Density functional theory of time-dependent phenomena

Bioassay-Guided Isolation and Identification of Cytotoxic Compounds from Melaleuca quinquenervia Fruits

The fruit extract of Melaleuca quinquenervia yielded a total of 19 compounds, including two novel spiro-biflavonoid enantiomers (1a and 1b) and a chalcone derivative (3). Their structures were determined through spectroscopic analysis. The enantiomers of the racemic mixture of compound 1 were successfully resolved into (+)-1 and (-)-1 using chiral-phase HPLC. Single-crystal X-ray diffraction analysis was also used to confirm the structure of 1. The enantiomeric configurations of 1 and 2 were determined through a comparison of the calculated and experimental electronic circular dichroism spectra. Compounds 2 (melanervin), 14 (methyl betulinate), 15 (3-O-acetylbetulinic acid), and 16 (pyracrenic acid) were found to be highly cytotoxic, with compound 16 showing superior growth inhibition of nonsmall cell lung cancer cells (A549 cells) (IC50 2.8 ± 0.1 μM) compared to cisplatin (IC50 3.3 ± 0.0 μM), a positive control chemotherapeutic drug. Both compound 16 and cisplatin were significantly more cytotoxic toward A549 lung cancer cells compared to nontumorigenic Vero E6 cells.

Primary photophysical and photochemical processes for cerium ammonium nitrate (CAN) in acetonitrile

Cerium ammonium nitrate (CAN) is an important photolytic source of NO3• radicals in aqueous nitric acid solutions and in acetonitrile. In this work we performed the study of primary photochemical processes for CAN in acetonitrile by means of ultrafast TA spectroscopy and quantum chemical calculations. Photoexcitation of CAN is followed by ultrafast (< 100 fs) intersystem crossing; the vibrationally cooled triplet state decays to pentacoordinated Ce(III) intermediate and NO3• radical with the characteristic time of ca. 40 ps. Quantum chemical (QM) calculations satisfactorily describe the UV-vis spectrum of the triplet state. An important feature of CAN photochemistry in CH3CN is the partial stabilization of the radical complex (RC) [(NH4)2CeIII(NO3)5…NO3•], which lifetime is ca. 2 μs. The possibility of the RC stabilization is supported by the QM calculations.

Chemical Investigation on the Mechanism and Kinetics of the Atmospheric Degradation Reaction of Trichlorofluoroethene by OH⋅ and Its Subsequent Fate in the Presence of O2 /NOx

The M06-2X/6-311++G(d,p) level of theory was used to examine the degradation of Trichlorofluoroethene (TCFE) initiated by OH⋅ radicals. Additionally, the coupled-cluster single-double with triple perturbative [CCSD(T)] method was employed to refine the single-point energies using the complete basis set extrapolation approach. The results indicated that OH-addition is the dominant pathway. OH⋅ adds to both the C1 and C2 carbons, resulting in the formation of the C(OH)Cl2 -⋅CClF and ⋅CCl2 -C(OH)ClF species. The associated barrier heights were determined to be 1.11 and -0.99 kcal mol-1 , respectively. Furthermore, the energetic and thermodynamic parameters show that pathway 1 exhibits greater exothermicity and exergonicity compared to pathway 2, with differences of 8.11 and 8.21 kcal mol-1 , correspondingly. The primary pathway involves OH addition to the C2 position, with a rate constant of 6.2×10-13  cm3 molecule-1 sec-1 at 298 K. This analysis served to estimate the atmospheric lifetime, along with the photochemical ozone creation potential (POCP) and ozone depletion potential (ODP). It yielded an atmospheric lifetime of 8.49 days, an ODP of 4.8×10-4 , and a POCP value of 2.99, respectively. Radiative forcing efficiencies were also estimated at the M06-2X/6-311++G(d,p) level. Global warming potentials (GWPs) were calculated for 20, 100, and 500 years, resulting in values of 9.61, 2.61, and 0.74, respectively. TCFE is not expected to make a significant contribution to the radiative forcing of climate change. The results obtained from the time-dependent density functional theory (TDDFT) indicated that TCFE and its energized adducts are unable to photolysis under sunlight in the UV and visible spectrum. Secondary reactions involve the [TCFE-OH-O2 ]⋅ peroxy radical, leading subsequently to the [TCFE-OH-O]⋅ alkoxy radical. It was found that the alkoxy radical resulting from the peroxy radical can lead to the formation of phosgene (COCl2 ) and carbonyl chloride fluoride (CClFO), with phosgene being the primary product.

Complex Linear Response Functions for a Multiconfigurational Self-Consistent Field Wave Function in a High Performance Computing Environment

We present novel developments for the highly efficient evaluation of complex linear response functions of a multiconfigurational self-consistent field (MCSCF) wave function as implemented in MultiPsi. Specifically, expressions for the direct evaluation of linear response properties at given frequencies using the complex polarization propagator (CPP) approach have been implemented, within both the Tamm-Dancoff approximation (TDA) and the random phase approximation (RPA). Purely real algebra with symmetric and antisymmetric trial vectors in a shared subspace is used wherein the linear response equations are solved. Two bottlenecks of large scale MC-CPP calculations, namely, the memory footprint and computational time, are addressed. The former is addressed by limiting the size of the subspace of trial vectors by using singular value decomposition (SVD) on either orbital or CI subspaces. The latter is addressed using an efficient parallel implementation as well as the strategy of dynamically adding linear response equations at near-convergence to neighboring roots. Furthermore, a novel methodology for decomposing MC-CPP spectra in terms of intuitive orbital excitations in an approximate fashion is presented. The performance of the code is illustrated with several numerical examples, including the X-ray spectrum of a molecule with nearly one hundred atoms. Additionally, for X-ray spectroscopy, the effect of including or excluding the core orbital in the active space on small covalent metal complexes is discussed.

Phosphorescent Properties of Heteroleptic Ir(III) Complexes: Uncovering Their Emissive Species

In this contribution, we assess the computational machinery to calculate the phosphorescence properties of a large pool of heteroleptic [Ir(C^N)2(N^N)]+ complexes (where N^N is an ancillary ligand and C^N is a cyclometalating ligand) including their phosphorescent rates and their emission spectra. Efficient computational protocols are next proposed. Specifically, different flavors of DFT functionals were benchmarked against DLPNO-CCSD(T) for the phosphorescence energies. The transition density matrix and decomposition analysis of the emitting triplet excited state enable us to categorize the studied complexes into different cases, from predominant triplet ligand-centered (3LC) character to predominant charge-transfer (3CT) character, either of metal-to-ligand charge transfer (3MLCT), ligand-to-ligand charge transfer (3LLCT), or a combination of the two. We have also calculated the vibronically resolved phosphorescent spectra and rates. Ir(III) complexes with predominant 3CT character are characterized by less vibronically resolved bands as compared to those with predominant 3LC character. Furthermore, some of the complexes are characterized by close-lying triplet excited states so that the calculation of their phosphorescence properties poses additional challenges. In these scenarios, it is necessary to perform geometry optimizations of higher-lying triplet excited states (i.e., Tn). We demonstrate that in the latter scenarios all of the close-lying triplet species must be considered to recover the shape of the experimental emission spectra. The global analysis of computed emission energies, shape of the computed emission spectra, computed rates, etc. enable us to unambiguously pinpoint for the first time the triplet states involved in the emission process and to provide a general classification of Ir(III) complexes with regard to their phosphorescence properties.

Direct UV photodegradation of nalidixic acid in aqueous solutions: A mechanistic study

Mechanism of direct UV photolysis of nalidixic acid (NA), a model quinolone antibiotic, was revealed using a combination of steady-state photolysis coupled with high resolution LC-MS and DFT quantum-chemical calculations. Both quantum yields of photodegradation and detailed identification of final products were performed for the first time for two main forms of NA: neutral and anionic. The quantum yield of NA photodegradation is 0.024 and 0.0032 for the neutral and anionic forms in the presence of dissolved oxygen and 0.016/0.0032 in deoxygenated solutions, respectively. The main process is photoionization with the formation of a cation radical, which undergoes transformation into three different neutral radicals and further into final photoproducts. It is shown that the triplet state does not play a role in the photolysis of this compound. The main products of photolysis are the products of the loss of carboxyl, methyl and ethyl groups in the NA molecule, as well as the dehydrogenation of the ethyl group. The results obtained may be important for understanding the fate of pyridine herbicides in the processes of disinfection by UV and in natural waters under the action of sunlight.

Curing the Divergence in Time-Dependent Density Functional Quadratic Response Theory

The adiabatic approximation in time-dependent density functional theory is known to give an incorrect pole structure in the quadratic response function, leading to unphysical divergences in excited state-to-state transition probabilities and hyperpolarizabilties. We find the form of the exact quadratic response kernel and derive a practical and accurate approximation that cures the divergence. We demonstrate our results on excited state-to-state transition probabilities of a model system and of the LiH molecule.

Anti-inflammatory Quinoline Alkaloids from the Roots of Waltheria indica

Sixteen new quinoline alkaloids (1a-7, 8a, 9, 10, 13-15, 17, and 21) and 10 known analogs (8b, 11, 12, 16, 18-20, and 22-24), along with three known cyclopeptide alkaloids (25-27), were isolated from the roots of Waltheria indica. The structures of the new compounds were elucidated by detailed NMR and circular dichroism with computational support and mass spectrometry data interpretation. Anti-inflammatory potential of isolates was evaluated based on inhibition of lipopolysaccharide (LPS)-induced nitric oxide (NO) production and tumor necrosis factor-alpha (TNF-α)-induced nuclear factor kappa B (NF-κB) activity with cell culture models. In the absence of cell growth inhibition, compounds 6, 8a, 9-11, 13, 21, and 24 reduced TNF-α-induced NF-κB activity with IC₅₀ values ranging from 7.1 to 12.1 μM, comparable to the positive control (BAY 11-7082, IC₅₀ = 9.7 μM). Compounds 6, 8a, 8b, and 11 showed significant NO-inhibitory activity with IC₅₀ values ranging from 11.0 to 12.8 μM, being more active than the positive control (l-NMMA, IC₅₀ = 22.7 μM). Structure-activity relationships indicated that NO inhibitory activity was significantly affected by C-8 substitution. Inhibition of LPS-induced nitric oxide synthase (iNOS) by 8b [(5S)-waltherione M, IC₅₀ 11.7 ± 0.8 μM] correlated with inhibition of iNOS mRNA expression. The biological potential of W. indica metabolites supports the traditional use of this plant for the treatment of inflammatory-related disorders.

Static/dynamic first and second order hyperpolarizabilities, optimized structures, IR, UV-Vis, 1H and 13C NMR spectra for effective charge transfer compounds: A DFT study

The effective charge transfer compounds, 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium m-trifluoromethylbenzene-sulfonate (DSMFS) and 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium p-trifluoromethylbenzene-sulfonate (DSPFS), were simulated in terms of geometric structure, IR, UV-Vis, ¹H NMR and ¹³C NMR spectra. UV-vis spectra for both molecules give two peaks at 290 and 436 nm assigned as n-π* and π-π* transitions. The HOMO-LUMO energy gap for DSMFS (2.8174 eV) was calculated as lower than that of DSPFS (4.6649 eV). The detailed frontier molecular orbital analysis also indicated that the intra- and inter-molecular charge transfers occur in DSMFS and DSPFS. The static and dynamic (ω = 532 and 1064 nm) nonlinear optical properties were also investigated by using B3LYP/6-311++G(d,p) level. Static first and second order hyperpolarizabilities (β and γ) of DSMFS were obtained 1.5726 × 10^-28 esu and 271.63 × 10^-36 esu, and those for DSPFS were obtained as 1.5528 × 10^-28 esu and 303.31 × 10^-36 esu. The dynamic β and γ were obtained as higher than the static corresponding parameters. However, the increasing wavelength in dynamic NLO calculations led to a decrease in β and γ parameters.

Coumarinolignans with Reactive Oxygen Species (ROS) and NF-κB Inhibitory Activities from the Roots of Waltheria indica

Seven new coumarinolignans, walthindicins A–F (1a, 1b, 2–5, 7), along with five known analogs (6, 8–11), were isolated from the roots of Waltheria indica. The structures of the new compounds are determined by detailed nuclear magnetic resonance (NMR), circular dichroism (CD) with extensive computational support, and mass spectroscopic data interpretation. Compounds were tested for their antioxidant activity in Human Cervical Cancer cells (HeLa cells). Compounds 1a and 6 showed higher reactive oxygen species (ROS) inhibitory activity at 20 μg/mL when compared with other natural compound-based antioxidants such as ascorbic acid. Considering the role of ROS in nuclear-factor kappa B (NF-κB) activation, compounds 1a and 6 were evaluated for NF-κB inhibitory activity and showed a concentration-dependent inhibition in Human Embryonic Kidney 293 cells (Luc-HEK-293).

Quantum simulations of thermally activated delayed fluorescence in an all-organic emitter

We investigate the prototypical NAI-DMAC thermally activated delayed fluorescence (TADF) emitter in the gas phase- and high-packing fraction limits at finite temperature, by combining first principles molecular dynamics with a quantum thermostat to account for nuclear quantum effects (NQE). We find a weak dependence of the singlet-triplet energy gap (ΔE_ST) on temperature in both the solid and the molecule, and a substantial effect of packing. While the ΔE_ST vanishes in the perfect crystal, it is of the order of ∼0.3 eV in the molecule, with fluctuations ranging from 0.1 to 0.4 eV at 300 K. The transition probability between the HOMOs and LUMOs has a stronger dependence on temperature than the singlet-triplet gap, with a desirable effect for thermally activated fluorescence; such temperature effect is weaker in the condensed phase than in the molecule. Our results on ΔE_ST and oscillator strengths, together with our estimates of direct and reverse intersystem crossing rates, show that optimization of packing and geometrical conformation is critical to increase the efficiency of TADF compounds. Our findings highlight the importance of considering thermal fluctuations and NQE to obtain robust predictions of the electronic properties of NAI-DMAC.

Spirovetivane- and Eudesmane-Type Sesquiterpenoids Isolated from the Culture Media of Two Cyanobacterial Strains

As part of a study examining polar metabolites produced by cyanobacterial strains, we examined media extracts of a Calothrix sp. (strain R-3-1) and a Scytonema sp. (strain U-3-3). The cell mass of each was separated from the media, and HP20 resin was added for adsorption of secreted metabolites, a relatively unexplored area of cyanobacterial chemistry. HPLC-UV-LCMS-guided isolation led to the discovery of seven sesquiterpenoid compounds with five new, one known, and one previously isolated as the methyl ester. Through a complement of 1D and 2D NMR spectroscopic techniques, the planar structures and relative configurations of the seven compounds were elucidated. Spironostoic acid (1), 11,12-didehydrospironostoic acid (2), and 12-hydroxy-2-oxo-11-epi-hinesol (4) are spirovetivane-type compounds from R-3-1, while stigolone (5), 11R,12-dihydroxystigolone (6), and 11S,12-dihydroxystigolone (7) are three eudesmane-type compounds from U-3-3. Circular dichroism was utilized to decipher the absolute configurations of new compounds 1, 2, 4, 5, 6, and 7. Due to the structural variety observed among the spirovetivane- and eudesmane-type compounds in the literature and often a lack of clarity in how determinations were made, computational spectra and model compounds were used to support the interpretation of ECD and NMR spectra. A straightforward process to determine the configuration of these systems is presented.

Prospect of DFT Utilization in Polymer-Graphene Composites for Electromagnetic Interference Shielding Application: A Review

The improvement in current materials science has prompted a developing need to capture the peculiarities that determine the properties of materials and how they are processed on an atomistic level. Quantum mechanics laws control the interface among atoms and electrons; thus, exact and proficient techniques for fixing the major quantum-mechanical conditions for complex many-particle, many-electron frameworks should be created. Density functional theory (DFT) marks an unequivocal advance in these endeavours. DFT has had a rapid influence on quintessential and industrial research during the last decade. The DFT system describes periodic structural systems of 2D or 3D electronics with the utilization of Bloch’s theorem in the direction of Kohn–Sham wavefunctions for the significant facilitation of these schemes. This article introduces and discusses the infinite systems modelling approach required for graphene-based polymer composites or their hybrids. Aiming to understand electronic structure computations as per physics, the impressions of band structures and atomic structure envisioned along with orbital predicted density states are beneficial. Convergence facets coupled with the basic functions number and the k-points number are necessary to explain for every physicochemical characteristic in these materials. Proper utilization of DFT in graphene-based polymer composites for materials in EMI SE presents the potential of taking this niche to unprecedented heights within the next decades. The application of this system in graphene-based composites by researchers, along with their performance, is reviewed.

Comparative analysis on the photolysis kinetics of four neonicotinoid pesticides and their photo-induced toxicity to Vibrio Fischeri: Pathway and toxic mechanism

Neonicotinoids are widely used pesticides all over the world and pose severe water pollution. Although they can be degraded via absorbing sunlight, few attentions have been paid to the environmental risks of their photolysis products. In this paper, the photo-toxicity was investigated for four neonicotinoids (dinotefuran, nitenpyram, thiamethoxam and clothianidin) based on a series of experiments (i.e., photolysis kinetics, radical scavenging, bioluminescent inhibition test to Vibrio Fischeri and intermediate identification) and in-silico calculation of photolysis pathway. The results show that direct photolysis dominates the photolysis of the four neonicotinoids under simulated sunlight radiation. The bioluminescent inhibition kinetics shows that all four neonicotinoids have photo-induced toxicity to V. fischeri, but with different light-induced responses. Scavenging radicals (·OH and ¹O₂) will decrease the photo-induced toxicity of all the four neonicotinoids, indicating radicals play important roles to the photo-chemical reactions of intermediates. Dissolved organic matters exhibit slightly shading effect to the photolysis rates of four parent compounds. However, the ROSs generated by DOM can accelerate the photo-chemical reactions of intermediates, leading to different photo-induced toxicity in present of DOM. According to the detected intermediates and Gaussian calculations, there are different photolysis pathways and mechanisms for the four neonicotinoids. The calculation for photo-sensitization reactions with ³O₂ indicates that both energy transfer reactions and electron transfer reactions can be produced under simulated sunlight radiation, which further consolidate that reactive oxygen species are involved in the photolysis process. A theoretical model has been developed to explain the toxicity variations of four neonicotinoids in different aqueous conditions.

Surface modeling of photocatalytic materials for water splitting

The photocatalyst surface is central to photocatalytic reactions. However, it has been a challenge to explicitly understand both the surface configuration and the structure-dependent photocatalytic properties at the atomic level. First-principles density functional theory (DFT) calculations provide a versatile method that makes up for the lack of experimental surface studies. In DFT calculations, the initial surface model greatly affects the accuracy of the calculation results. Consequently, establishing a more realistic and more reliable material surface models is undoubtedly the first step and the most important link in theoretical calculations. The aim of this Perspective is to provide a general understanding of the methods for the surface modeling of photocatalytic materials in recent years. We begin with a discussion of the basic theories applied in photocatalytic surface research, followed by an explanation of the importance of surface modeling in photocatalysis. We then elaborate on the advantages and disadvantages of the basic surface model and briefly describe the latest surface modeling methods. Finally, we evaluate the rationality of current surface modeling methods. We summarize this Perspective by prospecting the developing directions of photocatalytic surface research in the future. It is believed that a reasonable surface model should be verified by both experimental characterization and theoretical computation with negative feedback.

Mechanism, Kinetics, and Ecotoxicity Assessment of ·OH-Initiated Oxidation Reactions of Sulfoxaflor

The ·OH-initiated reaction mechanism and kinetics of sulfoxaflor were investigated by using electronic structure calculations. The possible hydrogen atom and cyano group abstraction reaction pathways were studied, and the calculated thermochemical parameters show that the hydrogen atom abstraction from the C7 carbon atom is the more favorable reaction pathway. The subsequent reactions for the favorable intermediate (I4) with other atmospheric reactive species, such as O₂, H₂O, HO₂·, and NO_x· (x = 1, 2), were studied in detail. The products identified from the subsequent reactions could contribute to secondary organic aerosol (SOA) formation in the atmosphere. The intermediates and products formed from the initial and subsequent reactions are equally as toxic as the parent sulfoxaflor. At 298 K, the rate constant calculated for the formation of the favorable intermediate I4 is 2.54 × 10^-12 cm³ molecule^-1 s^-1, which shows that the lifetime of sulfoxaflor is 54 h. The excited-state calculation performed through time-dependent density functional theory shows that the photolysis of the title molecule is unlikely in the atmosphere. The global warming potentials (GWPs) for different time horizons, photochemical ozone creation potential (POCP), and ecotoxicity analysis were also studied for the insecticide sulfoxaflor.

Computational Protocol to Calculate the Phosphorescence Energy of Pt(II) Complexes: Is the Lowest Triplet Excited State Always Involved in Emission? A Comprehensive Benchmark Study

The reliable calculation of phosphorescence energies of phosphor materials is at the core of designing efficient phosphorescent organic light-emitting diodes (PhOLEDs). Therefore, it is of paramount importance to have a robust computational protocol to perform those calculations in a black-box manner. In this work, we use Domain-Based Local Pair Natural Orbital Coupled Cluster theory with single, double, and perturbative triple excitation (DLPNO-CCSD(T)) calculations to attain the phosphorescence energies of a large pool of Pt(II) complexes. Several approaches to incorporate relativistic effects in our calculations were tested. In addition, we have used the DLPNO-CCSD(T) values (i.e., our best theoretical values) to assess the performance of different flavors of density functional theory including pure, hybrid, meta-hybrid, and range-separated functionals. Among the tested functionals, the M06HF functional provides the best values compared with the DLPNO-CCSD(T) ones, with a mean absolute deviation (MAD) value of 0.14 eV. In its turn, and thanks to the increased accuracy achieved in the calculation of phosphorescence energies, we also demonstrate that not all of the investigated complexes emit from their lowest-lying triplet state (T₁). The outlier complexes include different complex photophysical scenarios and both Kasha and anti-Kasha types of complexes. Finally, we provide a general computational protocol to pre-screen whether T₁ is actually the emissive state and to accurately calculate the phosphorescence energies of Pt(II) complexes.

Hydroxyaromatic Fluorophores

Many fluorophores that are widely used in analytical biochemistry and in biological microscopy contain a hydroxyaromatic component. One could also find fascinating chemistries of hydroxyaromatic dyes, especially those capable of excited state proton transfer (ESPT) to produce dual emission, in the literature of materials and physical chemistry. The ESPT-capable compounds have attracted interest based on their fundamental intellectual values in molecular photophysics and their potential utilities as light emitters in organic light-emitting diodes (LEDs) or fluorescent sensors. The hydroxyaromatic dyes could undergo either intra- or intermolecular proton transfer in either electronic ground or excited states. Although having long been applied for various purposes, some of their absorption and emission properties have not always been clearly described because of the insufficient attention given to proton transfer equilibria in either the ground or excited state and the challenges in computationally modeling the true emitters of these dyes under any given conditions. In this article, an attempt is made to summarize the spectroscopic properties of a few common hydroxyaromatic dyes that have been studied for both fundamental and practical purposes, with the help from quantum chemical calculations of the absorption and emission energies of these dyes in neutral and anion forms. The goal of this article is to provide readers some clarity in the optical properties of these compounds and the tools to understand and to predict the photon-initiated behaviors of hydroxyaromatic fluorophores.

Structurally various sorbicillinoids from the deep-sea sediment derived fungus Penicillium sp. SCSIO06871

Two new hybrid sorbicillinoids (1 and 5), three new bisorbicillinoids (2-4), and three monomeric sorbicillinoids (6-8), along with eighteen known sorbicillinoids (9-26) were isolated from cultures of the deep-sea sediment derived fungus Penicillium sp. SCSIO06871. Their structures and absolute configurations were elucidated based upon the extensive spectroscopic analysis, X-ray crystallography analysis and the comparison of the experimental and calculated ECD data. Bisorbicillpyrone A (4) is the first example of bisorbicillinoid containing an α-pyrone derivative unit. All of the isolated compounds were evaluated for their antibacterial, antifungal and enzyme inhibitory activities against α-glycosidase and acetylcholinesterase (AChE) in vitro. Compound 6 displayed more potent inhibitory activity against α-glycosidase than acarbose with IC₅₀ value of 36.0 μM and compounds 4, 12, 18, 22, 23 exhibited moderate inhibitory activity with IC₅₀ values ranging from 115.8 to 208.5 μM. Compounds 10 and 22 showed weak enzyme inhibitory activities against AChE with 55.1% and 51.1% inhibitions at concentration of 50 μg/mL, respectively. Besides, compounds 11 and 12 exhibited significant antibacterial activities against Staphylococcus aureus with MIC values of 10.0 and 5.0 μg/mL, respectively. The hypothetical biosynthetic pathway of the isolated sorbicillinoids with three different structural types was discussed.

The ONIOM/PMM Model for Effective Yet Accurate Simulation of Optical and Chiroptical Spectra in Solution: Camphorquinone in Methanol as a Case Study

This paper deals with the development and first validation of a composite approach for the simulation of chiroptical spectra in solution aimed to strongly reduce the number of full QM computations without any significant accuracy loss. The approach starts from the quantum mechanical computation of reference spectra including vibrational averaging effects and taking average solvent effects into account by means of the polarizable continuum model. Next, the snapshots of classical molecular dynamics computations are clusterized and one reference configuration from each cluster is used to compute a reference spectrum. Local fluctuation effects within each cluster are then taken into account by means of the perturbed matrix model. The performance of the proposed approach is tested on the challenging case of the optical and chiroptical spectra of camphorquinone in methanol solution. Although further validations are surely needed, the results of this first study are quite promising also taking into account that agreement with experimental data is reached by just a couple of full quantum mechanical geometry optimizations and frequency computations.

A new abyssomicin polyketide with anti-influenza A virus activity from a marine-derived Verrucosispora sp. MS100137

Marine microorganisms live in dramatically different environments and have attracted much attention for their structurally unique natural products with potential strong biological activity. Based on the one strain-many compounds (OSMAC) strategy and liquid chromatography mass spectrometry (LC-MS) methods, our continuing efforts on the investigation of novel active compounds from marine Verrucosispora sp. MS100137 has led to the identification of a new polycyclic metabolite, abyssomicin Y (1), together with six known abyssomicin and proximicin analogs (2-7). Abyssomicin Y is a type I abyssomicin with an epoxide group at C-8 and C-9. Compounds 1-3 showed potent inhibitory effects against the influenza A virus; their observed inhibition rates were 97.9%, 98.3%, and 95.9%, respectively, at a concentration of 10 μM, and they displayed lower cytotoxicity than 4. The structures were determined by different NMR techniques and HRMS experiments. This investigation revealed that OSMAC could serve as a useful method for enabling the activation of the silent genes in the microorganism and for the formation of previously unreported active secondary metabolites.

Long-range corrected exchange-correlation kernels to describe excitons in second-harmonic generation

We investigate the role of excitons in second-harmonic generation (SHG) through the long-range corrected (LRC) exchange-correlation kernels: empirical LRC, Bootstrap, and jellium-with-a-gap model. We calculate the macroscopic second-order frequency-dependent susceptibility χ⁽²⁾. We also present the frequency-dependent macroscopic dielectric function ϵ_M which is a fundamental quantity in the theoretical derivation of χ⁽²⁾. We assess the role of the long-range kernels in describing excitons in materials with different symmetry types: cubic zincblende, hexagonal wurtzite, and tetragonal symmetry. Our studies indicate that excitons play an important role in χ⁽²⁾ bringing a strong enhancement of the SHG signal. Moreover, we found that the SHG enhancement follows a simple trend determined by the magnitude of the long-range corrected α-parameter. This trend is material dependent.

DFT Study of Photochemical Properties and Radiative Forcing Efficiency Features of the Stereoisomers cis- and trans-CHCl═CH-CF3

The accurate assessment of radiative forcing efficiency (RFE) of a greenhouse gas is based on the precise knowledge of its structure and infrared absorption spectrum. The present work investigates the UV-vis absorption spectra and IR absorption spectra that are used for the determination of RFE of the short-lived compounds, cis- and trans-CHCl═CHCF₃ (CTFP). These investigations were carried out with six different density functional theory (DFT) methods B3LYP, CAM-B3LYP, M06, M06-2X, TPSS0, and ωB97X-D associated to the basis set 6-31G(3df). Therefrom, the relative populations of the two states cis and trans for temperatures over the range 220-370 K at 1 atm and along the atmospheric altitude were assessed. It turns out that trans-CTFP is the abundant component between the two states. This review reveals that B3LYP and M06 reproduce well the experimental results of UV-vis spectra of trans-CTFP. As for cis-CTFP, EOM-CCSD is not well fitted by DFT methods. The cis- to trans-CTFP isomerization leads to the red shift for DFT methods and to the blue shift in regard to EOM-CCSD and experimental results. The IR absorption spectra are well fitted by B3LYP over the range 500-1600 cm^-1 and TPSS0 over 1300-2000 cm^-1 for both stereoisomers. Moreover, the root-mean-square errors (RMSEs) of frequencies from experimental data are lower for B3LYP and TPSS0 for both systems. The computed IR absorption band strengths over 500-2000 cm^-1 for cis- and over 600-1800 cm^-1 for trans-CTFP are consistent with the experiment. The relevant descriptor RFEs of the climate effect were calculated using a narrow band model for a constant vertical profile and then corrected with a lifetime factor for different computational methods. The computed values correlate well with the experimental results for both stereoisomers except M06-2X and TPSS0. It is worth noting that, for both systems, the intense radiative forcing spectra are located at frequencies ranging in 1000-1200 cm^-1. The lower forcings of trans-CTFP lying in the atmospheric window region 800-1000 cm^-1 are greater than those of cis-CTFP. Therefore, RFE(trans-CTFP) = 1.127 RFE(cis-CTFP).

Four New Picrotoxane-Type Sesquiterpenes From Dendrobium nobile Lindl

Four picrotoxane-type sesquiterpenes, dendroterpene A–D (1–4), together with four known compounds (5–8), were isolated from the stems of Dendrobium nobile Lindl. Their structures were elucidated by spectroscopic analysis, X-ray diffraction analysis, analysis of the ECD data according to the Klyne's lactone sector rule, and quantum ECD calculation. Compounds 1 and 2 are two new picrotoxane-type sesquiterpenes with a new carbon skeleton containing a formamide group, which may be derived from the previously reported dendrobiumane B skeleton by the C(9)-C(11) carbon bond cleavage. Compounds 3, 5, 6, and 8 exhibited inhibitory activity against α-glycosidase. Compounds 5 and 6 were cytotoxic against SGC-7901, K562, A549, BEL-7402, and Hela cell lines.

Myrmenaphthol A, Isolated from a Hawaiian Sponge of the Genus Myrmekioderma

Four compounds (1-4) were isolated from a Hawaiian sponge of the genus Myrmekioderma. Myrmenaphthol A (1) incorporates two unusual elements into an oxidized steroidal core: a naphthyl AB-ring system and a hydroxy group at C-2. A comparison of the experimental and predicted electronic circular dichroism (ECD) spectra of 1 assigned an S configuration to the lone stereocenter (Δ_ESI = 0.75; similarity factor 0.8137). Known compounds, cinanthrenol A (2), 3,4-dihydroxypregna-5,17-diene-10,2-carbolactone (3), and 3,4-dihydroxypregna-5,20-diene-10,2-carbolactone (4), were also isolated. Despite literature reports of competitive inhibition at nanomolar levels for 2, neither 2 nor the structurally related 1 showed any activity against estrogen receptors at the concentrations tested.

Thermodynamic of solvation, solute - Solvent electron transfer and ionization potential of BSCAPE molecule and its UV-vis spectra in aqueous solution

The molecular system 2-Phenylethyl (2E)-3-(1-benzenesulfonyl-4,5-dihydroxyphenyl) acrylate (BSCAPE) is a phenolic acid that covers a large spectrum of biological properties. The investigations of solvation and oxidation processes of BSCAPE molecule by computational means were the challenge of this present work. Water was required for solvation throughout the work. The explicit H₂O were sequentially added to form the complexes BSCAPE(H₂O)_n=0-11. The discrete - continuum model was at the heart of this work. DFT and TD-DFT both associated to the continuum model SMD were required. Hence, the structures, the solvation energies, the energies of solute - solvent electron transfer (SSET), the ionisation potential (IP), and the UV-vis spectra were studied. It comes out that, the structure of the CAPE part included in BSCAPE agrees well with the available experimental values of CAPE but with a minor influence due to the presence of benzensulfonyl group. The enthalpy and free energy of solvation increase linearly with nH₂O. The global reactivity indexes were assessed to appreciate the oxidation of BSCAPE. The latter quality was strongly assessed by the enthalpy and free energy of SSET and IP. The SSET potential increase with nH₂O and the size of water clusters. The values 723.16 and 711.62 kJ/mol were found for enthalpy and free energy of IP respectively. Then in aqueous solution, the results fall down and upon addition of nH₂O, they approach gas phase value for 11H₂O and still are not stabilized. Therefore, the resistance to oxidation starts to raise at this level. Elsewhere, the UV-vis spectra of BSCAPE present four important peaks about 279.3, 234.8, 208.4 and 199.4 nm in gaseous state. The excitation shifts to the red as the number of H₂O increase. Their oscillator strengths also increase with solvation.

High-resolution tip-enhanced Raman scattering probes sub-molecular density changes

Tip-enhanced Raman spectroscopy (TERS) exhibits new selection rule and sub-nanometer spatial resolution, which is attributed to the plasmonic near-field confinement. Despite recent advances in simulations of TERS spectra under highly confined fields, a simply physical mechanism has remained elusive. In this work we show that single-molecule TERS images can be explained by local sub-molecular density changes induced by the confined near-field during the Raman process. The local sub-molecular density changes determine the spatial resolution in TERS and the gradient-based selection rule. Using this approach we find that the four-fold symmetry of meso-tetrakis(3,5-di-tert-butylphenyl)porphyrin (H₂TBPP) TERS images observed in experiments arises from the combination of degenerate normal modes localized in the functional side groups rather than the porphyrin ring as previously considered. As an illustration of the potential of the method, we demonstrate how this new theory can be applied to microscopic structure characterization.

Despite recent advances in simulations of tip-enhanced Raman spectroscopy (TERS) under highly confined fields, a simply physical mechanism has remained elusive. Here, the authors show that single molecule TERS images can be explained by local sub-molecular density changes induced by the confined near-field during the Raman process.

Graphene Nanobuds: A New Second-Generation Phosgene Sensor with Ultralow Detection Limit in Aqueous Solution

Selective and sensitive detection of highly toxic chemicals by a suitable, fast, inexpensive, and trustworthy method is vital due to its serious health threats to humankind and breach of public security caused by unexpected terrorist attacks and industrial accidents. Phosgene or carbonyl dichloride is widely employed in many chemical industries and pharmaceuticals, and in pesticide production, which is extremely toxic by severe (short-term) inhalation exposure. Because of the non-existence of a phosgene sensor in aqueous solution and the immense emphasis gained by nanomaterials, especially carbonaceous materials, augmented attention has been given to the development of a fluorophore-functionalized carbon-based method to detect this noxious substance. In this study, surfactant free 1,8-diaminonaphthalene (DAN)-functionalized graphene quantum dots (DAN-GQDs) were prepared to detect phosgene in aqueous solution. The FESEM (field emission scanning electron microscopy) and HRTEM (high-resolution transmission electron microscopy) analyses confirm the as-prepared DAN-GQD morphology as nanobuds (NBs) with an average diameter of ca. 35-40 nm. The crystalline nature, elemental composition, and chemical state of DAN-GQDs were analyzed by standard physiochemical techniques. The edge-termination at the carboxyl functional group of GQDs with DAN was examined by XPS, Raman, FT-IR, and ¹H NMR spectroscopy analyses. The aqueous solution of DAN-GQDs (4.89 × 10^-9 M) exhibits a strong emission peak at 423 nm upon excitation at 328 nm. The addition of the phosgene molecule (0 → 88 μL) quenches the initial fluorescence intensity of DAN-GQDs (Φ_F 53.6 → 34.6%) through the formation of a stable six-membered cyclized product. The DAN-GQDs displayed excellent selectivity and sensitivity for phosgene ( K_a = 3.84 × 10² M^-1 and LoD (limit of detection) = 2.26 ppb) over other competing toxic pollutants in water. The time-resolved fluorescence analysis confirms that the quenching of DAN-GQDs follows nonradiative relaxation of excited electrons. Furthermore, bioimaging experiments of phosgene in living human breast cancer (HeLa) cells and cell viability test successfully demonstrated the practicability of DAN-GQDs.

Intramolecular Path Determination of Active Electrons on Push-Pull Oligocarbazole Dyes-Sensitized Solar Cells

Several push‐pull oligocarbazole dye‐sensitizers have been studied using theoretical methods in order to better understand the relationship between structural electronic or optical properties and intramolecular path of active electrons during the ionization and injection processes. DFT/TD‐DFT calculations were performed on a series of five dye sensitizers. They differ by the presence of electron donating group (EDG) by inductive effect (noted+I) or electron releasing group (ERG) by mesomeric effect (noted+M) or electron withdrawing group by inductive effect (noted‐I) on the pushed part of the dyes studied. Our work focused on the internal distribution of electrons in the different parts of dye that are the push/pull moieties and the π‐bridge. The study concerned the ground state, the electronic transition process and the excited state. In each situation, the fragment acting in the ionization or transition phenomena were identified. In the ground state, the electrons of the push part appear to be the least bound because they have the highest probabilities of ionization. In the excited state, the ionized atoms are essentially positioned in the pushing part and some neighboring atoms of the bridge. In the electronic transition, the active atoms are located in the π‐conjugated part but only on the side adjacent to the acceptor group. To arrive to this conclusion, we optimized the structures of the five dyes in their ground and excited states. We calculated the atomic charges, the wavelengths and intensities of electronic transitions in the visible domain, the reorganization energies as well as the oxidation potential. It appears that +M donor ligands improve the performance of a dye because the great distribution of atoms to be ionized in the push parts.

Nucleotide conjugated (ZnO)3 cluster: Interaction and optical characteristics using TDDFT

Binding of four DNA nucleotide units with (ZnO)₃ cluster in an aqueous phase has been investigated using density functional theory (DFT) and time dependent-density functional theory (TDDFT) method and the stability order for (ZnO)₃-nucleobases/sugar/phosphate systems is predicted as phosphate > C > A > S > T ∼ G. The order of binding energy for (ZnO)₃-nucleotide hybrid systems is observed to be (ZnO)₃ + nuc-C ˃ (ZnO)₃ + nuc-A ˃ (ZnO)₃ + nuc-G ˃ (ZnO)₃ + nuc-T. The binding of nucleotide units with the cluster has been explained on the basis of molecular electrostatic potential (MEP) plots, hydrogen bonding, glycosidic torsion angles, density of state (DOS) plots. The photophysical properties of (ZnO)₃-nucleotide complexes have been studied using TDDFT approach. Among all (ZnO)₃-nucleotide complexes, the absorption spectra of (ZnO)₃ + nuc-A and (ZnO)₃ + nuc-C complexes are seen to undergo red shift with respect to their bare nucleotide units that would be useful in the optical sensing of the respective nucleotides of DNA. It is interesting to note that binding of the nucleotide unit with the cluster makes it fluorescent, the study reports the fluorescence activity of (ZnO)₃ + nuc-T complex.

Spiro-Phthalides and Isocoumarins Isolated from the Marine-Sponge-Derived Fungus Setosphaeria sp. SCSIO41009

Fourteen new polyketides classified as four phthalides, setosphalides A and B, 5- O-desmethylcolletotrialide, and ( S)-colletotrialide (1-4), three isocoumarin derivatives, exserolides I-K (5-7), four pyrones, setosphapyrones A-D (8-11), one furanone (12), and two depsidones (13 and 14), along with 17 known polyketides were isolated from cultures of the sponge-derived fungus Setosphaeria sp. SCSIO41009. The structures and absolute configurations of these new compounds (1-14) were determined by spectroscopic analyses, X-ray diffraction, chiral-phase HPLC analysis, modified Mosher's method, and comparison of ECD spectra to calculations. Setosphalides A (1) and B (2) are the first examples possessing a 5,5 spiroketal skeleton in phthalide derivatives. Botryorhodines I (13) and J (14) showed moderate antifungal activities against the phytopathogenic fungi Colletotrichum asianum and Colletotrichum acutatum. Compound 18 (7- O-demethylmonocerin) exhibited potent radical scavenging activity against DPPH.

Perylenequione Derivatives with Anticancer Activities Isolated from the Marine Sponge-Derived Fungus, Alternaria sp. SCSIO41014

Seven new secondary metabolites classified as two perylenequinone derivatives (1 and 2), an altenusin derivative (3), two phthalide racemates (4 and 5), and two phenol derivatives (6 and 7), along with twenty-one known compounds (8–28) were isolated from cultures of the sponge-derived fungus, Alternaria sp. SCSIO41014. The structures and absolute configurations of these new compounds (1–7) were determined by spectroscopic analysis, X-ray single crystal diffraction, chiral-phase HPLC separation, and comparison of ECD spectra to calculations. Altertoxin VII (1) is the first example possessing a novel 4,8-dihydroxy-substituted perylenequinone derivative, while the phenolic hydroxy groups have commonly always substituted at C-4 and C-9. Compound 1 exhibited cytotoxic activities against human erythroleukemia (K562), human gastric carcinoma cells (SGC-7901), and hepatocellular carcinoma cells (BEL-7402) with IC₅₀ values of 26.58 ± 0.80, 8.75 ± 0.13, and 13.11 ± 0.95 μg/mL, respectively. Compound 11 showed selectively cytotoxic activity against K562, with an IC₅₀ value of 19.67 ± 0.19 μg/mL. Compound 25 displayed moderate inhibitory activity against Staphylococcus aureus with an MIC value of 31.25 μg/mL.

Dispersion interactions between neighboring Bi atoms in (BiH3 )2 and Te(BiR2 )2

Triggered by the observation of a short Bi⋯Bi distance and a BiTeBi bond angle of only 86.6° in the crystal structure of bis(diethylbismuthanyl)tellurane quantum chemical computations on interactions between neighboring Bi atoms in Te(BiR₂ )₂ molecules (R = H, Me, Et) and in (BiH₃ )₂ were undertaken. Bi⋯Bi distances atoms were found to significantly shorten upon inclusion of the d shells of the heavy metal atoms into the electron correlation treatment, and it was confirmed that interaction energies from spin component-scaled second-order Møller-Plesset theory (SCS-MP2) agree well with coupled-cluster singles and doubles theory including perturbative triples (CCSD(T)). Density functional theory-based symmetry-adapted perturbation theory (DFT-SAPT) was used to study the anisotropy of the interplay of dispersion attraction and steric repulsion between the Bi atoms. Finally, geometries and relative stabilities of syn-syn and syn-anti conformers of Te(BiR₂ )₂ (R = H, Me, Et) and interconversion barriers between them were computed. © 2018 Wiley Periodicals, Inc.

Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions

This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies (Ees) usually constitute 95% of the total interaction energy. The Ees energies in this study were several times larger in absolute value when compared, for example, with dimers of neutral nucleobases. However, they were not as large as some theoretical calculations have predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from charge transfer from chlorine to the protonated nucleobases, small but visible charge redistribution within the nucleobase cations was observed. Some dimers of singly protonated bases in the studied crystals, namely a cytosinium-cytosinium trans sugar/sugar edge pair and an adeninium-adeninium trans Hoogsteen/Hoogsteen edge pair, exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. The pairs are metastable as a result of strong hydrogen bonding between bases which overcompensates the overall cation-cation repulsion, the latter being weakened due to charge transfer and molecular charge-density polarization.

Cytotoxic and Antibacterial Eremophilane Sesquiterpenes from the Marine-Derived Fungus Cochliobolus lunatus SCSIO41401

Three new eremophilane sesquiterpenes, dendryphiellins H-J (1-3), and three new phthalide natural products (4-6) were isolated from the marine-derived fungus Cochliobolus lunatus SCSIO41401. Their structures including absolute configurations were determined by spectroscopic and calculated ECD analyses. Dendryphiellin I (2) showed cytotoxic and antibacterial activities against five cancer cell lines (IC₅₀ 1.4 to 4.3 μM) and three bacterial species (MIC 1.5 to 13 μg/mL), respectively. Dendryphiellin J (3), a rare naturally occurring aldoxime analogue, displayed cytotoxicities against ACHN and HepG-2 cells with IC₅₀ values of 3.1 and 5.9 μM, respectively. Further studies indicated that 3 induced apoptosis in ACHN cells in a dose- and time-dependent manner.