the energies and the corresponding optical transitions obtained from the absorption bands (0-0 peaks) measured in dichloromethane as well as providing a good evaluation of the bathochromic shifts caused by the increase in the conjugation length or by the presence of extra alkyl chains on the nitrogen atoms in TRIMER 3P compared to TRIMER 2P.     

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.     

Origin of substituent effects in the absorption spectra of peroxy radicals: time dependent density functional theory calculations.

We investigate the assignment of electronic transitions in alkyl peroxy radicals. Past experimental work has shown that the phenyl peroxy radical exhibits a transition in the visible region; however, previous high level calculations have not reproduced this observed absorption. We use time dependent density functional theory (TDDFT) to characterize the electronic excitations of the phenyl peroxy radical as well as other hydrocarbon substituted peroxy radicals. TDDFT calculations of the phenyl peroxy radical support an excitation in the visible spectrum. Further, we investigate the nature of this visible absorption using electron attachment/detachment density diagrams of the peroxy radicals and present a qualitative picture of the origin of the visible absorption based on molecular orbital perturbations. The peroxy radical substituent is also compared against isoelectronic radical groups. The visible absorption is determined to be dependent on mixing of the alkyl and radical substituent orbitals.     

Synthesis, structure and characterization of fac-[Re(CO)3] complexes derived from hydrazone Schiff bases: DFT-TDDFT investigation on electronic structures

The syntheses, structural and spectroscopic characterization of the complexes of general formula [ReL(CO)₃Cl] bearing bifunctional hydrazone Schiff base ligand L are presented in this paper. The structure of one of the complexes is determined by X-ray crystallography. The solid-state structure of the compound is involved in a secondary interaction in lattice forming a supramolecular array. The gas phase geometry optimization and electronic calculation have been performed using density functional theory without any symmetry constraints. On the basis of structural and theoretical studies, ligand in the complexes is considered to be in the keto, not in enol form. Experimental ground state IR and NMR data set agree with those calculated by DFT calculations. The electronic spectra of the complexes are calculated by time dependent density functional theory (TDDFT) using conductor like polarizable continuum model (CPCM). The computed vertical excitation energies in solution are in good agreement with experimental one showing that the metal-to-ligand charge transfer transitions in visible region dominate over ligand based ILCT transition. The TDDFT excited states calculation of the electronic spectra in solution provides evidence towards luminescence spectra.     

Role of polyols (erythritol, xylitol and sorbitol) on the structural stabilization of collagen

A state-specific scheme for time-dependent density functional theory (SS-TDDFT) based on the Davidson algorithm is presented. SS-TDDFT is a method devised for speeding up TDDFT calculations by screening transitions that contribute to a specific excitation. By applying this method to calculations of the low-lying excitation energies of test molecules (N₂, CO, H₂CO, C₂H₄ and C₆H₆), water clusters and polyenes, we found that SS-TDDFT accurately reproduced the excitation energies of standard TDDFT while drastically reducing the rank of the TDDFT response matrix without loss of accuracy. We have thus formulated TDDFT that works more efficiently and economically for memory storage.     

Modelling of UV-molecular spectra of several bis-pyrazolopyridines derivatives

Quantum chemical simulations of UV-absorption spectra in substituted bis-pyrazolopyridines were done. As a theoretical tool time dependent density functional theory (TDDFT) method with Vosko-Wilk-Nusair parameterisation was applied. Comparison of the theoretically simulated UV-absorption spectra with experimental data was performed. Crucial role of pi-conjugated bonds within the backside phenyl rings is demonstrated. Physical insight of the several observed discrepancies between the calculations and experimental data is discussed. A comparison of the TDDFT and several semi-empirical approaches is given.     

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units

Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response Tamm-Dancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results).     

The role of the beta-ionone ring in the photochemical reaction of rhodopsin

Time-dependent density functional theory (TDDFT) calculations on the photoabsorption process of the 11-cis retinal protonated Schiff base (PSB) chromophore show that the Franck-Condon relaxation of the first excited state of the chromophore involves a torsional twist motion of the beta-ionone ring relative to the conjugated retinyl chain. For the ground state, the beta-ionone ring and the retinyl chain of the free retinal PSB chromophore form a -40 degrees dihedral angle as compared to -94 degrees for the first excited state. The double bonds of the retinal are shorter for the fully optimized structure of the excited state than for the ground state suggesting a higher cis-trans isomerization barrier for the excited state than for the ground state. According to the present TDDFT calculations, the excitation of the retinal PSB chromophore does not primarily lead to a reaction along the cis-trans torsional coordinate at the C11-C12 bond. The activation of the isomerization center seems to occur at a later stage of the photo reaction. The results obtained at the TDDFT level are supported by second-order M?ller-Plesset (MP2) and approximate singles and doubles-coupled cluster (CC2) calculations on retinal chromophore models; the MP2 and CC2 calculations yield for them qualitatively the same ground state and excited-state structures as obtained in the density functional theory and TDDFT calculations.     

采用优化的DFTB参数对铜(111)表面碳二聚化的分子动力学研究

针对铜表面化学反应,我们发展了一套铜-碳体系的密度泛函紧束缚(DFTB)参数。测试结果表明这套参数可以很好的描述吸附铜或碳原子前后铜表面的几何结构和能量。基于这套参数,我们对Cu(111)表面的碳二聚化过程进行了分子模拟研究。即使在高温下,直接的分子动力学模拟也很难观察到碳二聚体的形成。这是因为高温下铜表面显著的结构弛豫一定程度上阻止了二聚化。为了研究高温下铜表面碳二聚化的机理,我们进行了赝动力学模拟。发现在二聚化的过程中,碳原子形成C-Cu-C桥状结构以后,会绕中间Cu原子转动,最后形成碳二聚体。1300 K下碳二聚化的自由能垒约0.9 eV。     

Modeling the absorption spectrum of tryptophan in proteins

We have applied time-dependent density functional theory (TDDFT) to study the valence pi-pi* excited states of the tryptophan chromophore in the environment of the proteins barnase and human serum albumin. The chromophore is represented by indole. Due to the approximate nature of TDDFT, in the gas phase the calculated vertical transition energies to the 1L valence states are reordered with respect to experiment. The 1L(a) state responds more than the 1L(b) state to the local environment, described fully at the TDDFT level, and to bulk environment, described by a set of point charges. Nevertheless, the vertical transitions are readily identified. For human serum albumin, our calculations predict distinct spectral characteristics between structures with different tryptophan side chain torsion angles. The computational tractability of TDDFT relative to more accurate ab initio methods allows a large part of the surrounding protein environment (up to 100 atoms) to be explicitly included in the TDDFT calculations.     

On low‐lying excited states of extended nanographenes

Low‐lying excited states of planarly extended nanographenes are investigated using the long‐range corrected (LC) density functional theory (DFT) and the spin‐flip (SF) time‐dependent density functional theory (TDDFT) by exploring the long‐range exchange and double‐excitation correlation effects on the excitation energies, band gaps, and exciton binding energies. Optimizing the geometries of the nanographenes indicates that the long‐range exchange interaction significantly improves the C C bond lengths and amplify their bond length alternations with overall shortening the bond lengths. The calculated TDDFT excitation energies show that long‐range exchange interaction is crucial to provide accurate excitation energies of small nanographenes and dominate the exciton binding energies in the excited states of nanographenes. It is, however, also found that the present long‐range correction may cause the overestimation of the excitation energy for the infinitely wide graphene due to the discrepancy between the calculated band gaps and vertical ionization potential (IP) minus electron affinity (EA) values. Contrasting to the long‐range exchange effects, the SF‐TDDFT calculations show that the double‐excitation correlation effects are negligible in the low‐lying excitations of nanographenes, although this effect is large in the lowest excitation of benzene molecule. It is, therefore, concluded that long‐range exchange interactions should be incorporated in TDDFT calculations to quantitatively investigate the excited states of graphenes, although TDDFT using a present LC functional may provide a considerable excitation energy for the infinitely wide graphene mainly due to the discrepancy between the calculated band gaps and IP–EA values. © 2017 Wiley Periodicals, Inc.     

A unified approach to the density-potential mapping in a family of time-dependent density functional theories

It is shown that the density-potential mapping and the V-representability problems in the time-dependent current density functional theory (TDCDFT) are reduced to the solution of a certain many-body nonlinear Schrödinger equation (NLSE). The derived NLSE for TDCDFT links the earlier NLSE-based formulations of the time-dependent deformation functional theory (TDDefFT) and the time-dependent density functional theory (TDDFT). We establish a close relation between the nonlinear many-body problems which control the existence of TDCDFT, TDDFT, and TDDefFT, and thus develop a unified point of view on the whole family of the TDDFT-type theories.     

Density Functional Study of Tetraphenylporphyrin Long-Range Exciton Coupling

The performance of time-dependent density functional theory (TDDFT) for calculations of long-range exciton circular dichroism (CD) is investigated. Tetraphenylporphyrin (TPP) is used as a representative of a class of strongly absorbing chromophores for which exciton CD with chromophore separations of 50 Å and even beyond has been observed experimentally. A dimer model for TPP is set up to reproduce long-range exciton CD previously observed for a brevetoxin derivative. The calculated CD intensity is consistent with TPP separations of over 40 Å. It is found that a hybrid functional with fully long-range corrected range-separated exchange performs best for full TDDFT calculations of the dimer. The range-separation parameter is optimally tuned for TPP, resulting in a good quality TPP absorption spectrum and small DFT delocalization error (measured by the curvature of the energy calculated as a function of fractional electron numbers). Calculated TDDFT data for the absorption spectra of TPP are also used as input for a ‘matrix method’ (MM) model of the exciton CD. For long-range exciton CD, comparison of MM spectra with full TDDFT CD spectra for the dimer shows that the matrix method is capable of producing very accurate results. A MM spectrum obtained from TPP absorption data calculated with the nonhybrid Becke88–Perdew86 (BP) functional is shown to match the experimental brevetoxin spectrum ‘best’, but for the wrong reasons.     

Rapid and accurate assessment of GPCR–ligand interactions Using the fragment molecular orbital‐based density‐functional tight‐binding method

The reliable and precise evaluation of receptor–ligand interactions and pair‐interaction energy is an essential element of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biological systems due to its high computational cost. Here, the fragment molecular orbital (FMO) method has been used to accelerate QM calculations, and by combining FMO with the density‐functional tight‐binding (DFTB) method we are able to decrease computational cost 1000 times, achieving results in seconds, instead of hours. We have applied FMO‐DFTB to three different GPCR–ligand systems. Our results correlate well with site directed mutagenesis data and findings presented in the published literature, demonstrating that FMO‐DFTB is a rapid and accurate means of GPCR–ligand interactions. © 2017 Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Analytical approach for the excited-state Hessian in time-dependent density functional theory: formalism, implementation, and performance

The paper presents the formalism, implementation, and performance of the analytical approach for the excited-state Hessian in the time-dependent density functional theory (TDDFT) that extends our previous work [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011)] on the analytical Hessian in TDDFT within Tamm-Dancoff approximation (TDA) to full TDDFT. In contrast to TDA-TDDFT, an appreciable advantage of full TDDFT is that it maintains the oscillator strength sum rule, and therefore yields more precise results for the oscillator strength and other related physical quantities. For the excited-state harmonic vibrational frequency calculation, however, full TDDFT does not seem to be advantageous since the numerical tests demonstrate that the accuracy of TDDFT with and without TDA are comparable to each other. As a common practice, the computed harmonic vibrational frequencies are scaled by a suitable scale factor to yield good agreement with the experimental fundamental frequencies. Here we apply both the optimized ground-state and excited-state scale factors to scale the calculated excited-state harmonic frequencies and find that the scaling decreases the root-mean-square errors. The optimized scale factors derived from the excited-state calculations are slightly smaller than those from the ground-state calculations.