Geometries and properties of excited states in the gas phase and in solution: theory and application of a time-dependent density functional theory polarizable continuum model

Aggregation induced blue-shifted emission – the molecular picture from a QM/MM study

Aggregation induced blue-shifted emission is a consequence of the restricted structural relaxation, excited-state planarization and freezing of low-frequency out-of-plane vibrations.

Quantum mechanical methods for the investigation of metalloproteins and related bioinorganic compounds

It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H2, O2, and N2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure-activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very versatile and often elusive chemistry. For this reason, computational methods are becoming very popular tools in the characterization of metalloproteins. In particular, since computing power is becoming less and less expensive, due to the continuous technological development of CPUs, the computational tools suited to investigate metalloproteins are becoming more accessible and therefore more commonly used also in molecular biology and biochemistry laboratories. Here, we present the main procedures and computational methods based on quantum mechanics, which are commonly used to study the structural, electronic, and reactivity properties of metalloproteins and related bioinspired compounds, with a specific focus on the practical and technical aspects that must be generally tackled to properly study such biomolecular systems.

New semiconducting naphthalene bisimides N-substituted with alkoxyphenyl groups: spectroscopic, electrochemical, structural and electrical properties

Air operating n-channel FETs are obtained from alkoxyphenyl-substituted naphthalene bisimides.

A TDDFT/MMPol/PCM model for the simulation of exciton-coupled circular dichroism spectra

A multiscale strategy is presented to simulate electronic CD spectra of multichromophoric systems using an excitonic approach in which all components are calculated self-consistently through a fully polarizable QM/MM/PCM method.

Reconciliation of chemical, enzymatic, spectroscopic and computational data to assign the absolute configuration of the DNA base lesion spiroiminodihydantoin

The diastereomeric spiroiminodihydantoin-2'-deoxyribonucleoside (dSp) lesions resulting from 2'-deoxyguanosine (dG) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (dOG) oxidation have generated much attention due to their highly mutagenic nature. Their propeller-like shape leads these molecules to display mutational profiles in vivo that are stereochemically dependent. However, there exist conflicting absolute configuration assignments arising from electronic circular dichroism (ECD) and NOESY-NMR experiments; thus, providing definitive assignments of the 3D structure of these molecules is of great interest. In the present body of work, we present data inconsistent with the reported ECD assignments for the dSp diastereomers in the nucleoside context, in which the first eluting isomer from a Hypercarb HPLC column was assigned to be the S configuration, and the second was assigned the R configuration. The following experiments were conducted: (1) determination of the diastereomer ratio of dSp products upon one-electron oxidation of dG in chiral hybrid or propeller G-quadruplexes that expose the re or si face to solvent, respectively; (2) absolute configuration analysis using vibrational circular dichroism (VCD) spectroscopy; (3) reinterpretation of the ECD experimental spectra using time-dependent density functional theory (TDDFT) with the inclusion of 12 explicit H-bonding waters around the Sp free bases; and (4) reevaluation of calculated specific rotations for the Sp enantiomers using the hydration model in the TDDFT calculations. These new insights provide a fresh look at the absolute configuration assignments of the dSp diastereomers in which the first eluting from a Hypercarb-HPLC column is (-)-(R)-dSp and the second is (+)-(S)-dSp. These assignments now provide the basis for understanding the biological significance of the stereochemical dependence of enzymes that process this form of DNA damage.

Electronic excitations in Fischer-type Cr and W aminocarbene complexes: a combined ab initio and experimental study

The influence of the substitution on the carbene ligand in the series of Fischer-type Cr and W aminocarbene complexes was studied experimentally by UV-vis spectroscopy and theoretically by comparative ab initio SA-CASSCF/MS-CASPT2 and TD-DFT methods. Both calculations interpreted the experimental UV-vis spectra and their variations caused by substitution effects well. TD-DFT analysis of individual transitions using electron density redistributions indicated that the variation of the absorption spectra due to substitution is accompanied by a change in the character of the low-lying excited states participating in the visible bands. Correlated MS-CASPT2 calculations confirmed the TD-DFT assignments of the lowest-lying transitions in the visible region almost quantitatively.

Manganese(II) complexes with thiosemicarbazones as potential anti-Mycobacterium tuberculosis agents

Through a systematic variation on the structure of a series of manganese complexes derived from 2-acetylpyridine-N(4)-R-thiosemicarbazones (Hatc-R), structural features have been investigated with the aim of obtaining complexes with potent anti-Mycobacterium tuberculosis activity. The analytical methods used for characterization included FTIR, EPR, UV-visible, elemental analysis, cyclic voltammetry, magnetic susceptibility measurement and single crystal X-ray diffractometry. Density functional theory (DFT) calculations were performed in order to evaluate the contribution of the thiosemicarbazonate ligands on the charge distribution of the complexes by changing the peripheral groups as well as to verify the Mn-donor atoms bond dissociation predisposition. The results obtained are consistent with the monoanionic N,N,S-tridentate coordination of the thiosemicarbazone ligands, resulting in octahedral complexes of the type [Mn(atc-R)2], paramagnetic in the extension of 5 unpaired electrons, whose EPR spectra are consistent for manganese(II). The electrochemical analyses show two nearly reversible processes, which are influenced by the peripheral substituent groups at the N4 position of the atc-R(1-) ligands. The minimal inhibitory concentration (MIC) of these compounds against M. tuberculosis as well as their in vitro cytotoxicity on VERO and J774A.1 cells (IC50) was determined in order to find their selectivity index (SI) (SI=IC50/MIC). The results evidenced that the compounds described here can be considered as promising anti-M. tuberculosis agents, with SI values comparable or better than some commercial drugs available for the tuberculosis treatment.

Synthesis, photophysics and reverse saturable absorption of bipyridyl platinum(II) bis(arylfluorenylacetylide) complexes

A series of Pt(II) bipyridyl complexes with different aryl substituents (Ar = naphthyl (1a), anthryl (1b), pyrenyl (1c) and phenothiazyl (1d)) on the fluorenylacetylide ligands are synthesized and investigated. The influence of the aryl substituent on the photophysics of these complexes is systematically investigated by spectroscopic methods and simulated by time dependent density functional theory (TD-DFT). All complexes exhibit ligand-centered (1)π,π* transitions significantly admixed with the metal-to-ligand charge transfer ((1)MLCT)/ligand-to-ligand charge transfer ((1)LLCT) transitions in the UV and blue spectral region, and broad, structureless (1)MLCT/(1)LLCT absorption bands in the visible spectral region. All complexes are emissive in solution at room temperature, with the fluorescence originating predominantly from the (1)MLCT/(1)LLCT states. The triplet emitting state is dominated by the (3)π,π* state localized on the fluorenylacetylide motif and mixed with some (3)ML'CT character (metal-to-fluorenylacetylide ligand charge transfer) for 1a, 1b and 1d. For 1c, the phosphorescence predominantly originates from the pyrene localized (3)π,π* state. The variation in the photophysical properties is related to the twisting angle of the aryl substituent from the fluorenyl plane, which defines the conjugation between the substituents and fluorenylacetylide ligands and, consequently, alters the energy and intensity of absorption and emission in these complexes. also exhibit broadband triplet excited-state absorption in the visible spectral region. Therefore, they show strong reverse saturable absorption at 532 nm for nanosecond laser pulses as demonstrated by the nonlinear transmission experiment.

General Time Dependent Approach to Vibronic Spectroscopy Including Franck-Condon, Herzberg-Teller, and Duschinsky Effects

An effective time-dependent (TD) approach to compute vibrationally resolved optical spectra from first principles is presented for the computation of one-photon electronic spectra induced by either electric or magnetic transition dipoles or by their mutual interaction, namely absorption, emission, and circular dichroism. Particular care has been devoted to generality, modularity, and numerical stability including all the contributions that play a role at the harmonic level of approximation, namely Franck-Condon, Herzberg-Teller, and Dushinsky (i.e., mode mixing) effects. The implementation shares the same general framework of our previous time-independent (TI) model, thus allowing an effective integration between both approaches with the consequent enhancement of their respective strengths (e.g., spectrum completeness and straightforward account of temperature effects for the TD route versus band resolution and assignment for the TI route) using a single set of starting data. Implementation of both models in the same general computer program allows comprehensive studies using several levels of electronic structure description together with effective account of environmental effects by atomistic and/or continuum models of different sophistication. A few medium-size molecules (furan, phenyl radical, anthracene, dimethyloxirane, coumarin 339) have been studied in order to fully validate the approach.

Probing charge transfer in benzodifuran-C60 dumbbell-type electron donor-acceptor conjugates: ground- and excited-state assays

Rigid electron donor-acceptor conjugates (1-3) that combine π-extended benzodifurans as electron donors and C60 molecules as electron acceptors with different linkers have been synthesized and investigated with respect to intramolecular charge-transfer events. Electrochemistry, fluorescence, and transient absorption measurements revealed tunable and structure-dependent charge-transfer processes in the ground and excited states. Our experimental findings are underpinned by density-functional theory calculations.

Calculating excited state properties using Kohn-Sham density functional theory

The accuracy of excited states calculated with Kohn-Sham density functional theory using the maximum overlap method has been assessed for the calculation of adiabatic excitation energies, excited state structures, and excited state harmonic and anharmonic vibrational frequencies for open-shell singlet excited states. The computed Kohn-Sham adiabatic excitation energies are improved significantly by post self-consistent field spin-purification, but remain too low compared with experiment with a larger error than time-dependent density functional theory. Excited state structures and vibrational frequencies are also improved by spin-purification. The structures show a comparable accuracy to time-dependent density functional theory, while the harmonic vibrational frequencies are found to be more accurate for the majority of vibrational modes. The computed harmonic vibrational frequencies are also further improved by perturbative anharmonic corrections, suggesting a good description of the potential energy surface. Overall, excited state Kohn-Sham density functional theory is shown to provide an efficient method for the calculation of excited state structures and vibrational frequencies in open-shell singlet systems and provides a promising technique that can be applied to study large systems.

Nonlinear absorbing cationic iridium(III) complexes bearing benzothiazolylfluorene motif on the bipyridine (N∧N) ligand: synthesis, photophysics and reverse saturable absorption

Four new heteroleptic cationic Ir(III) complexes bearing benzothiazolylfluorene motif on the bipyridine (N∧N) (1 and 2) and phenylpyridine (C∧N) (3 and 4) ligands are synthesized and characterized. The influence of the position of the substituent and the extent of π-conjugation on the photophysics of these complexes is systematically investigated by spectroscopic methods and simulated by time-dependent density functional theory (TDDFT). The complexes exhibit ligand-centered (1)π,π* transitions with admixtures of (1)ILCT (π(benzothiazolylfluorene) → π*(bpy)) and (1)MLCT (metal-to-ligand charge transfer) characters below 475 nm, and very weak (1,3)MLCT and (1,3)LLCT (ligand-to-ligand charge transfer) transitions above 475 nm. The emission of these complexes at room temperature in CH2Cl2 solutions is ascribed to be predominantly from the (3)MLCT/(3)LLCT states for 1 and from the (3)π,π* state for 2, while the emitting state of 3 and 4 are assigned to be an admixture of (3)MLCT, (3)LLCT, and (3)π,π* characters. The variations of the photophysical properties of 1-4 are attributed to different degrees of π-conjugation in the bipyridine and phenylpyridine ligands induced by different positions of the benzothiazolylfluorenyl substituents on the bipyridine ligand and different extents of π-conjugation in the phenylpyridine ligands, which alters the energy and lifetime of the lowest singlet and triplet excited states. 1-4 all possess broadband transient absorption (TA) upon nanosecond laser excitation, which extends from the visible to the NIR region. Therefore, 1-4 all exhibit strong reverse saturable absorption (RSA) at 532 nm for ns laser pulses. However, the TA of complexes 1, 2, and 3 are much stronger than that of 4. This feature, combined with the difference in ground-state absorption and triplet excited-state quantum yield, result in the difference in RSA strength, which follows this trend: 1 ≈ 2 ≈ 3 > 4. Therefore, complexes 1-3 are strong reverse saturable absorbers at 532 nm and could potentially be used as broadband nonlinear absorbing materials.

Circular dichroism and optical rotation of lactamide and 2-aminopropanol in aqueous solution

The performance of implicit and explicit solvent models (polarizable continuum model (PCM) and microsolvation with positions of water molecules obtained either from molecular dynamics (MD) simulations or quantum mechanical geometry optimization) for calculations of electronic circular dichroism (CD) and optical rotation (OR) is examined for two polar and flexible molecules: lactamide and 2-aminopropanol. The vibrational structure of the CD spectrum is modeled for lactamide. The results are compared with the newly obtained experimental data. The signs of the bands are correctly reproduced using all three methods under investigation and the CAM-B3LYP functional for the CD spectrum of lactamide, but not for 2-aminopropanol. The sign of the calculated optical rotation is correctly predicted by means of PCM, but its magnitude is somewhat underestimated in comparison with experiment for lactamide and overestimated for 2-aminopropanol. To some extent it is rectified by employing explicit hydration. Overall, microsolvation with geometry optimization seems more cost-effective than classical MD, but this is likely to be a consequence of inadequate classical potential and electronic structure model.

Insights for an Accurate Comparison of Computational Data to Experimental Absorption and Emission Spectra: Beyond the Vertical Transition Approximation

In this work we carefully investigate the relationship between computed data and experimental electronic spectra. To that end, we compare both vertical transition energies, EV, and characteristic frequencies of the spectrum like the maximum, ν(max), and the center of gravity, M(1), taking advantage of an analytical expression of M(1) in terms of the parameters of the initial- and final-state potential energy surfaces. After pointing out that, for an accurate comparison, experimental spectra should be preliminarily mapped from wavelength to frequency domain and transformed to normalized lineshapes, we simulate the absorption and emission spectra of several prototypical chromophores, obtaining lineshapes in very good agreement with experimental data. Our results indicate that the customary comparison of experimental ν(max) and computational EV, without taking into account vibrational effects, is not an adequate measure of the performance of an electronic method. In fact, it introduces systematic errors that, in the investigated systems, are on the order of 0.1-0.3 eV, i.e., values comparable to the expected accuracy of the most accurate computational methods. On the contrary, a comparison of experimental and computed M(1) and/or 0-0 transition frequencies provides more robust results. Some rules of thumbs are proposed to help rationalize which kind of correction one should expect when comparing EV, M(1), and ν(max).

Determination of absolute configuration and conformation of a cyclic dipeptide by NMR and chiral spectroscopic methods

Increasing precision of contemporary computational methods makes spectroscopies such as vibrational (VCD) and electronic (ECD) circular dichroism attractive for determination of absolute configurations (AC) of organic compounds. This is, however, difficult for polar, flexible molecules with multiple chiral centers. Typically, a combination of several methods provides the best picture of molecular behavior. As a test case, all possible stereoisomers with known AC (RS, SR, SS, and RR) of the cyclic dipeptide cyclo(Arg-Trp) (CAT) were synthesized, and the performances of the ECD, infrared (IR), VCD, Raman, Raman optical activity (ROA), and nuclear magnetic resonance (NMR) techniques for AC determination were investigated. The spectra were interpreted with the aid of density functional theory (DFT) calculations. Folded geometries stabilized by van der Waals and electrostatic interactions between the diketopiperazine (DKP) ring and the indole group are predicted to be preferred for CAT, with more pronounced folding due to Arg-Trp stacking in the case of SS/RR-CAT. The RS/SR isomers prefer a twist-boat puckering of the DKP ring, which is relatively independent of the orientation of the side chains. Calculated conformer-averaged VCD and ECD spectra explain most of the experimentally observed bands and allow for AC determination of the tryptophan side-chain, whereas the stereochemical configuration of the arginine side-chain is visible only in VCD. NMR studies provide characteristic long-range (2)J(C,H) and (3)J(C,H) coupling constants, and nuclear Overhauser effect (NOE) correlations, which in combination with either ECD or VCD also allow for complete AC determination of CAT.