Theoretical analysis of the porphyrin-porphyrin exciton interaction in circular dichroism spectra of dimeric tetraarylporphyrins

Chiral bis-porphyrins are currently the subject of intense interest as chiral receptors and as probes in the determination of structure and stereochemistry. To provide an improved framework for interpreting the circular dichroism (CD) spectra of bis-porphyrins, we have calculated the CD spectra of chiral bis-porphyrins from three classes: I, where porphyrins can adopt a relatively wide range of orientations relative to each other; II, porphyrins have a fixed relative orientation; III, porphyrins undergo pi-stacking. The calculations primarily utilized the classical polarizability theory of DeVoe, but were supplemented by the quantum mechanical matrix method. Class I was represented by three isomers of the diester of 5alpha-cholestane-3,17-diol with 5-(4'-carboxyphenyl)-10,15,20-triphenylporphin (2-alphabeta, 2-betaalpha, 2-betabeta). Careful analysis of the torsional degrees of freedom led to two to four minimum-energy conformers for each isomer, in each of which the phenyl-porphyrin bonds had torsional angles near 90 degrees. Libration about these bonds is relatively unrestricted over a range of +/-45 degrees. CD spectra in the Soret region were calculated as Boltzmann-weighted averages over the low-energy conformers for each isomer. Three models were used: the effective transition moment model, in which only one of the degenerate Soret components is considered, along the 5-15 direction; the circular oscillator model, in which both Soret components are given equal weight; and the hybrid model, in which the 10-20 oscillator is given half the weight of the 5-15 oscillator, to mimic the effect of extensive librational averaging about the 5-15 direction. All three models predict Soret exciton couplets with signs in agreement with experiment. Quantitatively, the best results are given by the hybrid and circular oscillator models. These results validate the widely used effective transition moment model for qualitative assignments of bis-porphyrin chirality and thus permit application of the exciton chirality model. However, for quantitative studies, the circular oscillator or hybrid models should be used. The simplified effective transition moment and hybrid models are justified by the librational averaging in the class I bis-porphyrins and should only be used with such systems. Two class II bis-porphyrins were also studied by DeVoe method calculations in the circular oscillator model, which yielded good agreement with experiment. Class III bis-porphyrins were represented by 2-alphaalpha, for which the calculations gave qualitative agreement. However, limitations in the conformational analysis with the close contacts and dynamic effects in these pi-stacked systems preclude quantitative results.     

Synthesis,characterization and biological activity of bis(3‐Aryl‐1‐hexahydropyrimidinyl)methanes. Novel heterocyclic polyamine derivatives

A method is described for the synthesis of bis(3‐aryl‐1‐hexahydropyrimidinyl)methanes 1, by condensation of N‐aryl‐1,3‐propanediarnines 2 with formaldehyde. The reaction mechanism involves N‐arylhexahydropyrimidines 3 as intermediates. Such compounds can also be prepared efficiently by a methylene exchange reaction between bis‐hexahydropyrimidines 1 and the corresponding diamines 2. The antimicrobial activity of compounds 1 was evaluated by the disk diffusion method and some of them showed moderate to good growth inhibition activity.     

TAT peptide internalization: seeking the mechanism of entry

During the last decade several peptides have been extensively studied for their ability to translocate across the plasma membrane. These peptides have been called "cell penetrating peptides" (CPP) or "protein transduction domains" (PTD). These peptides also promote the cellular uptake of various cargo molecules. Their mechanism of cellular entry appeared very intriguing since most publications in the field highlighted an energy-independent process. Indeed, cellular uptake of these peptides was still observed by fluorescence microscopy at low temperature or in the presence of several drugs known to inhibit active transport. In addition, internalization was reported to be much faster than known endocytic processes. However the involvement of a specific cellular component responsible for this uptake process appeared unlikely following intensive structure activity relationship studies using a wide panel of Tat analogues. Several reports about a possible artefactual redistribution of CPPs, and their associated cargos, during the cell fixation step commonly used for fluorescence microscopy have recently emerged in the literature. Moreover strong ionic interactions of CPPs with the cell surface also led to an overestimation of the recorded cell-associated fluorescent signal. It now seems well established that arginine-rich peptides are internalized by an energy dependent process involving endocytosis. Whatever the case, however, an increasing number of data indicate that the conjugation of non-permeant molecules to these CPPs allows their cellular uptake and leads to the expected biological responses, thus pointing to the interest of this delivery strategy. However, initial structure activity relationship studies of these CPPs will have to be reconsidered and the relative potency of each peptide (and their analogues) to vectorize the cargos to their most appropriate subcellular compartment will require careful re-evaluation.     

Net analyte signal as a deconvolution-oriented resolution criterion in the optimisation of chromatographic techniques

The performance of two multivariate calibration measurements, multivariate selectivity (SEL(s)) and scalar net analyte signal (scalar NAS), as chromatographic objective functions (COFs), was investigated. Since both assessments are straightforwardly related to the quantification of analytes in the presence of interferents, they were expected to confer new features in the optimisation of compound resolution, not present in conventional assessments. These capabilities are especially interesting in situations of low resolution, where peak deconvolution becomes an attractive alternative. For comparison purposes, chromatographic resolution (R(s)) and peak purity (p(s)) were used as reference COFs. In order to correlate COFs with the probability of deconvolution error, an artificial peak crossing was used to generate 73 different peak arrangements, which were deconvolved using three different methods. SEL(s) exhibited the best correlation, which allowed predicting properly the risk of obtaining inaccurate deconvolutions. The optimisation of a poorly resolved mixture of 16 aromatic compounds by reversed-phase liquid chromatography with methanol-water and acetonitrile-water mobile phases was examined to investigate the differences in performance among the resolution criteria. In situations like these, SEL(s) tends to consider acceptable mobile phase compositions with partial coelution, which permits however the deconvolution with low errors. In contrast, p(s) selects compositions where the resolution of some compounds is sacrificed to enhance the separation of others. Scalar NAS was not so favourable as expected, since it depends on sampling frequency and peak widening. SEL(s) was not affected by these factors.     

Comparison of low-order multireference many-body perturbation theories

Tests have been made to benchmark and assess the relative accuracies of low-order multireference perturbation theories as compared to coupled cluster (CC) and full configuration interaction (FCI) methods. Test calculations include the ground and some excited states of the Be, H(2), BeH(2), CH(2), and SiH(2) systems. Comparisons with FCI and CC calculations show that in most cases the effective valence shell Hamiltonian (H(v)) method is more accurate than other low-order multireference perturbation theories, although none of the perturbative methods is as accurate as the CC approximations. We also briefly discuss some of the basic differences among the multireference perturbation theories considered in this work.     

Ab initio calculations and vibrational energy level fits for the lower singlet potential-energy surfaces of C3

Ab initio multireference configuration interaction potential energy surfaces are computed for the eight lowest singlet surfaces of C(3). These reveal several important features, including several conical intersections in linear, nonlinear, and equilateral triangle geometries. These intersections are important because, particularly for the excited A (1)Pi(u) state, reasonable ab initio results could only be obtained by including nearby, near degenerate, (1)Sigma(u) (-) and (1)Delta(u) states that cross the A (1)Pi(u) state around 4500 cm(-1) above the equilibrium geometry, and a (1)Pi(g) state whose potential in turn crosses the other states about 2000 cm(-1) further up. These states are probably responsible for the complexity of the shorter wavelength UV absorption spectrum of C(3). The computed potential energy surface for the ground, X (1)Sigma(g) (+), state and for the lowest two excited singlet surfaces (which both correlate with the A (1)Pi(u) state in a collinear geometry) are fitted to analytic functional forms. Vibrational energy levels are calculated for both states, taking account of the Renner-Teller coupling in the excited A (1)Pi(u) state. The potential parameters for both states are then least-squares fitted to experimental data. The ground-state fit covers a range of approximately 8500 cm(-1) above the lowest level, and reproduces 100 observed vibrational levels with an average error of 2.8 cm(-1). The A (1)Pi(u) state surfaces cover a range of 3250 cm(-1) above the zero-point level, and reproduce the 44 observed levels in this range with an average error of 2.8 cm(-1).     

Beyond generative models: superfast traversal,optimization, novelty,exploration and discovery (STONED) algorithm for molecules using SELFIES

Inverse design allows the generation of molecules with desirable physical quantities using property optimization. Deep generative models have recently been applied to tackle inverse design, as they possess the ability to optimize molecular properties directly through structure modification using gradients. While the ability to carry out direct property optimizations is promising, the use of generative deep learning models to solve practical problems requires large amounts of data and is very time-consuming. In this work, we propose STONED – a simple and efficient algorithm to perform interpolation and exploration in the chemical space, comparable to deep generative models. STONED bypasses the need for large amounts of data and training times by using string modifications in the SELFIES molecular representation. First, we achieve non-trivial performance on typical benchmarks for generative models without any training. Additionally, we demonstrate applications in high-throughput virtual screening for the design of drugs, photovoltaics, and the construction of chemical paths, allowing for both property and structure-based interpolation in the chemical space. Overall, we anticipate our results to be a stepping stone for developing more sophisticated inverse design models and benchmarking tools, ultimately helping generative models achieve wider adoption.

Interpolation and exploration within the chemical space for inverse design.