Origin of the unusual ultraviolet absorption of Arsenicin A

This paper presents a combined experimental and theoretical study of the electronic spectrum of the natural adamantane-type polyarsenical Arsenicin A. Experiments reveal that this molecule strongly absorbs UV light in the absence of an obvious chromophore. The observed absorbance is supported by the time-dependent density functional (TD-DFT) calculations with B3LYP, M06-L, and M06-2X functionals combined with the 6-311+G(3df,2pd) basis set, as well as by symmetry-adapted cluster/configuration interaction (SAC-CI) theory. The theoretical investigations reveal that the absorption is facilitated by through-space and through-bond interactions, between the lone pairs on the arsenic and oxygen atoms and the σ-bonding framework of the molecule, that destabilize occupied and stabilize unoccupied molecular orbitals.     

Influence of the halogen ligand on the near-UV-visible spectrum of [Ru(X)(Me)(CO)2(alpha-diimine)] (X = Cl, I; alpha-diimine = Me-DAB, iPr-DAB; DAB = 1,4-diaza-1,3-butadiene): an ab initio and TD-DFT analysis

The near-UV-vis electronic spectroscopy of [Ru(X)(Me)(CO)(2)(iPr-DAB)] (X = Cl or I; iPr-DAB = N,N'-di-isopropyl-1,4-diaza-1,3-butadiene) is investigated through CASSCF/CASPT2 and TD-DFT calculations on the model complexes [Ru(X)(Me)(CO)(2)(Me-DAB)] (X = Cl or I). Convergence of the calculated transition energies for the low-lying metal-to-ligand charge-transfer (MLCT), X-to-ligand charge-transfer (XLCT, X halide ligand), or sigma-bond-to-ligand charge-transfer (SBLCT) to experimental values is analyzed for both methods. On the basis of these accurate calculations, it is shown that whereas the lowest singlet state can be assigned to a nearly pure XLCT state in [Ru(I)(Me)(CO)(2)(Me-DAB)], its character is mainly MLCT in [Ru(Cl)(Me)(CO)(2)(Me-DAB)]. These results are in agreement with time-resolved emission/IR and resonance Raman experimental data. The experimental UV-vis bands are well reproduced by the CASSCF/CASPT2 calculations. The TD-DFT transition energies to the long-range charge transfer states are dramatically affected by the nature of the functional, with lowering leading to meaningless values in the case of nonhybrid functionals. Both methods reproduce well the red shift of the absorption bands on going from the chloride to the iodide complex as well as the shift of the strongly absorbing higher MLCT transition from the visible to the UV domain of energy.     

Substituents destabilize the molecule by increasing biradicaloid character and stabilize by intramolecular charge transfer in the derivatives of benzobis(thiadiazole) and thiadiazolothienopyrazine: a computational study

Keeping in view the possible applications of singlet open-shell molecules as semiconductors, non-classical derivatives of the heterocyclic rings benzobis(thiadiazole) (BBT) and its positional isomer thiadiazolothienopyrazine (TTP) are characterized using DFT methodologies. M06-2X, B3LYP and BHandHLYP functionals were used to optimize the geometries and estimate the vertical transition energies. It is observed that unlike the BHandHLYP functional (50% exchange), which gives rise to spin-contaminated solutions for all molecules in the series, M06-2X (54% exchange) affords a wavefunction either with no instability or negligible instability for most of the molecules. The results are compared with the earlier reported experimental data and those obtained herein using the spin-flip (SF)-5050 method. It is found that B3LYP does not fare well while on the other hand the M06-2X and SF-50-50 are in good agreement with the experimental results. It is seen that M06-2X TD-DFT for the molecules can be carried out without major spin contamination and also that the more time-consuming CI can be avoided for the calculation of transition energies. The biradical nature of the molecules is estimated by the singlet-triplet gap. Intramolecular charge transfer is calculated. It is found that the ring substituents donate charge in the ground state, creating a zwitterionic structure. Thus the substituents play an interesting dual role, decreasing the stability of the molecule by increasing the biradical character (small HOMO-LUMO gap), and stabilization of this ground state by intramolecular charge transfer.     

Predicting absorption spectra of silver-ligand complexes

The detailed structures of most of ligand-stabilized metal nanoclusters (NCs) remain unknown due to the absence of crystal structure data for them. In such a situation, quantum-chemical modeling is of particular interest. We compared the performance of different theoretical methods of geometry optimization and absorption spectra calculation for silver-thiolate complexes. We showed that the absorption spectra calculated with the ADC(2) method were consistent with the spectra obtained with CC2 method. Three DFT functionals (B3LYP, CAM-B3LYP, and M06-2X) failed to reproduce the CC2 absorption spectra of the silver-thiolate complexes.     

Optical absorption and emission properties of fluoranthene, benzo[k]fluoranthene, and their derivatives. A DFT study

Fluoranthene and benzo[k]fluoranthene-based oligoarenes are good candidates for organic light-emitting diodes (OLEDs). In this work, the electronic structure and optical properties of fluoranthene, benzo[k]fluoranthene, and their derivatives have been studied using quantum chemical methods. The ground-state structures were optimized using the density functional theory (DFT) methods. The lowest singlet excited state was optimized using time-dependent density functional theory (TD-B3LYP) and configuration interaction singles (CIS) methods. On the basis of ground- and excited-state geometries, the absorption and emission spectra have been calculated using the TD-DFT method with a variety of exchange-correlation functionals. All the calculations were carried out in chloroform medium. The results show that the absorption and emission spectra calculated using the B3LYP functional is in good agreement with the available experimental results. Unlikely, the meta hybrid functionals such as M06HF and M062X underestimate the absorption and emission spectra of all the studied molecules. The calculated absorption and emission wavelength are more or less basis set independent. It has been observed that the substitution of an aromatic ring significantly alters the absorption and emission spectra.     

Nickel-catalyzed alkyl coupling reactions: evaluation of computational methods

The B3LYP, M06, M06L, M062X, MPW1K, and PBE1PBE DFT methods were evaluated for modeling nickel-catalyzed coupling reactions. The reaction consists of a nucleophilic attack by a carbanion equivalent on the nickel complex, S(N)2 attack by the anionic nickel complex on an alkyl halide, and reductive elimination of the coupled alkane product, regenerating the nickel catalyst. On the basis of CCSD(T)//DFT single-point energies, the B3LYP, M06, and PBE1PBE functionals were judged to generate the best ground state geometries. M06 energies are generally comparable or superior to B3LYP and PBE1PBE energies for transition state calculations. The MP2 and CCSD methods were also evaluated for single-point energies at the M06 geometries. The rate-determining step of this reaction was found to be nucleophilic attack of a L(2)NiR anion on the alkyl halide.     

Switchable Nonlinear Optical Properties of η(5)-Monocyclopentadienylmetal Complexes: A DFT Approach

Density functional theory (DFT) calculations have been carried out to investigate the switching of the second-order nonlinear optical (NLO) properties of η(5)-monocyclopentadienyliron(II) and ruthenium(II) model complexes presenting 5-(3-(thiophen-2-yl)benzo[c]thiophen-1-yl)thiophene-2-carbonitrile as a ligand. The switching properties were induced by redox means. Both oxidation and reduction stimulus have been considered, and calculations have been performed both for the complexes and for the free benzo[c]thiophene derivative ligand in order to elucidate the role played by the organometallic fragment on the second-order NLO properties of these complexes. B3LYP, CAM-B3LYP, and M06 functionals were used for our calculations. The results show some important structural changes upon oxidation/reduction that are accompanied by significant differences on the corresponding second-order NLO properties. TD-DFT calculations show that these differences on the second-order NLO response upon oxidation/reduction are due to a change in the charge transfer pattern, in which the organometallic iron and ruthenium moieties play an important role. The calculated static hyperpolarizabilities were found to be strongly functional dependent. CAM-B3LYP, however, seems to predict more reliable structural and optical data as well as hyperpolarizabilities when compared to experimental data. The use of this functional predicts that the studied complexes can be viewed as acting as redox second-order NLO switches, in particular using oxidation stimulus. The β(tot) value of one-electron oxidized species is at least ～8.3 times (for Ru complex) and ～5.5 times (for Fe complex) as large as that of its nonoxidized counterparts.     

Electronic structures and spectroscopic properties of mono- and binuclear d(8) complexes: a theoretical exploration on promising phosphorescent materials

The structures of trans-[M(2)(CN)(4)(PH(2)CH(2)PH(2))(2)] (M = Pt (1), Pd (2), and Ni (3)), trans-[Pt(2)X(4)(PH(2)CH(2)PH(2))(2)] (X = Cl (4) and Br (5)), and trans-[M(CN)(2)(PH(3))(2)] (M = Pt (6), Pd (7), and Ni (8)) in the ground state were optimized using the MP2 method. Frequency calculations reveal that the weak metal-metal interaction is essentially attractive for 1, 2, 4, and 5 but not for 3. The TD-DFT calculations associated with the polarized continuum model (PCM) were performed to predict absorption spectra in CH(2)Cl(2) solution. Experimental spectra are well reproduced by our results. With respect to analogous mononuclear d(8) complexes (6-8), a large red shift of the absorption wavelength was calculated for the binuclear d(8) complexes (1-3). Relative to 1 with unsaturated CN- donors, introduction of saturated halogen donors into 4 and 5 changes their electronic structures, especially the HOMO and LUMO. The TD-DFT and subsequent unrestricted MP2 calculations predict that 1 produces the lowest-energy d --> p emission while 2-5 favor the d --> d emissions, agreeing with experimental observations.     

Solvent effects on electron-driven proton-transfer processes: adenine-thymine base pairs

Time-Dependent Density Functional Theory (TD-DFT) computations, with M05-2X and PBE0 functionals, have been employed for a detailed study of the Electron-Driven Proton-Transfer (PT) processes in an Adenine-Thymine Watson-Crick Base Pair in the gas phase and in solution, with the bulk solvent described by the polarizable continuum model. In the gas phase, TD-DFT computations predict that the Adenine → Thymine Charge Transfer (CT) excited state undergoes a barrierless PT reaction, in agreement with CC2 computations (S. Perun, A. Sobolewski, W. Domcke, J. Phys. Chem. A, 2006, 110, 9031.). The good agreement between the TD-DFT approach and CC2 results validates the former for the studies of excited state properties, excited state proton transfer reaction, and deactivation mechanisms in the DNA base pairs. Next, it is shown that inclusion of solvent effects significantly influences the possibility of both barrier-less excited state proton transfer and radiation-less deactivation through conical intersection with the ground state, affecting the energy of the CT excited state in the Franck-Condon region, the energy barrier associated to the PT process and the energy gap with the ground electronic state. These findings clearly indicate that environmental effects, with a special attention to proper treatment of dynamical solvation effects, have to be included for reliable computational analysis of photophysical and photochemical processes occurring in condensed phases.     

Assessment of the accuracy of density functionals for prediction of relative energies and geometries of low-lying isomers of water hexamers

Water hexamers provide a critical testing ground for validating potential energy surface predictions because they contain structural motifs not present in smaller clusters. We tested the ability of 11 density functionals (four of which are local and seven of which are nonlocal) to accurately predict the relative energies of a series of low-lying water hexamers, relative to the CCSD(T)/aug'-cc-pVTZ level of theory, where CCSD(T) denotes coupled cluster theory with an interative treatment of single and double excitations and a quasi-perturbative treatment of connected triple excitations. Five of the density functionals were tested with two different basis sets, making a total of 16 levels of density functional theory (DFT) tested. When single-point energy calculations are carried out on geometries obtained with second-order M?ller-Plesset perturbation theory (MP2), only three density functionals, M06-L, M05-2X, and M06-2X, are able to correctly predict the relative energy ordering of the hexamers. These three functionals predict that the range of energies spanned by the six isomers is 3.2-5.6 kcal/mol, whereas the other eight functionals predict ranges of 1.0-2.4 kcal/mol; the benchmark value for this range is 3.1 kcal/mol. When the hexamers are optimized at each level of theory, all methods are able to reproduce the MP2 geometries well for all isomers except the boat and bag isomers, and DFT optimization changes the energy ordering for seven of the 16 methods tested. The addition of zero-point energy changes the energy ordering for all of the density functionals studied except for M05-2X and M06-2X. The variation in relative energies predicted by the different methods highlights the necessity for exercising caution in the choice of density functionals used in future studies. Of the 11 density functionals tested, the most accurate results for energies were obtained with the PWB6K, MPWB1K, and M05-2X functionals.     

Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA

The ability of a dinucleoside monophosphate to mimic the conformation of B-DNA was tested using a combination of different phosphate models (anionic, neutral, counterion), environments (gas, water), and density functionals (B3LYP, MPWB1K, M06-2X) with the 6-31G(d,p) basis set. Three sequences (5'-GX(Py)-3', where X(Py) = T, U or (Br)U) were considered, which vary in the (natural or modified) 3' pyrimidine nucleobase (X(Py)). These bases were selected due to their presence in natural DNA, structural similarity to T and/or applications in radical-initiated anti-tumour therapies. The accuracy of each of the 54 model, method and sequence combinations was judged based on the ability to reproduce key structural features of natural B-DNA, including the stacked base-base orientation and important backbone torsion angles. B3LYP yields distorted or tilted relative base-base orientations, while many computational challenges were encountered for MPWB1K. Despite wide use in computational studies of DNA, the neutral (protonated) phosphate model could not consistently predict a stacked arrangement for all sequences. In contrast, stacked base-base arrangements were obtained for all sequences with M06-2X in conjunction with both the anionic and (sodium) counterion phosphate models. However, comparison of calculated and experimental backbone conformations reveals the charge-neutralized counterion phosphate model best mimics B-DNA. Structures optimized with implicit solvent (water) are comparable to gas-phase structures, which suggests similar results should be obtained in an environment of intermediate polarity. We recommend the use of either gas-phase or water M06-2X optimizations with the counterion phosphate model to study the structure and/or reactivity of natural or modified DNA with a dinucleoside monophosphate.     

Gas‐phase doubly charged complexes of cyclic peptides with copper in +1, +2 and +3 formal oxidation states: formation,structures and electron capture dissociation

Copper complexes with a cyclic D‐His‐β‐Ala‐L‐His‐L‐Lys and all‐L‐His‐β‐Ala‐His‐Lys peptides were generated by electrospray which were doubly charged ions that had different formal oxidation states of Cu(I), Cu(II) and Cu(III) and different protonation states of the peptide ligands. Electron capture dissociation showed no substantial differences between the D‐His and L‐His complexes. All complexes underwent peptide cross‐ring cleavages upon electron capture. The modes of ring cleavage depended on the formal oxidation state of the Cu ion and peptide protonation. Density functional theory (DFT) calculations, using the B3LYP with an effective core potential at Cu and M06‐2X functionals, identified several precursor ion structures in which the Cu ion was threecoordinated to pentacoordinated by the His and Lys side‐chain groups and the peptide amide or enolimine groups. The electronic structure of the formally Cu(III) complexes pointed to an effective Cu(I) oxidation state with the other charge residing in the peptide ligand. The relative energies of isomeric complexes of the [Cu(c‐HAHK + H)]²⁺ and [Cu(c‐HAHK ? H)]²⁺ type with closed electronic shells followed similar orders when treated by the B3LYP and M06‐2X functionals. Large differences between relative energies calculated by these methods were obtained for open‐shell complexes of the [Cu(c‐HAHK)]²⁺ type. Charge reduction resulted in lowering the coordination numbers for some Cu complexes that depended on the singlet or triplet spin state being formed. For [Cu(c‐HAHK ? H)]²⁺ complexes, solution H/D exchange involved only the N–H protons, resulting in the exchange of up to seven protons, as established by ultra‐high mass resolution measurements. Contrasting the experiments, DFT calculations found the lowest energy structures for the gas‐phase ions that were deprotonated at the peptide C_α positions. Copyright © 2012 John Wiley & Sons, Ltd.     

Accurate description of van der Waals complexes by density functional theory including empirical corrections

An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT-D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R(-6). The use of pure, gradient-corrected density functionals (BLYP and PBE), together with the resolution-of-the-identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The "double counting" of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene. H2O and four H-bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT-D-BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT-D data may either be used to calibrate much simpler (e.g., force-field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies.     

A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error

We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP.     

Assessment of density functionals and force field methods on anion–π interaction in heterocyclic calix complexes

The performance of ten density functionals and four force field methods in describing non-covalent interactions have been assessed by studying the interaction energies and structures of the four anion–π complexes involving tetraoxacalix[2]arene[2]triazine and various anions. Their structures are optimized at MP2/6-311++G(d,p) level, and interaction energies are obtained at DF-MP2-F12/aug-cc-pVDZ level. The result shows that the functional M06-2X predicts the most reliable interaction energy, followed by wB97XD and BHandH. B97D slightly overestimates the interaction energy. Other functionals and force field methods seriously overestimate the interaction energy. For the structures, three functionals M06-2X, wB97XD and BH and H predict the most reliable results, followed by B97D. The force field methods predict the largest deviations. The present work suggests that the functional M06-2X is a reliable method to describe energies and structural properties of the large molecules involving the anion–π interactions.     

Can TD‐DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case

By using calculations rooted in the time dependent density functional theory (TD-DFT) we have investigated how the lowest energy excited states of a face-to-face pi-stacked cytosine dimer vary with the intermonomer distance (R). The perfomances of different density functionals have been compared, focussing mainly on the lowest energy single excited state of the dimer (S(1))(2). TD-PBE0, TD-LC-omegaPBE, and TD-M05-2X provide a picture very similar to that obtained at the CASPT2 level by Merchan et al. (J Chem Phys 2006, 125, 231102), predicting that (S(1))(2) has a minimum for R approximately 3 A, with a binding energy of approximately 0.5 eV, whereas TD-B3LYP, TD-CAM-B3LYP, and TD-PBE understimate the binding energy. However, independently of the functional employed, no low-energy spurious charge transfer transitions are predicted by TD-DFT calculations, also when a nonsymmetric dimer is investigated, providing encouraging indications for the use of TD-DFT for studying the excited state of pi-stacked nucleobases.     

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

We present two new hybrid meta exchange- correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals.The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree–Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree–Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Contribution to the Mark S. Gordon 65th Birthday Festschrift Issue.     

Charge-transfer excited states in a pi-stacked adenine dimer, as predicted using long-range-corrected time-dependent density functional theory

The lowest few electronic excitations of a pi-stacked adenine dimer in its B-DNA geometry are investigated, in the gas phase and in a water cluster, using a long-range-corrected version of time-dependent density functional theory (TD-DFT) that asymptotically incorporates Hartree-Fock exchange. Long-range correction is shown to eliminate the catastrophic underestimation of charge-transfer (CT) excitation energies that plagues conventional TD-DFT, at the expense of introducing one adjustable parameter, mu, that determines the length scale on which Hartree-Fock exchange is turned on. This parameter allows us to interpolate smoothly between hybrid density functionals and time-dependent Hartree-Fock theory. Excitation energies for CT states (in which an electron is transferred from one adenine molecule to the other) are found to increase dramatically as a function of mu. Uncorrected hybrid functionals underestimate the CT excitation energies, placing them well below the valence excitations, while time-dependent Hartree-Fock calculations place these states well above the valence states. Values for mu determined from certain benchmark calculations place the CT states well above the valence pipi* and npi* states at the Franck-Condon point.