2015-2019 | Publication Types |
The stability of a variety of linear and cyclic (BN)n (n = 1–3) adducts with N-heterocyclic carbene (ImMe2; ImMe2 = [(HCNMe)2C:]), N-heterocyclic olefin (ImMe2CH2) and Wittig (Me3PCH2) donors has been examined using M05-2X/cc-pVTZ computations. The strength and nature of the bonds have been investigated using natural bond orbital (NBO) and atoms- in-molecules (AIM) analyses. Complementary energy decomposition analysis (EDA-NOCV) has been carried out based on BP86/TZ2P computations. In agreement with NBO and AIM analyses, the orbital interaction energy obtained from EDA con- tributes at least 50% to the total attractive interactions for the carbon–boron bonds indicating their largely covalent nature. The feasibility of isolating monomeric (BN)n units using a donor/acceptor protocol was also investigated in a series of adducts of the general form: LB·(BN)n·BH3 and LB·(BN)n·W(CO)5 (n = 1-3; LB = Lewis bases). Moreover, EDA-NOCV analysis of ImMe2·BN·W(CO)5 and ImMe2·B3N3·W(CO)5 shows that the carbene–boron bonds are stronger in the presence of W(CO)5 as a Lewis acid mainly because of a dramatic decrease in the amount of Pauli repulsion rather than an increase in the electro- static/orbital attraction terms.
The zirconium-mediated syntheses of pinacolboronate (BPin) appended benzo[b]tellurophenes and two phenyl/BPin substituted tellurophene isomers with different colors of emission have been achieved. These species are new additions to an emerging class of inorganic heterocycles that display visible phosphorescence in the solid state under ambient conditions.
The resonance Raman spectra of the 5-halogenated (F, Cl, and Br) uracils are simulated via the Herzberg-Teller (HT) short-time dynamics formalism. The gradient of the S1 excited state is computed at the CAMB3LYP/aug-cc-pVTZ level of theory in the conductor-like Polarizable Continuum Model for water (C-PCM, H2O}), based on the equilibrium geometry determined using PBE0/aug-cc-pVTZ in H2O (C-PCM). The simulated resonance Raman spectra show good agreement with the experimental spectra both in terms of peak positions and intensities. The differences between the resonance Raman spectra of the three 5-halogenated uracils, caused by the effect of halogen substitution, are examined in terms of ground state normal mode eigenvectors and excited state Cartesian gradients, according to the HT formalism. The differences in the normal mode eigenvectors and excited state Cartesian gradients between 5-fluorouracil and 5-chlorouracil are used to interpret the dissimilarity between their resonance Raman spectra. Meanwhile, the similarity between the spectra of 5-chlorouracil and 5-bromouracil is explained by the correspondence between their normal modes and excited state gradients.
Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool characterized by deep tissue penetration and little damage. However, two-photon spectroscopy has lower sensitivity than one-photon microscopy alternatives and hence a protein with a large two-photon absorption cross-section is needed. We use time-dependent density functional theory (TD-DFT) at the B3LYP/6-31+G(d,p) level of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the green fluorescent protein (GFP) chromophore with a non-canonical amino acid. A proposed chromophore with a nitro substituent was found to have a large two-photon absorption cross-section (29 GM) compared to other fluorescent protein chromophores as determined at the same level of theory. Classical molecular dynamics are then performed on a nitro-modified fluorescent protein to test its stability and study the effect of the conformational flexibility of the chromophore on its two-photon absorption cross-section. The theoretical results show that the large cross-section is primarily due to the difference between the permanent dipole moments of the excited and ground states of the nitro-modified chromophore. This large difference is maintained through the various conformations assumed by the chromophore in the protein cavity. The nitro-derived protein appears to be very promising as a two-photon absorption probe.
The vertical excitation energies of 17 boron-dipyrromethene (BODIPY) core structures with a variety of substituents and ring sizes are benchmarked using time-dependent density functional theory (TD-DFT) with nine different functionals combined with the cc-pVTZ basis set. When compared to experimental measurements, all functionals provide mean absolute errors (Mean AEs) greater than 0.3 eV; larger than the 0.1-0.3 eV differences typically expected from TD-DFT. Due to the high linear correlation of TD-DFT results with experiment, most functionals can be used to predict excitation energies if corrected empirically. Using the CAM–B3LYP functional, 0-0 transition energies are determined and, while the absolute difference is improved (Mean AE = 0.478 eV compared to 0.579 eV), the correlation diminishes substantially (R2 of 0.961 to 0.862). Two very recently introduced charge transfer (CT) indices, qCT and dCT, and electron density difference (EDD) plots demonstrate that CT does not play a significant role for most of the BODIPYs examined, and, thus cannot be the source of error in TD-DFT. Therefore, vertical excitation energies are determined utilizing TD-HF, configuration interaction CIS and CIS(D), equation of motion EOM-CCSD, SAC-CI, and Laplace-transform based local coupled-cluster singles and doubles LCC2* methods. Moreover, multi-reference CASSCF and CASPT2 vertical excitation energies were also obtained for all species (except CASPT2 was not feasible for the 4 largest systems). The SAC-CI/cc-pVDZ, LCC2*/cc-pVDZ, and CASPT2/cc-pVDZ approaches are shown to have the smallest Mean AEs of 0.154 eV, 0.109 eV, and 0.100 eV, respectively; the utility of the LCC2* approach is demonstrated for 8 extended BODIPYs and aza-BODIPYs. The problems with TD-DFT arise from difficulties in dealing with the differential electron correlation (as assessed by comparing CCS, CC2, LR-CCSD, CCSDR(T), and CCSDR(3) vertical excitation energies for 5 compounds) and from contributions of multi-reference character and double excitations (from analysis of the CASSCF wave functions).
We present a computational study on two flavonols that were recently isolated from Loranthaceae family plant extracts: kaempferol 3-O-α-L-arabinofuranosyl-(1 → 3)-α-L-rhamnoside and quercetin 3-O-α-L-arabinofuranosyl-(1 → 3)-α-L-rhamnoside. Their structures and energetics have been investigated at the density functional level of theory, up to B3LYP/6-31+G(d,p), incorporating solvent effects with polarizable continuum models. In addition, their potential antioxidant activities were probed through the computation of the (i) bond dissociation enthalpies (BDEs), which are related to the hydrogen-atom transfer mechanism (HAT), and (ii) ionization potentials (IPs), which are related to the single-electron transfer mechanism (SET). The BDEs were determined in water to be 83.23 kcal/mol for kaempferol 3-O-α-L-arabinofuranosyl-(1 → 3)-α-L-rhamnoside and 77.49 kcal/mol for quercetin 3-O-α-L-arabinofuranosyl-(1 → 3)-α-L-rhamnoside. The corresponding IPs were obtained for both compounds as 133.38 and 130.99 kcal/mol, respectively. The BDEs and IPs are comparable to those probed for their parental molecules kaempferol and quercetin; this is in marked contrast to previous studies where glycosylation at the 3-position increases the corresponding BDEs, and, hence, decreases subsequent antioxidant activity. The BDEs and IPs obtained suggest both compounds are promising for antioxidant activity and thus further experimental tests are encouraged.
A series of 11 different boron−dipyrromethene
(BODIPY) dimers is carefully examined by means of ab initio and
Tamm−Dancoff approximated density functional theory meth-
ods. Vertical and 0−0 excitation energies along with the
tetraradical character of these dimers are determined. Possible
application of a series of linked dimers for photodynamic therapy
(PDT) was investigated through computing their excitation
energies, spin−orbit coupling matrix elements, and singlet−triplet
energy gaps. Finally through a systematic investigation of a series of 36 different BODIPY and aza-BODIPY dimers, a new class of near-IR heavy atom free photosensitizers for PDT action is introduced.
The tetrameric red fluorescent protein from Discosoma sp. coral (DsRed) has previously been engineered to produce dimeric and monomeric fluorescent variants with excitation and emission profiles that span the visible spectrum. The brightest of the effectively monomeric DsRed variants is tdTomato − a tandem fusion of a dimeric DsRed variant. Here we describe the engineering of brighter red (RRvT), green (GGvT), and green-red heterodimeric (GRvT), tdTomato variants. GRvT exhibits 99% intramolecular Förster resonance energy transfer (FRET) efficiency, resulting in long Stokes shift red fluorescence. These new variants may prove useful for multicolor live cell imaging applications.
We have constructed a (semi)-global six-dimensional potential energy surface (PES) for HFCO, incorporating the equilibrium, cis- and trans-isomers (HOCF) as well as the transition states connecting them. The PES is based on a fit to 15000 CCSD(T)-F12/cc-pVTZ-F12 ab initio energies. The sum-of-products PES, obtained using neural network exponential fitting functions, was used to compute vibrational state frequencies using block improved relaxation with the multiconfiguration time dependent Hartree (MCTDH) approach. The PES is accurate (RMSE = 130 cm-1) up to 40000 cm-1 above the minimum energy. The equilibrium region of the PES was fit very well based on a comparison of the vibrational frequencies with those from a recent local HFCO PES [J. Chem. Phys. 144, 174305 (2016)] and experimental measurements (RMSE = 10.9 cm-1 compared to experiment). The vibrational frequencies for the trans- and cis-isomers are computed from the PES and compared to anharmonic MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ results; the trans-and cis-isomers have yet to be detected experimentally. Based on the accuracy of the vibrational energies at equilibrium, the present results for the cis- and trans-isomers could facilitate the identification of these species. The PES will also enable the study of intramolecular vibrational energy redistribution and its control leading to the elusive equilibrium to trans-conversion.
Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool known for deep tissue penetration and little cellular damage. Being less sensitive than the one-photon microscopy alternatives, a protein with a large two-photon absorption (TPA) cross-section is needed. Here, we use time-dependent density functional theory (TD-DFT) at the B3LYP and CAM-B3LYP/6-31+G(d,p) levels of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the red fluorescent protein (RFP) chromophore with a non-canonical amino acid. The two-level model for TPA was used to assess the properties (i.e., transition dipole moment, permanent dipole moment difference, and the angle between them) leading to the TPA cross-sections determined via response theory. Computing TPA cross-sections with B3LYP and CAM-B3LYP yield similar overall trends. Results using both functionals agree that the RFP-derived model of the Gold Fluorescent Protein chromophore (Model 20) has the largest intrinsic TPA cross-section. TPA was further computed for selected chromophores following conformational changes: variation of both the dihedral angle of the acylimine moiety and the tilt and twist angles between the rings of the chromophore. The TPA cross-section assumed an oscillatory trend with the rotation of the acylimine dihedral, and the TPA is maximized in the planar conformation for almost all models. Model 21 (a hydroxyquinoline derivative) is shown to be comparable to model 20 in terms of TPA cross-section. The conformational study on Model 21 shows that the acylimine angle has a much stronger effect on the TPA than its tilt and twist angles. Having an intrinsic TPA ability that is more than 7 times that of the native RFP chromophore, Models 20 and 21 appear to be very promising for future experimental investigation.
The HBrO2 isomers have been analyzed computationally to confirm the previous experimental assignments for HOOBr and HOBrO, and to assist in future identification of the as yet unobserved HBr(O)O isomer. Optimized geometries of the HOOBr, HOBrO and HBr(O)O isomers and the transition states connecting them were obtained at the CCSD(T)/O, H: aug-cc-pVTZ, Br: aug-cc-pVTZ-PP level of theory. The corresponding harmonic vibrational frequencies for the HOOBr, HOBrO and HBr(O)O isomers are reported for all isotopologues considered in the experimental measurements, i.e., those involving hydrogen, deuterium, 79Br, 81Br, 16O, and 18O. The relative energetics of the stationary point geometries were determined through extrapolation of energies to the complete basis set limit. To explain the photodestruction observed experimentally for HOOBr and HOBrO, the three lowest low-lying singlet and triplet excited electronic states for each of the three isomers were computed using the equation-of-motion coupled-cluster with inclusion of single and double excitations (EOM-CCSD) and time-dependent density functional theory (TD-B3LYP and TD-CAM-B3LYP) approaches; all utilizing the all-electron aug-cc-pVTZ basis sets for all atoms. Multi-reference configuration interaction (MRCI)/aug-cc-pVTZ computations were carried out for the lowest singlet and lowest two triplet excited states. The vertical excitation energies for the low-lying excited states of the most stable isomer (HOOBr) are reported for the first time. The vibrational frequencies for the HBrO2 isomers are used along with new anharmonic vibrational frequency computations (at the PBE0/aug-cc-pVTZ level of theory) and vertical excitation energies (at the TD-B3LYP/aug-cc-pVTZ, TD-CAMB3LYP/aug-cc-pVTZ, and EOM-CCSD/aug-cc-pVTZ levels of theory) for the HBrO3 isomers, HOOOBr and HOOBrO, to determine that previously unassigned peaks in the experimental spectrum generated from HBr/O2 photolysis in a Ne-matrix belong to HOOOBr.
Two-photon absorption (TPA) leads to higher-energy excited electronic states via the simultaneous absorption of two photons. In TPA, the absorption is directly proportional to the square of incident light intensity, and thus lasers are required for excitation. The advantages of TPA microscopy include better focus and less out-of-focus bleaching, together with absorption at longer wavelengths than in one-photon absorption, which leads to deeper penetration in scattering media, such as tissues. However, TPA probes are usually associated with less sensitivity, and thus designing TPA fluorophores with large absorption probability is an important area of research. TPA of biological molecules like fluorescent proteins and nucleic acids is of particular interest. These molecules are experimentally produced through utilization of the naturally present transcription mechanism in the cell and thus pose less cell toxicity. In this chapter, we review the theory of TPA highlighting the computational approaches used to study biological molecules. We discuss the computational methods available for exploring TPA and recent computational studies on the TPA of fluorescent proteins and nucleic acid base analogues. The chapter concludes by highlighting possible research avenues and unanswered questions.
A six-dimensional potential energy surface (PES) for formyl fluoride (HFCO) is fit in a sum-of-products form using neural network exponential fitting functions. The ab initio data upon which the fit is based were computed at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations [CCSD(T)-F12]/cc-pVTZ-F12 level of theory. The PES fit is accurate (RMSE = 10 cm−1) up to 10 000 cm−1 above the zero point energy and covers most of the experimentally measured IR data. The PES is validated by computing vibrational energies for both HFCO and deuterated formyl fluoride (DFCO) using block improved relaxation with the multi-configuration time dependent Hartree approach. The frequencies of the fundamental modes, and all other vibrational states up to 5000 cm−1 above the zero-point energy, are more accurate than those obtained from the previous MP2-based PES. The vibrational frequencies obtained on the PES are compared to anharmonic frequencies at the MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ levels of theory obtained using second-order vibrational perturbation theory. The new PES will be useful for quantum dynamics simulations for both HFCO and DFCO, e.g., studies of intramolecular vibrational redistribution leading to unimolecular dissociation and its laser control.
The minimum energy structures, i.e., trans-HONO, cis-HONO, HNO2, and OH + NO, as well as the corresponding transition states, i.e., TStrans↔cis, TS1,2H−shift, and TS1,3H−shift, on the ground state potential energy surface (PES) of HONO have been characterized at the CCSD(T)-F12/cc-pVTZ- F12 level of theory. Using the same level of theory, a six-dimensional (6D) PES, encompassing the trans- and cis-isomers as well as the associated transition state, is fit in a sum-of-products form using neural network exponential fitting functions. A second PES is developed based on ab initio data from CCSD(T) computations extrapolated to the complete basis set (CBS) limit. The PES fits, based on 90 neurons, are accurate (RMSEs ≈ 10 cm−1) up to 10000 cm−1 above the energy minimum. The PESs are validated by computing vibrational energies using block im- proved relaxation with the multi configuration time dependent Hartree (MCTDH) approach. The vibrational frequencies obtained on the PESs are compared to available experimental measure- ments, previous theoretical computations based on a CCSD(T)/cc-pVQZ(-g functions) PES, and anharmonic frequencies at the MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ levels of theory ob- tained using second-order vibrational perturbation theory. The results suggest that these are the best available PESs for HONO, and thus, should be suitable for a variety of dynamics studies, including quantum dynamics with MCTDH where the sum-of-products form can be exploited for computational efficiency.
The authors study adjustable bandgap properties of the novel triple chalcogenophene-based polymer poly-(3-hexyl-2(3-(4-hexylthiophene-2-yl)-4,5-butylselenophene-1-yl)-5-(4,5-butyltellurophene-1-yl)thiophene) through a combination of morphological, spectroscopic, and computational techniques. The bandgap can be tuned after polymerization by means of mild temperature annealing, which will allow for a partnership with a broader range of donor/acceptor molecules, a property that makes it potentially suitable for organic photovoltaic implementation. The bandgap is modified by selection of the annealing temperatures, and the process is arguably related to the aggregation of tellurophene units, as similar effects are observed in polytellurophenes. Moreover, adequate chemistry engineering ensures easy solution processability and attainment of homogeneous films, which is also essential for applications.
The effects of explicit hydrogen bonding with H2O on the resonance Ra- man spectra of uracil and thymine are examined computationally. The three bonding sites in uracil and thymine that form the lowest energy uracil-H2O and thymine-H2O complexes, as well as a more limited number of low-lying ones containing two waters, are considered. The ground state structures are optimized at the PBE0/aug-cc-pVTZ level of theory in H2O (C-PCM), and the gradients of the bright excited state (S1) are computed at the TD-CAM- B3LYP/aug-cc-pVTZ level of theory in H2O (C-PCM). As the resonance Raman spectrum is governed by the ground state normal modes and the excited state Cartesian gradient (within the Herzberg-Teller formalism), the differences between spectra of uracil- and thymine-(H2O)n, n = 1 or 2, are compared in terms of these two factors. Explicit hydrogen bonding to wa- ter is found to cause changes in both relative peak positions and intensities for the resonance Raman spectra of uracil and thymine when compared to the isolated molecules. The effect of hydrogen bonding is primarily on the ground state normal mode character, especially for the high frequency modes (> 1600 cm−1), rather than on the excited state Cartesian gradients. Dif- ferent hydrogen bonding sites are found to have different contributions to the resulting resonance Raman spectra, and inclusion of explicit hydrogen bonding on the carbonyl bond opposite to the ring nitrogen is necessary to obtain good agreement between the simulated and experimental resonance Raman spectra for uracil and thymine.
In this review, the use of the neural network method with exponential neurons for directly fitting ab initio data to generate potential energy surfaces (PESs) in sum-of-product form will be discussed. The utility of the approach will be highlighted using fits of CS2, HFCO, and HONO ground state PESs based upon high-level ab initio data. Using a generic interface between the neural network PES fitting, which is performed in MATLAB, and the Heidelberg multi-configuration time-dependent Hartree (MCTDH) software package, the PESs have been tested via comparison of vibrational energies to experimental mea- surements. The review demonstrates the potential of the PES fitting method, combined with MCTDH, to tackle high-dimensional quantum dynamics problems.
Previous research in our group showed that tellurophenes with pinacolboronate (BPin) units at the 2- and/or 5-positions displayed efficient phosphorescence in the solid state, both in the presence of oxygen and water. In this current study, we show that luminescence from a tellurophene is possible when various aryl-based substituents are present, thus greatly expanding the family of known (and potentially accessible) Te-based phosphors. Moreover, for the green phosphorescent perborylated tellurium heterocycle, 2,3,4,5-TeC4BPin4 (4BTe), oxygen-mediated quenching of phosphorescence is an important contributor to the lack of emission in solution (when exposed to air); thus this system displays aggregation-enhanced emission (AEE). These discoveries should facilitate the future design of color tunable tellurium-based luminogens.
In this article our attempts to tune the color of luminescence within a new class of aggregation-induced emission (AIE) active tellurophenes is reported along with computational details that include spin-orbit coupling effects so as to better undestand the nature of emission in the phosphorescent tellurophene (B-Te-6-B). Despite not meeting some of the initial synthetic targets, the emission within a borylated tellurophene can be altered by addition of an N-heterocyclic carbene.
A well-defined Ir-allyl complex catalyzes the Z-selective cross-coupling of allyl carbonates with α-aryl diazo esters. The process overrides the large thermodynamic preference for E-products typically observed in metal-mediated coupling reactions to enable the synthesis of Z,E-dieneoates in good yield with selectivities consistently approaching or greater than 90:10. This transformation represents the first productive merger of Ir-carbene and Ir-allyl species, which are commonly encountered intermediates in allylation and cyclopropanation/E–H insertion catalysis. Potentially reactive functional groups (aryl halides, ketones, nitriles, olefins, amines) are tolerated owing to the mildness of reaction conditions. Kinetic analysis of the reaction suggests oxidative addition of the allyl carbonate to an Ir-species is rate-determining. Mechanistic studies uncovered a pathway for catalyst activation mediated by NEt3.