Efficient calculation of electronic coupling integrals with the dimer projection method via a density matrix tight-binding potential

Designing organic semiconductors for practical applications in organic solar cells, organic field-effect transistors, and organic light-emitting diodes requires understanding charge transfer mechanisms across different length and time scales. The underlying electron transfer mechanisms can be efficiently explored using semiempirical quantum mechanical (SQM) methods. The dimer projection (DIPRO) method combined with the recently introduced non-self-consistent density matrix tight-binding potential (PTB) [Grimme et al., J. Chem. Phys. 158, 124111 (2023)] is used in this study to evaluate charge transfer integrals important for understanding charge transport mechanisms. PTB, parameterized for the entire Periodic Table up to Z = 86, incorporates approximate non-local exchange, allowing for efficient and accurate calculations for large hetero-organic compounds. Benchmarking against established databases, such as Blumberger's HAB sets, or our newly introduced JAB69 set and comparing with high-level reference data from ωB97X-D4 calculations confirm that DIPRO@PTB consistently performs well among the tested SQM approaches for calculating coupling integrals. DIPRO@PTB yields reasonably accurate results at low computational cost, making it suitable for screening purposes and applications to large systems, such as metal-organic frameworks and cyanine-based molecular aggregates further discussed in this work.

TBMaLT, a flexible toolkit for combining tight-binding and machine learning

Tight-binding approaches, especially the Density Functional Tight-Binding (DFTB) and the extended tight-binding schemes, allow for efficient quantum mechanical simulations of large systems and long-time scales. They are derived from ab initio density functional theory using pragmatic approximations and some empirical terms, ensuring a fine balance between speed and accuracy. Their accuracy can be improved by tuning the empirical parameters using machine learning techniques, especially when information about the local environment of the atoms is incorporated. As the significant quantum mechanical contributions are still provided by the tight-binding models, and only short-ranged corrections are fitted, the learning procedure is typically shorter and more transferable as it were with predicting the quantum mechanical properties directly with machine learning without an underlying physically motivated model. As a further advantage, derived quantum mechanical quantities can be calculated based on the tight-binding model without the need for additional learning. We have developed the open-source framework-Tight-Binding Machine Learning Toolkit-which allows the easy implementation of such combined approaches. The toolkit currently contains layers for the DFTB method and an interface to the GFN1-xTB Hamiltonian, but due to its modular structure and its well-defined interfaces, additional atom-based schemes can be implemented easily. We are discussing the general structure of the framework, some essential implementation details, and several proof-of-concept applications demonstrating the perspectives of the combined methods and the functionality of the toolkit.

N-Methylimidazolidin-4-one organocatalysts: gas-phase fragmentations of radical cations by experiment and theory

Electron ionisation mass spectra of N-methylimidazolidin-4-one organocatalysts were studied by experimental and theoretical means. The molecular ions mostly undergo alpha cleavages of exocyclic substituents that leave the five-membered ring intact. The type of substituent strongly dominates the appearance of the spectra. Fragmentation cascades are corroborated by metastable ion mass spectra. Quantum Chemistry Electron Ionisation Mass Spectra calculations correlate reasonably well with the experimental electron ionisation spectra and reveal mechanistic details of fragmentation pathways. The drawbacks and benefits of such calculations are discussed. Copyright © 2017 John Wiley & Sons, Ltd.

Synthesis of a monomolecular anionic FLP complex

Despite intense research in FLP chemistry, nothing is known about monomolecular anionic FLPs and/or complexes thereof. Herein, synthesis and reaction of the first anionic FLP complex is described using [(OC)₅W{(Me₃Si)₂HCP(H)OLi(12-crown-4)}], Cy₂BCl and subsequent deprotonation by KHMDS. The obtained anionic FLP complex reacts readily with CO₂ in a concerted manner.

Synthesis of novel pyridyl containing phospholanes and their polynuclear luminescent copper(i) complexes

A novel type of cyclic P,N-ligands, pyridyl containing phospholanes, has been synthesized in a moderate yield by the reaction of primary phosphines with 1,4-dichlorobutane in a superbasic medium. A series of homo tetranuclear octahedral Cu4I4L2, dinuclear tetrahedral Cu2I2L3, and dinuclear "head-to-tail" Cu2I2L2 luminescent complexes with these ligands were obtained. All the compounds were characterized using a range of spectroscopic and computational techniques, and in the case of some Cu4I4L2 and Cu2I2L3 complexes, by single crystal X-ray diffraction. The structural diversity of the obtained complexes was reflected in their photophysical properties: phosphorescence spectra of the compounds display emission in broad spectral range of 471-615 nm. TD-DFT computations allow the assignment of a single emission band around 550 nm for Cu2I2L3 complexes and 471 nm for Cu2I2L2 complex to a vertical triplet-singlet transition from a metal-to-ligand and halide-to-ligand charge-transfer (3)(M + X)LCT excited state, whereas a second band at around 600 nm in the spectra of octahedral Cu4I4L2 complexes was assigned predominantly to Cu4I4 cluster-centered ((3)CC) excited state.

Quantum Chemical Investigation of Spin-Forbidden Transitions in Dithiosuccinimide

The vertical and adiabatic electronic spectra of dithiosuccinimide have been investigated by means of multi-reference Møller–Plesset perturbation theory and combined densitiy functional/multi-reference configuration interaction methods. Geometries of the electronic ground state and several low-lying excited states have been optimised at the level of time-dependent density functional theory. We have determined spin-orbit coupling for correlated wavefunctions utilising a non-empirical spin-orbit mean-field approach. Because of the two thiocarbonyl groups present in the molecule, dithiosuccinimide exhibits a dense spectrum of low-lying valence states. The first two excited singlet states (S 1 and S 2) originate from n → π* excitations. Nearby, three triplet states are located, two n → π* states (T 1 and T 2), and a π → π* triplet excitation (T 3). The experimentally observed strong absorption band with maximum at 3.96 eV arises from the π → π* excited 1 B 2 (S 3) state. Computed radiative lifetimes are presented for the experimentally known phosphorescence from the n → π* excited T 1 state. Further, we find nearly equal probabilities for the spin-forbidden S 0 → T 2 and the spin-allowed S 0 → S 1 transitions in absorption. On these grounds, we assign band number 3 in the spectra measured by Meskers et al. [J. Phys. Chem. 99 (1995) 1134] to this spin-forbidden transition.

A comparative quantum chemical study of the ruthenium catalyzed olefin metathesis

The accurate quantum mechanical description of homogeneous catalysis involving transition-metal complexes is a complicated and computationally demanding task. Hence, in this study the performance of different quantum chemical approaches with respect to the ruthenium catalyzed olefin metathesis of ethylene and RuCl(2)(PH(3))(2)CH(2) as a model system is investigated. All intermediates and transition states that are relevant for the rate determining steps of competing reaction mechanisms (associative and two dissociative pathways) are considered. Results from density functional theory calculations employing B-P86, B97-D, B3-LYP, TPSSh, and B2-PLYP functionals, as well as from MP2 and SCS-MP2 perturbation theory are compared to reference values (relative and reaction energies) obtained at the QCISD(T) level of theory. In particular, the applicability of AO basis sets of increasing size ranging from double-zeta to quadruple-zeta quality is evaluated for representative methods. For some reaction steps, large basis set effects on the order of 10 kcal mol(-1) (50% of Delta E) are observed. Double-zeta type basis sets yield very unreliable results while properly polarized triple-zeta sets provide reaction energies quite close to the basis set limit. The performance of recommended methods is B2-PLYP>TPSSh>B-86 approximately B97-D>SCS-MP2. The often used standard approaches B3-LYP and MP2 provide overall the largest errors. The accurate QCISD(T) computations predict in conclusion (and in agreement with a recent other study) that for the model system considered, the dissociative trans pathway is favored over the dissociative cis pathway and also over the associative reaction mechanism.

Systematic quantum chemical study of DNA-base tautomers

The relative energies of the energetically low-lying tautomers of pyridone, cytosine, uracil, thymine, guanine, and iso-cytosine are studied by a variety of different quantum chemical methods. In particular, we employ density functional theory (DFT) using the six functionals HCTH407, PBE, BP86, B-LYP, B3-LYP, and BH-LYP, and the ab initio methods Hartree-Fock (HF), standard second-order Møller-Plesset perturbation theory (MP2), an improved version of it (SCS-MP2), and quadratic configuration interaction including single and double excitations (QCISD) and perturbative triple corrections [QCISD(T)]. A detailed basis set study is performed for the formamide/formamidic acid tautomeric pair. In general, large AO basis sets of at least valence triple-zeta quality including f-functions (TZV) are employed, which are found to be necessary for an accurate energetic description of the various structures. The performance of the more approximate methods is evaluated with QCISD(T)/TZV(2df,2dp) data taken as reference. In general it is found that DFT is not an appropriate method for the problem. For the tautomers of pyridone and cytosine, most density functionals, including the popular B3-LYP hybrid, predict a wrong energetic order, and only for guanine, the correct sequence of tautomers is obtained with all functionals. Out of the density functionals tested, BH-LYP, which includes a rather large fraction of HF exchange, performs best. A consistent description of the nonaromatic versus aromatic tautomers seems to be a general problem especially for pure, nonhybrid functionals. Tentatively, this could be assigned to the exchange potentials used while the functional itself, including the correlation part, seems to be appropriate. Out of the ab initio methods tested, the new SCS-MP2 approach seems to perform best because it effectively reduces some outliers obtained with standard MP2. It outperforms the much more costly QCISD method and seems to be a very good compromise between computational effort and accuracy.

High level ab initio calculations of the optical gap of small silicon quantum dots

Using state of the art time-dependent density functional theory and multireference second-order perturbation theory, we have accurately calculated (within 0.3 eV) in real space the optical gap of small silicon quantum dots, with diameters up to 25 A. Our results, which support the quantum confinement hypothesis, are in excellent agreement with recent and earlier experimental data on oxygen-free samples and the conclusions of Wilcoxon et al. [Phys. Rev. B 60, 2704 (1999)]. We have found that the diameter of the smallest dot, which could emit photoluminescence in the visible region of the spectrum, is around 22 A. Our work can resolve existing controversies and bridge diverse experimental and theoretical results.

Endocytosis of insulin-like growth factor II by a mini-receptor based on repeat 11 of the mannose 6-phosphate/insulin-like growth factor II receptor

The mannose 6-phosphate/insulin-like growth factor II receptor (M6P/IGF-II receptor) plays an important role in controlling the extracellular level of the insulin-like growth factor II (IGF-II) by mediating its binding at the cell surface and delivery to lysosomes. Loss of the receptor is associated with an accumulation of IGF-II, which can cause perinatal lethality if it is systemic, or local proliferation and tumorgenesis if it is spatially restricted. The extracytoplasmic domain of the receptor consists of 15 homologous repeats, of which repeat 11 carries the IGF-II-binding site of the multifunctional receptor. To investigate whether repeat 11 is sufficient to mediate binding and internalization of IGF-II, a construct consisting of repeat 11 fused to the transmembrane and cytoplasmic domain of the M6P/IGF-II receptor was transfected into mouse embryonic fibroblasts. The construct was expressed as a stable membrane protein which binds IGF-II with a 10-fold lower affinity as observed for the M6P/IGF-II receptor and is found at the cell surface and in endosomes. It mediates the internalization of IGF-II and its delivery to lysosomes, suggesting that it can function as a IGF-II mini-receptor controlling the extracellular IGF-II level.

Characterization of cobalt(II)-substituted peptide deformylase: function of the metal ion and the catalytic residue Glu-133

Peptide deformylase (PDF) catalyzes the hydrolytic removal of the N-terminal formyl group from nascent ribosome-synthesized polypeptides in eubacteria. PDF represents a novel class of mononuclear iron protein, which utilizes an Fe(2+) ion to catalyze the hydrolysis of an amide bond. This Fe(2+) enzyme is, however, extremely labile, undergoing rapid inactivation upon exposure to molecular oxygen, and is spectroscopically silent. In this work, we have replaced the native Fe(2+) ion with the spectroscopically active Co(2+) ion through overexpression in the presence of Co(2+). Co(2+)-substituted PDF (Co-PDF) has an activity 3-10-fold lower than that of the Fe(2+)-PDF but is highly stable. Steady-state kinetic assays using a series of substrates of varying deformylation rates indicate that Co-PDF has the same substrate specificity as the native enzyme. Co-PDF and Fe-PDF also share the same three-dimensional structure, pH sensitivity, and inhibition pattern by various effector molecules. These results demonstrate that Co-PDF can be used as a stable surrogate of Fe-PDF for biochemical characterization and inhibitor screening. The electronic absorption properties of the Co(2+) ion were utilized as a probe to monitor changes in the enzyme active site as a result of site-directed mutations, inhibitor binding, and changes in pH. Mutation of Glu-133 to an alanine completely abolishes the catalytic activity, whereas mutation to an aspartate results in only approximately 10-fold reduction in activity. Analysis of their absorption spectra under various pH conditions reveals pK(a) values of 6.5 and 5.6 for the metal-bound water in E133A and E133D Co-PDF, respectively, suggesting that the metal ion alone is capable of ionizing the water molecule to generate the catalytic nucleophile, a metal-bound hydroxide. On the other hand, substrate binding to the E133A mutant induces little spectral change, indicating that in the E.S complex the formyl carbonyl oxygen is not coordinated with the metal ion. These results demonstrate that the function of the active-site metal is to activate the water molecule, whereas Glu-133 acts primarily as a general acid, donating a proton to the leaving amide ion during the decomposition of the tetrahedral intermediate.

Deoxycytidine kinase and deoxyguanosine kinase of Lactobacillus acidophilus R-26 are colinear products of a single gene

Three of the four deoxynucleoside kinases required for growth of Lactobacillus acidophilus R-26 exist as heterodimeric pairs specific for deoxyadenosine (dAK) and deoxycytidine (dCK) or dAK and deoxyguanosine (dGK). However, only two tandem genes, dak/dgk, are found, and are expressed only as dAK/dGK in transformed Escherichia coli. Sequencing peptides spanning 63% of the native dCK subunit revealed a sequence identical to that deduced from dgk (beginning MTVIVL...), except that dCK lacks residues 2 and 3 (dCK is M..IVL; dGK is .TVIVL). Also, mass spectrometry indicates that native dCK and dGK subunits are identical in mass adjusted for the first three residues. Furthermore, the native enzymes have identical isoelectric pH values, indicating an equal number of charged residues. To enable E. coli to express peptide having the native dCK sequence, codons 2 and 3 were deleted from the dgk portion of the tandem genes, resulting in expression of protein having the specificities and regulatory properties of native dAK/dCK, including heterotropic stimulation of dAK activity by deoxycytidine or dCTP (not deoxyguanosine or dGTP) and end-product inhibition of the respective activities by dATP and dCTP. Subcloning normal and mutant dgk yielded homodimeric dGK and dCK, respectively. The dCK homodimer strongly resembles human dCK, with a low K(m) for deoxycytidine, the ability to phosphorylate deoxyadenosine and deoxyguanosine at much higher K(m) values, and end-product inhibition by dCTP. Thus two distinct and specific enzymes evidently are derived from a single Lactobacillus gene. The mechanism by which this occurs in vivo has yet to be elucidated.

A highly sensitive, nonradioactive DNA labeling and detection system

A highly sensitive method for detecting specific nucleotide sequences was recently developed. The method uses digoxigenin-labeled nucleic acid probes for hybridization to immobilized target nucleic acids. Probes can be labeled by the random-primed method, nick translation, oligonucleotide tailing, cDNA synthesis, photodigoxigenin or SP6/T7/T3 polymerase-mediated transcription. Hybrids are detected by an enzyme-linked immunoassay using an anti-digoxigenin antibody conjugate. Visualization of the bound antibody is accomplished by an enzymatic color reaction, enzymatic chemiluminescent reaction or immunofluorescence, depending on the antibody conjugate and enzymatic substrate used. Here we report the successful application of this technology in the detection of specific cloned DNA in colony and plaque hybridizations, specific detection of a single mRNA species in Northern blots and single-copy gene detection in genomic Southern blots.