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.     

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.     

Bare and ligand protected planar hexacoordinate silicon in SiSb3M3+ (M = Ca,Sr, Ba) clusters

The occurrence of planar hexacoordination is very rare in main group elements. We report here a class of clusters containing a planar hexacoordinate silicon (phSi) atom with the formula SiSb₃M₃⁺ (M = Ca, Sr, Ba), which have D_3h (¹A₁′) symmetry in their global minimum structure. The unique ability of heavier alkaline-earth atoms to use their vacant d atomic orbitals in bonding effectively stabilizes the peripheral ring and is responsible for covalent interaction with the Si center. Although the interaction between Si and Sb is significantly stronger than the Si–M one, sizable stabilization energies (−27.4 to −35.4 kcal mol⁻¹) also originated from the combined electrostatic and covalent attraction between Si and M centers. The lighter homologues, SiE₃M₃⁺ (E = N, P, As; M = Ca, Sr, Ba) clusters, also possess similar D_3h symmetric structures as the global minima. However, the repulsive electrostatic interaction between Si and M dominates over covalent attraction making the Si–M contacts repulsive in nature. Most interestingly, the planarity of the phSi core and the attractive nature of all the six contacts of phSi are maintained in N-heterocyclic carbene (NHC) and benzene (Bz) bound SiSb₃M₃(NHC)₆⁺ and SiSb₃M₃(Bz)₆⁺ (M = Ca, Sr, Ba) complexes. Therefore, bare and ligand-protected SiSb₃M₃⁺ clusters are suitable candidates for gas-phase detection and large-scale synthesis, respectively.

The global minimum of SiSb₃M₃⁺ (M = Ca, Sr, Ba) is a D_3h symmetric structure containing an elusive planar hexacoordinate silicon (phSi) atom. Most importantly, the phSi core remains intact in ligand protected environment as well.

Exploring the bonding capacity of main-group elements (such as carbon or silicon) beyond the traditional tetrahedral concept has been a fascinating subject in chemistry for five decades. The 1970 pioneering work of Hoffmann and coworkers¹ initiated the field of planar tetracoordinate carbons (ptCs), or more generally, planar hypercoordinate carbons. The past 50 years have witnessed the design and characterization of an array of ptC and planar pentacoordinate carbon (ppC) species.^2–14 However, it turned out to be rather challenging to go beyond ptC and ppC systems. The celebrated CB₆²⁻ cluster and relevant species^15,16 were merely model systems because C avoids planar hypercoordination in such systems.^17,18 In 2012, the first genuine global minimum D_3h CO₃Li₃⁺ cluster was reported to have six interactions with carbon in planar form, although electrostatic repulsion between positively charged phC and Li centers and the absence of any significant orbital interaction between them make this hexacoordinate assignment questionable.¹⁹ It was only very recently that a series of planar hexacoordinate carbon (phC) species, CE₃M₃⁺ (E = S–Te; M = Li–Cs), were designed computationally by the groups of Tiznado and Merino (Fig. 1; left panel),²⁰ in which there exist pure electrostatic interactions between the negative C^δ− center and positive M^δ+ ligands. These phC clusters were achieved following the so-called “proper polarization of ligand” strategy.Open in a separate windowFig. 1The pictorial depiction of previously reported phC CE₃M₃⁺ (E = S–Te; M = Li–Cs) clusters and the present SiE₃M₃⁺ (E = S–Te and N–Sb; M = Li–Cs and Ca–Ba) clusters. Herein the solid and dashed lines represent covalent and ionic bonding, respectively. The opposite double arrows illustrate electrostatic repulsion.The concept of planar hypercoordinate carbons has been naturally extended to their next heavier congener, silicon-based systems. Although the steric repulsion between ligands decreases due to the larger size, the strength of π- and σ-bonding between the central atom and peripheral ligands dramatically decreases, which is crucial for stability. Planar tetracoordinate silicon (ptSi) was first experimentally observed in a pentaatomic C_2v SiAl₄⁻ cluster by Wang and coworkers in 2000.²¹ Very recently, this topic got a huge boost by the room-temperature, large-scale syntheses of complexes containing a ptSi unit.²² A recent computational study also predicted the global minimum of SiMg₄Y⁻ (Y = In, Tl) and SiMg₃In₂ to have unprecendented planar pentacoordinate Si (ppSi) units.²³ Planar hexacoordinate Si (phSi) systems seem to be even more difficult to stabilize. Previously, a C_2v symmetric Cu₆H₆Si cluster was predicted as the true minimum,²⁴ albeit its potential energy surface was not fully explored. A kinetically viable phSi SiAl₃Mg₃H₂⁺ cluster cation was also predicted.²⁵ However, these phSi systems^24,25 are only local minima and not likely to be observed experimentally. In 2018, the group of Chen identified the Ca₄Si₂²⁻ building block containing a ppSi center and constructed an infinite CaSi monolayer, which is essentially a two-dimensional lattice of the Ca₄Si₂ motif.²⁶ Thus, it is still an open question to achieve a phSi atom to date.Herein we have tried to find the correct combination towards a phSi system as the most stable isomer. Gratifyingly, we found a series of clusters, SiE₃M₃⁺ (E = N, P, As, Sb; M = Ca, Sr, Ba), having planar D_3h symmetry with Si at the center of the six membered ring, as true global minimum forms. Si–E bonds are very strong in all the clusters, and alkaline-earth metals interact with the Si center by employing their d orbitals. However, electrostatic repulsion originated from the positively charged Si and M centers for E = N, P, and As dominates over attractive covalent interaction, making individual Si–M contacts repulsive in nature. This makes the assignment of SiE₃M₃⁺ (E = N, P, As; M = Ca, Sr, Ba) as genuine phSi somewhat skeptical. SiSb₃M₃⁺ (M = Ca, Sr, Ba) clusters are the sole candidates which possess genuine phSi centers as both electrostatic and covalent interactions in Si–M bonds are attractive. The d orbitals of M ligands play a crucial role in stabilizing the ligand framework and forming covalent bonds with phSi. Such planar hypercoordinate atoms are, in general, susceptible to external perturbations. However, the present title clusters maintain the planarity and the attractive nature of the bonds even after multiple ligand binding at M centers in SiSb₃M₃(NHC)₆⁺ and SiSb₃M₃(Bz)₆⁺. This would open the door for large-scale synthesis of phSi as well.Two major computational efforts were made before reaching our title phSi clusters. The first one is to examine SiE₃M₃⁺ (E = S–Po; M = Li–Cs) clusters, which adopt D_3h or C_3v structures as true minima (see Table S1 in ESI^†), being isoelectronic to the previous phC CE₃M₃⁺ (E = S–Po; M = Li–Cs) clusters. In the SiE₃M₃⁺ (E = S–Po; M = Li–Cs) clusters, the Si center always carries a positive charge ranging from 0.01 to +1.03|e|, in contrast to the corresponding phC species (see Fig. 1). Thus, electrostatic interactions between the Si^δ+ and M^δ+ centers would be repulsive (Fig. 1). Given that the possibility of covalent interaction with an alkali metal is minimal, it would be a matter of debate whether they could be called true coordination. A second effort is to tune the electronegativity difference between Si and M centers so that the covalent contribution in Si–M bonding becomes substantial. Along this line, we consider the combinations of SiE₃M₃⁺ (E = N, P, As, Sb; M = Be, Mg, Ca, Sr, Ba). The results in Fig. S1^† show that for E = Be and Mg, the phSi geometry has a large out-of-plane imaginary frequency mode, which indicates a size mismatch between the Si center and peripheral E₃M₃ (E = N–Bi; M = Be, Mg) ring. On the other hand, the use of larger M = Ca, Sr, Ba atoms effectively expands the size of the cavity and eventually leads to perfect planar geometry with Si atoms at the center as minima. In the case of SiBi₃M₃⁺, the planar isomer possesses a small imaginary frequency for M = Ca. Although planar SiBi₃Sr₃⁺ and SiBi₃Ba₃⁺ are true minima, they are 2.2 and 2.5 kcal mol⁻¹ higher in energy than the lowest energy isomer, respectively (Fig. S2^†). Fig. 2 displays some selected low-lying isomers of SiE₃M₃⁺ (E = N, P, As, Sb; M = Ca, Sr, Ba) clusters (see Fig. S3–S6^† for additional isomers). The global minimum structure is a D_3h symmetric phSi with an ¹A₁′ electronic state for all the twelve cases. The second lowest energy isomer, a ppSi, is located more than 49 kcal mol⁻¹ above phSi for E = N. This relative energy between the most stable and nearest energy isomer gradually decreases upon moving from N to Sb. In the case of SiSb₃M₃⁺ clusters, the second-lowest energy isomer is 4.6–6.1 kcal mol⁻¹ higher in energy than phSi. The nearest triplet state isomer is very high in energy (by 36–53 kcal mol⁻¹, Fig. S3–S6^†) with respect to the global minimum.Open in a separate windowFig. 2The structures of low-lying isomers of SiE₃M₃⁺ (E = N, P, As, Sb; M = Ca, Sr, Ba) clusters. Relative energies (in kcal mol⁻¹) are shown at the single-point CCSD(T)/def2-TZVP//PBE0/def2-TZVP level, followed by a zero-energy correction at PBE0. The values from left to right refer to Ca, Sr, and Ba in sequence. The group symmetries and electronic states are also given.Born–Oppenheimer molecular dynamics (BOMD) simulations at room temperature (298 K), taking SiE₃Ca₃⁺ clusters as case studies, were also performed. The results are displayed in Fig. S7.^† All trajectories show no isomerization or other structural alterations during the simulation time, as indicated by the small root mean square deviation (RMSD) values. The BOMD data suggest that the global minimum also has reasonable kinetic stability against isomerization and decomposition.The bond distances, natural atomic charges, and bond indices for SiE₃Ca₃⁺ clusters are given in † for M = Sr, Ba). The Si–E bond distances are shorter than the typical Si–E single bond distance computed using the self-consistent covalent radii proposed by Pyykkö.²⁷ In contrast, the Si–M bond distance is almost equal to the single bond distance. This gives the first hint of the presence of covalent bonding therein. However, the Wiberg bond indices (WBIs) for the Si–M links are surprisingly low (0.02–0.04). We then checked the Mayer bond order (MBO), which can be seen as a generalization of WBIs and is more acceptable since the approach of WBI calculations assumes orthonormal conditions of basis functions while the MBO considers an overlap matrix. The MBO values for the Si–M links are now sizable (0.13–0.18). These values are reasonable considering the large difference in electronegativity between Si and M, and, therefore, only a very polar bond is expected between them. In fact, the calculations of WBIs after orthogonalization of basis functions by the Löwdin method gives significantly large bond orders (0.48–0.55), which is known to overestimate the bond orders somewhat. The above results indicate that the presence of covalent bonding cannot be ruled out only by looking at WBI values.Bond distances (r, in Å), different bond orders (WBIs) {MBOs} [WBI in orthogonalized basis], and natural atomic charges (q, in |e|) of SiE₃Ca₃⁺ (E = N, P, As, Sb) clusters at the PBE0/def2-TZVP level

Inhibition of Bacterial Adhesion and Biofilm Formation by Seed-Derived Ethanol Extracts from Persea americana Mill

The increase in antibiotic resistance demands innovative strategies to combat microorganisms. The current study evaluated the antibacterial and antivirulence effects of ethanol extracts from Persea americana seeds obtained by the Soxhlet (SE) and maceration (MaE) methods. The UHPLC-DAD-QTOF analysis showed mainly the presence of polyphenols and neolignan. Ethanol extracts were not cytotoxic to mammalian cells (CC₅₀ > 500 µg/mL) and displayed a moderate antibacterial activity against Pseudomonas aeruginosa (IC₅₀ = 87 and 187 µg/mL) and Staphylococcus aureus (IC₅₀ = 144 and 159 µg/mL). Interestingly, no antibacterial activity was found against Escherichia coli. SE and MaE extracts were also able to significantly reduce the bacterial adhesion to A549 lung epithelial cells. Additionally, both extracts inhibited the biofilm growth at 24 h and facilitated the release of internal cell components in P. aeruginosa, which might be associated with cell membrane destabilization. Real-time PCR and agarose electrophoresis gel analysis indicated that avocado seed ethanol extracts (64 µg/mL) downregulated virulence-related factors such as mexT and lasA genes. Our results support the potential of bioproducts from P. americana seeds as anti-adhesive and anti-biofilm agents.