Accuracy of Effective Core Potentials and Basis Sets for Density Functional Calculations, Including Relativistic Effects, As Illustrated by Calculations on Arsenic Compounds

Tube-like Gold Clusters M2@Au17 q (M = W, Mo; q = 0, ±1): Structure, Electronic Property, and Optical Nonlinearity

Density functional theory (DFT) calculations are carried out to determine the geometries and electronic and nonlinear optical (NLO) properties of the doubly doped gold clusters in three charge states M2 @ Au17 q with M = W, Mo and q = 0, ±1. At their lowest-lying equilibrium structures, the impurities that are vertically encapsulated inside a cylindrical gold framework, significantly enhance the stability and modify properties of the host. The presence of M2 units results in the formation of a tube-like ground state, which is identified for the first time for gold clusters. Having 30 itinerant electrons, the electron shell of M2@Au17 - can be described as 1S21P61D102S2{1F xz 2 21F yz 2 2}1F z 3 2{1F xyz 21F z(x 2-y 2) 2}{1F y(3x 2 -y 2),1F x(x 2 -3y 2)}. The species is thus stabilized upon doping, but it is not a magic cluster. The optical transitions are shifted to the lower-energy region upon doping Mo and W atoms into Au17 q . The static and dynamic NLO properties of M2@Au17 q are also computed and compared to those of the pure Au19 q (having the same number of atoms) and an external reference molecule, i.e., para-nitroaniline (p-NA). For hyperpolarizabilities, the doped clusters possess smaller values than those of their pure counterparts but much larger values than the p-NA. Of the doubly doped systems, the neutral M2@Au17 exhibits particularly high first and second hyperpolarizability tensors. The doped cluster units can also be used as building blocks for the design of gold-based nanowires with outstanding electronic and optical characteristics.

The smallest triple-ring tubular gold clusters M2@Au15 with M = Mo, W: stability, electronic properties and nonlinear optical response

The smallest triple ring tube-like gold clusters M2@Au15q with M = Mo, W and q = 1, 0, -1 are reported for the first time. Incorporation of an M2 dimer results in a remarkable modification of both atomic and electronic structures of the gold host. While the bare Au15 cluster exhibits a 3D cage shape, the doubly doped clusters M2@Au15 in all charge states are found to prefer a tubular form composed of three five-membered Au rings in an anti-prism arrangement and stabilized by an M2 unit placed inside the tube-like Au15 gold framework. The equilibrium geometry of both M2@Au15 and M2@Au15- is not much modified upon electron detachment from or attachment to their pure gold counterpart. The anion M2@Au15- with 28 itinerant electrons establishes an electron shell configuration of 1S21P61D102S21F8, in which the 1F shell splits into four different sub-levels. These stable clusters are thus not magic. Computed results on the first and second hyper-polarizability parameters of the doped clusters show a strong dependence on the charge. Overall, the neutral M2@Au15 is found to exhibit a particularly strong nonlinear optical (NLO) response. These clusters can also be extended to 1D nanowires, providing helpful guidance for the design of novel gold-based nanowires with rich optoelectronic properties.

The Use of Effective Core Potentials with Multiconfiguration Pair-Density Functional Theory

The reliable and accurate prediction of chemical properties is a key goal in quantum chemistry. Transition-metal-containing complexes can often pose difficulties to quantum mechanical methods for multiple reasons, including many electron configurations contributing to the overall electronic description of the system and the large number of electrons significantly increasing the amount of computational resources required. Often, multiconfigurational electronic structure methods are employed for such systems, and the cost of these calculations can be reduced by the use of an effective core potential (ECP). In this work, we explore both theoretical considerations and performances of ECPs applied in the context of multiconfiguration pair-density functional theory (MC-PDFT). A mixed-basis set approach is used, using ECP basis sets for transition metals and all-electron basis sets for nonmetal atoms. We illustrate the effects that an ECP has on the key parameters used in the computation of MC-PDFT energies, and we explore how ECPs affect the prediction of physical observables for chemical systems. The dissociation curve for a metal dimer was explored, and ionization energies for transition metal-containing diatomic systems were computed and compared to experimental values. In general, we find that ECP approaches employed with MC-PDFT are able to predict ionization energies with improved accuracy compared to traditional Kohn-Sham density functional theory approaches.

Perhalogenated Anilines as Bifunctional Donors of Hydrogen and Halogen Bonds in Cocrystals with Ditopic Nitrogen-Containing Acceptors

In this study, we examine the experimental and theoretical capabilities of two perhalogenated anilines, 2,3,5,6-tetrafluoro-4-bromoaniline (btfa) and 2,3,5,6-tetrafluoro-4-iodoaniline (itfa) as hydrogen and halogen bond donors. A series of 11 cocrystals derived from the two anilines and selected ditopic nitrogen-containing acceptors (4,4'-bipyridine, 1,2-bis(4-pyridyl)ethane, and 1,4-diazabicyclo[2.2.2]octane) in 1:1 and 2:1 stoichiometries were prepared by liquid-assisted grinding and crystallization from solution. Crystallographic analysis revealed bifunctional donor properties in both anilines. The dominant supramolecular interaction in four cocrystals of btfa is the N-H···Nacceptor hydrogen bond between btfa and acceptor molecules, while in the one remaining cocrystal, donor and acceptor molecules are connected via the N-H···Nacceptor hydrogen bond and the Br···Nacceptor halogen bond. In two cocrystals of itfa, the dominant supramolecular interaction is the I···Nacceptor halogen bond between itfa and acceptor molecules, while in the remaining four cocrystals, donor and acceptor molecules are additionally connected by the N-H···Nacceptor hydrogen bond. Periodic density-functional theory (DFT) calculations have been conducted to assess the formation energies of these cocrystals and the strengths of the established halogen and hydrogen bonds. Molecular DFT calculations on btfa and itfa indicate that the differences in electrostatic potential between the competing sites on the molecules are 261.6 and 157.0 kJ mol-1 e-1, respectively. The findings suggest that itfa, with a smaller electrostatic potential difference between donor sites, is more predisposed to act as a bifunctional donor.

Distinguishing the responsive mechanisms of fluorescent probes to hydrogen peroxide, proteins, and DNA/RNA

The responsive mechanisms of cationic quinolinium-vinyl-N,N-dimethylaniline boronate (QVD-B) derivative probes to hydrogen peroxide (H2O2), proteins and DNA/RNA are theoretically investigated in this study. The potential energy curves of QVD-B scanned on a dihedral angle (N+-C-CC) in the first singlet (S1) state exhibit large torsional energy barriers. Additionally, the energy of the lowest unoccupied molecular orbital (LUMO) of an acceptor moiety (-3.14 eV) is lower than that of a donor moiety (-1.13 eV) in QVD-B. This demonstrates that photoinduced electron transfer (PET) quenches the fluorescence of QVD-B, as opposed to the previous report of intramolecular single-bond rotation. After reacting with H2O2, the reaction product of quinoline-vinyl-N,N-dimethylaniline (QVD) turns off the PET pathway and turns on the fluorescence at 550 nm, which is consistent with the experimental results (580 nm). Among the possible configurations of QVD-B that forms with proteins and DNA, the calculated fluorescence values of corresponding twisted QVD-B-P (638 nm) and QVD-B-D (686 nm) are consistent with the experimental results (632 and 688 nm). The frontier molecular orbital and electron-hole analysis show that the charge transfer distance follows the order of QVD (1.88 Å) < QVD-B-P (4.49 Å) < QVD-B-D (6.39 Å), which induces the fluorescence red-shifts of QVD-B-P and QVD-B-D compared to that of QVD. The multi-detection mechanism of the fluorescent probe QVD-B is attributed to PET progress and different degrees of local charge transfer after photoexcitation.

Scalar Relativistic Effects with Multiwavelets: Implementation and Benchmark

The importance of relativistic effects in quantum chemistry is widely recognized, not only for heavier elements but throughout the periodic table. At the same time, relativistic effects are strongest in the nuclear region, where the description of electrons through a linear combination of atomic orbitals becomes more challenging. Furthermore, the choice of basis sets for heavier elements is limited compared with lighter elements where precise basis sets are available. Thanks to the framework of multiresolution analysis, multiwavelets provide an appealing alternative to overcoming this challenge: they lead to robust error control and adaptive algorithms that automatically refine the basis set description until the desired precision is reached. This allows one to achieve a proper description of the nuclear region. In this work, we extended the multiwavelet-based code MRChem to the scalar zero-order regular approximation framework. We validated our implementation by comparing the total energies for a small set of elements and molecules. To confirm the validity of our implementation, we compared both against a radial numerical code for atoms and the plane-wave-based code EXCITING.

Error of relativistic effective core potentials for closed-shell diatomic molecules of p-block heavy and superheavy elements in DFT and TDDFT calculations

Pseudopotentials (PP) are extensively used in electronic structure calculations, particularly for molecules containing heavy elements. Parameters in PPs are mainly determined from ab initio results, and errors of such PPs in density functional theory (DFT) calculations have been studied previously. However, PP errors on results with spin-orbit coupling and those in time-dependent DFT (TDDFT) calculations have not been reported previously. In this work, we investigate the error of the small-core energy-consistent Stuttgart/Koln pseudopotentials in DFT and TDDFT calculations with and without spin-orbit coupling. Ground state bond lengths, harmonic frequencies, dissociation energies, and vertical excitation energies for a series of closed-shell diatomic heavy and superheavy p-block molecules are calculated using several popular exchange-correlation functionals. PP errors are estimated by comparing with results using the all-electron Dirac-Coulomb (-Gaunt) Hamiltonian. Our results show that the difference between ground state properties and most excitation energies in scalar-relativistic calculations with the PP and those of all-electron calculations is quite small. This difference becomes somewhat larger when spin-orbit coupling (SOC) is present, especially for properties that are affected by SOC to some extent. In addition, the errors of the PPs are insensitive to the employed exchange-correlation functionals in most cases. Our results indicate that reasonable DFT and TDDFT results can be obtained using the small-core energy-consistent Stuttgart/Koln pseudopotentials for heavy and super-heavy p-block molecules.

Physicochemical properties and density functional theory calculation of octahedral UiO-66 with Bis(Trifluoromethanesulfonyl)imide ionic liquids

In this study, the physicochemical properties and molecular interactions between zirconium-based metal-organic framework (UiO-66) and three different ionic liquids based on bis(trifluoromethanesulfonyl)imide anion (EMIM+, BMIM+ and OMIM+) was performed via a combined experimental and computational approach. The ionic liquid loaded UiO-66 or IL@UiO-66 was synthesized and characterized to understand the host-guest interaction. Density functional theory calculation was performed to analyse the electronic structure of IL@UiO-66 to provide molecular insight on the dominant interactions occurred in the hybrid material. Results showed that all ILs were successfully incorporated into the micropores of UiO-66. The 3D framework was retained even after loaded with ILs as analyzed from XRD pattern. FTIR spectrum reveals that interactions of ILs with UiO-66 influenced by the alkyl chain length of the cation. The anion has a profound affinity with the UiO-66 due to the presence of electronegative atoms. Phase transition study from DSC suggested that the incorporation of ILs has stabilized the framework of UiO-66 by shifting the endothermic peak to a higher state. These findings were further elaborated with DFT calculation. Geometrical optimizations confirmed the structural parameter changes of UiO-66 when loaded with ILs. These was mainly contributed by the non-covalent interactions which was confirmed by the reduced density gradient scattered plot. Another important findings are the strength of hydrogen bonding at the host-guest interface was influenced by the alkyl chain length. The molecular orbital analysis also shows that the size of alkyl chain influence the reactivity of the hybrid material. The present study provides fundamental insights on the molecular interaction of UiO-66 and ILs as a hybrid material, which can open new possibilities for advanced material for metal-organic framework applications in energy storage system, catalysis, gas storage and medicinal chemistry.

Dissociative electron attachment to gold(I)-based compounds: 4,5-dichloro-1,3-diethyl-imidazolylidene trifluoromethyl gold(I)

With the use of proton-NMR and powder XRD (XRPD) studies, the suitability of specific Au-focused electron beam induced deposition (FEBID) precursors has been investigated with low electron energy, structure, excited states and resonances, structural crystal modifications, flexibility, and vaporization level. 4,5-Dichloro-1,3-diethyl-imidazolylidene trifluoromethyl gold(I) is a compound that is a uniquely designed precursor to meet the needs of focused electron beam-induced deposition at the nanostructure level, which proves its capability in creating high purity structures, and its growing importance in other AuIm_x and AuCl_nB (where x and n are the number of radicals, B = CH, CH₃, or Br) compounds in the radiation cancer therapy increases the efforts to design more suitable bonds in processes of SEM (scanning electron microscopy) deposition and in gas-phase studies. The investigation performed of its powder shape using the XRPD XPERT³ panalytical diffractometer based on CoK_α lines shows changes to its structure with change in temperature, level of vacuum, and light; the sensitivity of this compound makes it highly interesting in particular to the radiation research. Used in FEBID, though its smaller number of C, H, and O atoms has lower levels of C contamination in the structures and on the surface, it replaces these bonds with C-Cl and C-N bonds that have lower bond-breaking energy. However, it still needs an extra purification step in the deposition process, either H₂O, O₂, or H jets.

Optical frequency comb-based measurements and the revisited assignment of high-resolution spectra of CH2Br2 in the 2960 to 3120 cm-1 region

Brominated organic compounds are toxic ocean-derived trace gases that affect the oxidation capacity of the atmosphere and contribute to its bromine burden. Quantitative spectroscopic detection of these gases is limited by the lack of accurate absorption cross-section data as well as rigorous spectroscopic models. This work presents measurements of high-resolution spectra of dibromomethane, CH₂Br₂, from 2960 cm^-1 to 3120 cm^-1 by two optical frequency comb-based methods, Fourier transform spectroscopy and a spatially dispersive method based on a virtually imaged phased array. The integrated absorption cross-sections measured using the two spectrometers are in excellent agreement with each other within 4%. A revisited rovibrational assignment of the measured spectra is introduced, in which the progressions of features are attributed to hot bands rather than different isotopologues as was previously done. Overall, twelve vibrational transitions, four for each of the three isotopologues CH₂⁸¹Br₂, CH₂⁷⁹Br⁸¹Br, and CH₂⁷⁹Br₂, are assigned. These four vibrational transitions are attributed to the fundamental ν₆ band and the nearby nν₄ + ν₆ - nν₄ hot bands (with n = 1-3) due to the population of the low-lying ν₄ mode of the Br-C-Br bending vibration at room temperature. The new simulations show very good agreement in intensities with the experiment as predicted by the Boltzmann distribution factor. The spectra of the fundamental and the hot bands show progressions of strong Q_Ka(J) rovibrational sub-clusters. The band heads of these sub-clusters are assigned and fitted to the measured spectra, providing accurate band origins and the rotational constants for the twelve states with an average error of 0.0084 cm^-1. A detailed fit of the ν₆ band of the CH₂⁷⁹Br⁸¹Br isotopologue is commenced after assigning 1808 partially resolved rovibrational lines, with the band origin, rotational, and centrifugal constants as fit parameters, resulting in an average error of 0.0011 cm^-1.

Performance of Density Functionals and Semiempirical 3c Methods for Small Gold-Thiolate Clusters

In light of the recent surge in computational studies of gold thiolate clusters, we present a comparison of popular density functionals (DFAs) and three-part corrected methods (3c-methods) on their performance by taking a data set named as AuSR18 consisting of 18 isomers of Au_n(SCH₃)_m (m ≤ n = 1-3). We have compared the efficiency and accuracy of the DFAs and 3c-methods in geometry optimization with RI-SCS-MP2 as the reference method. Similarly, the performance for accurate and efficient energy evaluation was compared with DLPNO-CCSD(T) as the reference method. The lowest energy structure among the isomers of the largest stoichiometry from our data set, AuSR18, i.e., Au₃(SCH₃)₃, is considered to evaluate the computational time for SCF and gradient evaluations. Alongside this, the numbers of optimization steps to locate the most stable minima of Au₃(SCH₃)₃ are compared to assess the efficiency of the methods. A comparison of relevant bond lengths with the reference geometries was made to estimate the accuracy in geometry optimization. Some methods, such as LC-BLYP, ωB97M-D3BJ, M06-2X, and PBEh-3c, could not locate many of the minima found by most of the other methods; thus, the versatility in locating various minima is also an important criterion in choosing a method for the given project. To determine the accuracy of the methods, we compared the relative energies of the isomers in each stoichiometry and the interaction energy of the gold core with the ligands. The dependence of basis set size and relativistic effects on energies are also compared. The following are some of the highlights. TPSS has shown accuracy, while mPWPW shows comparable speed and accuracy. For the relative energies of the clusters, the hybrid range-separated DFAs are the best option. CAM-B3LYP excels, whereas B3LYP performs poorly. Overall, LC-BLYP is a balanced performer considering both the geometry and relative stability of the structures, but it lacks diversity. The 3c-methods, although fast, are less impressive in relative stability.

Inorganic Drugs as a Tool for Protein Structure Solving and Studies on Conformational Changes

Inorganic drugs are capable of tight interactions with proteins through coordination towards aminoacidic residues, and this feature is recognized as a key aspect for their pharmacological action. However, the "protein metalation process" is exploitable for solving the phase problem and structural resolution. In fact, the use of inorganic drugs bearing specific metal centers and ligands capable to drive the binding towards the desired portions of the protein target could represent a very intriguing and fruitful strategy. In this context, a theoretical approach may further contribute to solve protein structures and their refinement. Here, we delineate the main features of a reliable experimental-theoretical integrated approach, based on the use of metallodrugs, for protein structure solving.

Ethanol Oxidation Reaction Mechanism on Gold Nanowires from Density Functional Theory

Thin gold nanowires (NWs) are materials that could be used as support in different chemical reactions. Using density functional theory (DFT) it was shown that NWs that form linear atomic chains (LACs) are suitable for stimulating chemical reactions. To this end, the oxidation reaction of ethanol supported on the LACs of Au-NWs was investigated. Two types of LACs were used for the study, one pure and the other with an oxygen impurity. The results showed that the oxygen atom in the LAC fulfills important functions throughout the reaction pathway. Before the chemical reaction, it was observed that the LAC with impurity gains structural stability, that is, the oxygen acts as an anchor for the gold atoms in the LAC. In addition, the LAC was shown to be sensitive to disturbances in its vicinity, which modifies its nucleophilic character. During the chemical reaction, the oxidation of ethanol occurs through two different reaction paths and in two stages, both producing acetaldehyde (CH₃ CHO). The different reaction pathways are a consequence of the presence of oxygen in the LAC (oxygen conditions the formation of reaction intermediates). In addition, the oxygen in the LAC also modifies the kinetic behavior in both reaction stages. It was observed that, by introducing an oxygen impurity in the LAC, the activation energy barriers decrease ∼69 % and ∼97 % in the first and second reaction stages, respectively.

Kinetics of IO radicals with C1, C2 aliphatic alcohols in tropospherically relevant conditions

Kinetics of the reaction of IO radicals with methanol (MeOH) and ethanol (EtOH) were experimentally studied in the gas phase using pulsed laser photolysis-cavity ring-down spectroscopy (PLP-CRDS). IO radicals were produced in situ at the reaction zone by photolysing a mixture of precursors (CH₃I + O₃ + N₂) at 248 nm and thereby electronically excited at 445.04 nm. The rate coefficients for the reactions of (IO + MeOH) and (IO + EtOH) were measured at a total pressure of 60 Torr/N₂ in the range of 258-360 K. At room temperature, the experimental rate coefficients of the title reactions were measured to be [Formula: see text] and [Formula: see text]. Dependencies of the kinetics with photolysis laser fluence and experimental pressures were verified. Effects of pressure over the kinetic behaviour of the studied systems were observed to be insignificant within the statistical uncertainties when studied in the range of ~ 30-150 Torr/N₂, whereas a minor and linear fluence dependency was observed within the studied limit. From the measured kinetic parameters, the atmospheric lifetimes of MeOH and EtOH were calculated in the tropospherically relevant conditions regarding their reactions with important atmospheric oxidants like Cl atom, OH and IO radicals. To complement experimental results, kinetics and thermochemistry for the title reactions were investigated theoretically via canonical variational transition state (CVT) theory in combination with small curvature tunnelling (SCT) corrections with a dual-level Interpolated Single Point Energy (ISPE) approach at the CCSD(T)/def2-QZVPP//M06-2X/def2-TZVPP level of theory/basis set in the temperatures between 200 and 400 K. Good degree of agreement was encountered between experimentally measured and theoretically calculated rate coefficients. This article also discusses the thermochemical parameters and kinetic branching ratios (BRs) of all the pathways involved in the title reactions.

Benchmarking Density Functionals, Basis Sets, and Solvent Models in Predicting Thermodynamic Hydricities of Organic Hydrides

Many renewable energy technologies, such as hydrogen gas synthesis and carbon dioxide reduction, rely on chemical reactions involving hydride anions (H^-). When selecting molecules to be used in such applications, an important quantity to consider is the thermodynamic hydricity, which is the free energy required for a species to donate a hydride anion. Theoretical calculations of thermodynamic hydricity depend on several parameters, mainly the density functional, basis set, and solvent model. In order to assess the effects of the above three parameters, we carry out hydricity calculations with different combinations of density functionals, basis sets, and solvent models for a set of organic molecules with known experimental hydricity values. The data are analyzed by comparing the R² and root-mean-squared error (RMSE) of linear fits with a fixed slope of 1 and using the Akaike Information Criterion to determine statistical significance of the RMSE rank ordering. Based on these results, we quantified the accuracy of theoretical predictions of hydricity and found that the best compromise between accuracy and computational cost was obtained by using the B3LYP-D3 density functional for the geometry optimization and free-energy corrections, either ωB97X-D3 or M06-2X-D3 for single-point energy corrections, combined with a basis set no larger than def-TZVP and the C-PCM ISWIG solvation model. At this level of theory, the RMSEs of hydricity calculations for organic molecules in acetonitrile and dimethyl sulfoxide were found to be <4 and <10 kcal/mol, respectively, for an experimental data set with a dynamic range of 20-150 kcal/mol.

Structure-based model of fucoxanthin-chlorophyll protein complex: Calculations of chlorophyll electronic couplings

Diatoms are a group of marine algae that are responsible for a significant part of global oxygen production. Adapted to life in an aqueous environment dominated by the blue-green light, their major light-harvesting antennae-fucoxanthin-chlorophyll protein complexes (FCPs)-exhibit different pigment compositions than of plants. Despite extensive experimental studies, until recently the theoretical description of excitation energy dynamics in these complexes was limited by the lack of high-resolution structural data. In this work, we use the recently resolved crystallographic information of the FCP complex from Phaeodactylum tricornutum diatom [Wang et al., Science 363, 6427 (2019)] and quantum chemistry-based calculations to evaluate the chlorophyll transition dipole moments, atomic transition charges from electrostatic potential, and the inter-chlorophyll couplings in this complex. The obtained structure-based excitonic couplings form the foundation for any modeling of stationary or time-resolved spectroscopic data. We also calculate the inter-pigment Förster energy transfer rates and identify two quickly equilibrating chlorophyll clusters.

Bonding in Nitrile Photo-dissociating Ruthenium Drug Candidates --A Local Vibrational Mode Study

In this work, we investigated bonding features 15 ruthenium complexes of the type [Ru(tpy)(L)-(CH3CN)]n+, containing the tridentate tpy ligand (tpy = 2,2':6',2'--terpyridine) and various bidentate ancillary ligands, 12 compounds originally synthesized by Loftus et al. (J. Phys. Chem. C 123, 10291-10299 (2019)) complemented with three additional complexes. The main focus of our work was to relate these local features to the experimental data of Loftus et al. which assess the efficiency of nitrile release in an indirect way via observed quantum yields for ruthenium water association after nitrile release. As a tool to quantitatively assess Ru-NC and Ru-L bonding we utilized the local vibrational mode analysis complemented by the topological analysis of the electron density and the natural bond orbital analysis. Interestingly, the stronger Ru-NC bonds have the greater observed quantum yields, leading to the conclusion that the observed quantum yields are a result of a complex interplay of several processes excluding a direct relationship between QY and Ru-NC or Ru-L bond strengths. We identified the ST splitting as one of the key players and not the Ru-NC bond strength, as one may have thought. In summary, this work has presented a modern computational tool set for the investigation of bonding features applied to nitrile photo-dissociating ruthenium drug candidates forming a valuable basis for future design and fine tuning of nitrile releasing ruthenium compounds, as well as for the understanding of how local properties affect overall experimental outcomes.

Photoexcited Intramolecular Charge Transfer in Dye Sensitizers: Predictive In Silico Screening for Dye-Sensitized Solar Cell Devices

Efficient photoinduced intramolecular charge transfer (ICT) from donor to acceptor in dye molecules is the functional basis and key property in the working of a dye-sensitized solar cell (DSSC). To understand the ICT process in photoexcited dye molecules, we analyze the electronic properties and structural parameters of a chosen set of experimentally synthesized donor-acceptor (D-A) and donor-π-spacer-acceptor (D-π-A) type dye molecules in their ground, excited, and cationic states. The correlation between structural modification and charge redistribution in different parts of the molecule helps to identify the extent of π-conjugation and spatial rearrangement of electron density localization along the molecular skeleton. We find that prominent twisting of several groups and the resulting molecular bond rearrangements in larger parts of the molecule promote efficient donor to acceptor ICT, such as in D-A type ADEKA1 and C275 dyes. Thus, based on the modest computation of structural and electronic properties of dye molecules in their respective ground, excited, and cationic states, we identify the desired structural changes that facilitate tunable intramolecular charge transfer to highlight a simple and direct prescription to screen out probable efficient dye molecules among many samples. Our approach complements recent experimental evidence of capturing the structural view of the excited-state charge transfer in molecules.

Kinetics of IO radicals with ethyl formate and ethyl acetate: a study using cavity ring-down spectroscopy and theoretical methods

The gas-phase kinetics of the reactions of IO radicals with ethyl formate (EF) and ethyl acetate (EA) were investigated experimentally using cavity ring-down spectroscopy (CRDS). IO radicals were generated in situ in the CRD reaction zone by photolyzing a mixture of (CH₃I + O₃ + N₂) at 248 nm and thereby probed at 445.04 nm. The rate coefficients for the reactions (IO + EF) and (IO + EA) were measured at a total pressure of 65 Torr of N₂ in the temperature range of 258-358 and 260-360 K, respectively. The rate coefficients for the reactions (IO + EF) and (IO + EA) were measured experimentally at room temperature to be kExpt,298KIO+EF = (3.38 ± 0.67) × 10^-14 and kExpt,298KIO+EA = (1.56 ± 0.30) × 10^-13 cm³ molecule^-1 s^-1, respectively. The effects of pressure and photolysis laser fluence on the kinetics of test reactions were found to be negligible within the experimental uncertainties for the studied range. To complement our experimental findings, the kinetics of the title reactions were investigated theoretically using canonical variational transition state theory (CVT) with small curvature tunnelling (SCT) at the CCSD(T)//M06-2X/def2-SV(P) level of theory in temperatures between 200 and 400 K. Very good agreement was observed between the experimentally measured and theoretically calculated rate coefficients for both the reactions at 298 K. The thermochemical parameters as well as the branching ratios for the title reactions are also discussed in this study.

Direct orange 26 dye environmental degradation: experimental studies (UV, mass, and thermal) in comparison with computational exploration hydrogen bonding analysis of TD-DFT calculations

The importance of this study stems from, it concentrates on new approach applying both practical and theoretical aspects to study structure stability of direct orange dye 26 (DO26) as an important dye widely used for dyeing of cotton or viscose for red orange direct printing. The stable dyes are so difficult to remove, decolorized and/or degrade, in pure solution or in wastewater samples, without using powerful removal environmental techniques electrochemical oxidations suggest and efficiently used in our Lab. Therefore, it is very important to compare between practical thermal and mass results as efficient techniques in studying dye stability, in comparison with theoretical results using Gaussian program for structural stability identification of DO26 dye, via careful inspection of various phenomena detected in its two symmetrical arms around urea center. Direct orange dye 26 (DO26) structure has been studied applying both practical spectroscopic and theoretical investigations. DFT-B3LYP/6-311 +  + G(d,p) calculations and the electronic vibrational properties are performed to investigate its structure stability and consequently its degradation and removal from its environmental media. Correlation is found between experimental and calculated data. An intra-molecular hydrogen bonding interaction had been detected and characterized in dye skeleton. The hydrogen bonding present in the dye structure affecting its vibrational properties had been discussed. Natural population analysis like HOMO and LUMO and high-quality molecular electrostatic potential plots along with various electronics had been presented at the same level of theory. Chemical reactivity descriptors from conceptual density functional theory point of view and structure activity relationship descriptor were obtained. The experimental UV/visible, FT-IR, mass and GC-mass spectral data of the dye DO26 (D1) had been presented. These data had been supported by TD-DFT calculations to simulate the experimental spectra with computing the natural transition orbitals (NTO) and the orbital composition. Actually there is a problem that the degradation of this dye in wastewater by different techniques leads to various unknown fragments, but on using theoretical possibilities, it can be expected what happened in practical work.

Automation of some macromolecular properties using a machine learning approach

In this study, we employed a newly developed method to predict macromolecular properties using a swarm artificial neural network (ANN) method as a machine learning approach. In this method, the molecular structures are represented by the feature description vectors used as training input data for a neural network. This study aims to develop an efficient approach for training an ANN using either experimental or quantum mechanics data. We aim to introduce an error model controlling the reliability of the prediction confidence interval using a bootstrapping swarm approach. We created different datasets of selected experimental or quantum mechanics results. Using this optimized ANN, we hope to predict properties and their statistical errors for new molecules. There are four datasets used in this study. That includes the dataset of 642 small organic molecules with known experimental hydration free energies, the dataset of 1475 experimental pKa values of ionizable groups in 192 proteins, the dataset of 2693 mutants in 14 proteins with given experimental values of changes in the Gibbs free energy, and a dataset of 7101 quantum mechanics heat of formation calculations. All the data are prepared and optimized using the AMBER force field in the CHARMM macromolecular computer simulation program. The bootstrapping swarm ANN code for performing the optimization and prediction is written in Python computer programming language. The descriptor vectors of the small molecules are based on the Coulomb matrix and sum over bond properties. For the macromolecular systems, they consider the chemical-physical fingerprints of the region in the vicinity of each amino acid.

Synthesis, spectral characterization, DFT calculations, pharmacological studies, CT-DNA binding and molecular docking of potential N, O-multidentate chelating ligand and its VO(II), Zn(II) and ZrO(II) chelates

The pharmacological efficacy of the variety tetradentate ligands encouraged us to design attractive compounds through effective synthetic procedure. The prepared Schiff base ligand 6,6'-((1E,1'E)-((4-chloro-1,2-phenylene)bis(azaneylylidene))bis(methaneylylidene))bis(2-ethoxy phenol (H₂L), which derived from 4-chloro-o-phenylenediamine and 3-ethoxy-salicylaldehyde and its VO(II), Zn(II) and ZrO(II) metal chelates, have been synthesized and characterized with aim of that it may struggle the invasion of drug resistance. The chemical structural of studied compounds were discussed by TGA, elemental analysis, UV-Vis., ¹H NMR, ¹³C NMR, FTIR, mass spectral, PXRD, molar conductance, magnetic susceptibility measurements and density functional theory. The results assigned square pyramid geometries for [VOL] and [ZrOL].2H₂O chelates and an octahedral geometry for [ZnL(H₂O)₂].2H₂O chelate. Powder XRD data showed that the complexes are monoclinic with polycrystalline nature. The results of CT-DNA interaction with the titled chelates showed that the binding between CT-DNA and the metal complexes occurs through intercalation mode. Their CT-DNA binding efficiency estimated in terms of their binding constants (K_b), which gave the order: VOL (6.9 × 10⁵) > ZrOL (6.3 × 10⁵) > ZnL(H₂O)₂ (5.5 × 10⁵). The antimicrobial activities of the synthesized compounds were tested against selected fungal and bacterial strains using well diffusion technique. The obtained chelates showed higher antifungal and antibacterial activities than their corresponding ligand. Furthermore, the M-complexes showed higher potent cytotoxic effect toward HEK-293, human colorectal HepG-2, HCT-116 and MCF-7 adenocarcinoma cell lines compared to the free H₂L ligand. Investigation of antioxidant property represented that all the prepared complexes have better radical scavenging potencies against DPPH radicals than the free H₂L ligand. To study the molecular docking of proposed compounds versus Tyrosine kinases receptor (TKR), we used AutoDock1.5.6rc3® suite. The current compounds (H₂L, VOL, ZrOL and ZnL(H₂O)₂) and STI were found to bind with C-kit of TKR with HBs at ILE789.A, ILE808.A, ASP810.A, GLU640.A and TYR846 amino acid residue and the binding energies were - 8.9, -8.93, -8.83, -1.48 and -10.39 kcal/mol respectively.

Tuning the reactivity of alkoxyl radicals from 1,5-hydrogen atom transfer to 1,2-silyl transfer

Controlling the reactivity of reactive intermediates is essential to achieve selective transformations. Due to the facile 1,5-hydrogen atom transfer (HAT), alkoxyl radicals have been proven to be important synthetic intermediates for the δ-functionalization of alcohols. Herein, we disclose a strategy to inhibit 1,5-HAT by introducing a silyl group into the α-position of alkoxyl radicals. The efficient radical 1,2-silyl transfer (SiT) allows us to make various α-functionalized products from alcohol substrates. Compared with the direct generation of α-carbon radicals from oxidation of α-C-H bond of alcohols, the 1,2-SiT strategy distinguishes itself by the generation of alkoxyl radicals, the tolerance of many functional groups, such as intramolecular hydroxyl groups and C-H bonds next to oxygen atoms, and the use of silyl alcohols as limiting reagents.

Revisiting the effect of f-functions in predicting the right reaction mechanism for hypervalent iodine reagents

To understand the effect of f-functions in predicting the right reaction mechanism for hypervalent iodine reagents, we adopt the Ahlrichs basis set family def2-SVP and def2-TZVP to revisit the potential energy surfaces of IBX-mediated oxidation and Togni I's isomerisation. Our results further prove that f-functions (in either Pople, Dunning, or Ahlrichs basis set series) are indispensable to predict the correct rate-determining step of hypervalent iodine reagents. The f-functions have a significant impact on the predicted reaction barriers for processes involving the IX (X = O, OH, CF₃ , etc.) bond cleavage and formation, for example, in the reductive elimination step or the hypervalent twist step. We furthermore explore two hypervalent twist modes that account for the different influences of f-functions for IBX and Togni I. Our findings may be helpful for theoretical chemists to appropriately study the reaction mechanism of hypervalent iodine reagents.

Role of oxygen functional groups in Pb2+ adsorption from aqueous solution on carbonaceous surface: A density functional theory study

The adsorption mechanism of Pb²⁺ from aqueous solution on carbonaceous surface modified with oxygen functional groups was investigated by using density functional theory method. The zigzag model with seven benzene rings and armchair model with four benzene rings were used to simulate the different structures of carbonaceous surfaces. It was found that the adsorption of Pb²⁺ on the pure zigzag surface was chemisorption with the adsorption energy of - 306.26 to - 322.36 kJ/mol, while that on the armchair surface was physisorption with the adsorption energy of - 32.39 kJ/mol. The introduction of oxygen functional groups significantly enhanced the Pb²⁺ adsorption on the armchair surface. The physisorption changed to chemisorption after adding carboxyl, phenolic hydroxyl, or carbonyl functional group, indicating the stronger adsorption ability of the carbonaceous surfaces after modification. On the zigzag surface, however, the studied functional groups cannot benefit the Pb²⁺ adsorption. The results showed that the Pb²⁺ tended to adsorb on the carbon atoms instead of moving to the oxygen atoms from the introduced functional groups for adsorption, which suggests that the oxygen functional groups promoted the Pb²⁺ adsorption by increasing the activity of their neighboring carbon atoms.

Towards H2O catalyzed N2-fixation over TiO2 doped Run clusters (n = 5, 6): a mechanistic and kinetic approach

H2O driven N2 fixation is known as the best alternative pathway to synthesise NH3 under ambient conditions. The thermodynamic non-spontaneous reaction can be accomplished by a photocatalytic water splitting reaction over a TiO2 supported surface with oxygen vacancies. Previous experiments have also shown N2 activation over a neutral Ru cluster whose catalytic activity was remarkably enhanced by TiO2 doping. In this article, we have investigated the detailed mechanism and kinetics of the H2O catalyzed nitrogen reduction reaction (NRR) over bare and TiO2 doped Ru5 clusters in conjunction with DFT and TST calculations. The lack of photochemical activity of the small model cluster provoked us to explore an alternative route of NH3 formation via H2O catalysis. For this, we have considered H2 as co-reactant. The partial reduction of N2 into NH3 or N2H4 could be achieved by a H2O oxidation reaction, however, catalytic regeneration requires additional H2 which effectively makes the overall reaction catalyzed by H2O. Above all, the present investigation suggests that NH3 is most favorably produced through the distal mechanism. Analysis of the rate constants demonstrates that the doping with TiO2 accelerates the kinetics of NRR by a few orders of magnitude. Furthermore, an increase of the size of the metal cluster would not significantly enhance the overall performance of NRR.

Theoretical study on conformational energies of transition metal complexes

Conformational energies are an important chemical property for which a performance assessment of theoretical methods is mandatory. Existing benchmark sets are often limited to biochemical or main group element containing molecules, while organometallic systems are generally less studied. A key problem herein is to routinely generate conformers for these molecules due to their complexity and manifold of possible coordination patterns. In this study we used our recently published CREST protocol [Pracht et al., Phys. Chem. Chem. Phys., 2020, 22, 7169-7192] to generate conformer ensembles for a variety of 40 challenging transition metal containing molecules, which were then used to form a comprehensive conformational energy benchmark set termed TMCONF40. Several low-cost semiempirical, density functional theory (DFT) and force-field methods were compared to high level DLPNO-CCSD(T1) and double-hybrid DFT reference values. Close attention was paid to the energetic ordering of the conformers in the statistical evaluation. With respect to the double-hybrid references, both tested low-cost composite DFT methods produce high Pearson correlation coefficients of rp,mean,B97-3c//B97-3c = 0.922 and rp,mean,PBEh-3c//B97-3c = 0.890, with mean absolute deviations close to or below 1 kcal mol-1. This good performance also holds for a comparison to DLPNO-CCSD(T1) reference energies for a smaller subset termed TMCONF5. Based on DFT geometries, the GFNn-xTB methods yield reasonable Pearson correlation coefficients of rp,mean,GFN1-xTB//B97-3c = 0.617 (MADmean = 2.15 kcal mol-1) and rp,mean,GFN2-xTB//B97-3c = 0.567 (MADmean = 2.68 kcal mol-1), outperforming the widely used PMx methods on the TMCONF40 test set. Employing the low-cost composite DFT method B97-3c on GFN2-xTB geometries yields an slightly improved correlation of rp,mean,B97-3c//GFN2-xTB = 0.632. Furthermore, for 68% of the investigated complexes at least one low-energy conformer was found that is more stable than the respective crystal structure conformation, which signals the importance of conformational studies. General recommendations for the application of the CREST protocol and DFT methods for transition metal conformational energies are given.

Synthesis and Computational and Experimental Investigations of a para-Nicotinic Acid-Bridged Dirhenium(I) Dimer Complex

The Re(I) dimer complex, [fac(CO)₃(phen)Re1-N(py)COORe2(phen)fac(CO)₃]⁺ (py = pyridine; phen = 1,10-phenanthroline), contains two different Re(I) centers 9.3 Å apart, one with a nitrogen donor and the other with an acetate donor from the bridging isonicotinate ligand. The complexes were characterized by ¹H NMR, UV-vis, fluorescence, and IR spectroscopy, elemental analysis, and single-crystal X-ray diffraction. The absorption and emission properties of the dimer dominated by charge transfer transitions are analyzed with respect to those of the monomers, [fac(CO)₃(phen)Re-N(pyCOOCH₃)]⁺ and [fac(CO)₃(phen)ReOOCCH₃]. Spectral comparison of these three complexes results in the unexpected finding that the dimer emission (575 nm) occurs near that of the nicotinate-containing monomer (580 nm) rather than near the lower energy-emitting state (650 nm) of the acetate-containing monomer. Density functional theory (DFT) calculations elucidate this unusual emission behavior. The geometries of the dimer and two monomers are optimized in the singlet ground and lowest-energy triplet excited states (LLTS's) to interpret absorption and emission behaviors, respectively. The singlet excited states calculated using time-dependent DFT correlate well with the absorption spectra in the lowest-energy and other major electronic transitions. The energy gaps and low-lying singlet excited states of the dimer are close to those of the acetate-containing monomer. The lowest-energy Franck-Condon triplet excited state of the dimer arising from electronic transitions localized on the acetate moiety is unstable. The next higher Franck-Condon triplet excited state arises from long-range charge transfer transition, and its energy is close to that of the nicotinate-containing monomer. Optimization of the dimer LLTS yields a stable state based on a long-range charge transfer transition involving occupied orbitals partially localized on the bridging nicotinate moiety. The LLTS energies of the dimer and nicotinate-containing monomer are in very good agreement as are the emission energies of these complexes. The correlated spectroscopic and computational results corroborate to the understanding of charge transfer states and transitions toward the development of photosensitive compounds for photoelectrochemical solar energy conversion cells.

Effect of Structure and Intramolecular Distances on Photoswitchable Magnetic Resonance Imaging Contrast Agents

Light-activated sensors are of great interest for biological applications but are limited by the depth of penetration of light. We have been interested in transducing light activation to a magnetic signal that can be detected through noninvasive imaging by magnetic resonance imaging (MRI). We have previously developed agents incorporating spiropyran derivatives as the sensing moiety and characterized features that influence photoswitching; however, we found the MRI response to be unpredictable. In this work, we delve deeper into the potential mechanisms for the observed MRI responses in an effort to better understand the structural effects on controlling magnetic properties. A series of light-activatable MRI contrast agents were synthesized and characterized to assess the effect of spiropyran positioning on contrast agent functions and properties. These compounds are based on the same spiropyran skeleton, also named 1',3',3'-trimethyl-6-nitrospiro[chromene-2,2-indoline], which is linked with an MRI contrast agent, gadolinium-1,4,7,10-tetraazacyclododecane-1,4,7-triacetate (DO3A). We investigated the photo-to-magnetic conversion properties of these novel compounds by adjusting linker lengths over a range from three to seven methylene groups. The primary results indicated that the contrast agent with a five-carbon linker (25) showed the highest light-sensing ability after irradiation with visible light. The results will aid in the design of future spiropyran-based MRI sensors.

In Silico Infrared Characterization of Synthetic Cannabinoids by Quantum Chemistry and Chemometrics

The concept of forensic sciences as mere trace analysis has been modified by the idea of forensic intelligence, which entails applying data to make decisions within the investigative process. Many countries are engaged in combating drug trafficking and drug use because they are related to public health and safety issues. Prohibiting the consumption of traditional drugs has led new psychoactive substances (NPSs) to emerge. NPSs consist of compounds that resemble the initially banned substance and which aim to mimic the traditional drug recreational effects while circumventing drug legislation. For example, synthetic cannabinoids are sprayed on herbal products to reproduce the cannabis recreational effects. According to the United Nations Office on Drugs and Crime (UNODC), the toxic effects of synthetic cannabis types are unknown, and harm and fatalities associated with the use of these drugs have been reported. Information on the characterization related to these species is lacking. The rate at which NPSs appear poses a significant challenge because employing conventional methods to understand the characteristics of these compounds may require time and be costly. This work uses in silico practices as an alternative to understand how NPSs related to cannabis behave. We apply quantum chemistry methods to evaluate several synthetic cannabinoids recognized in forensic samples. More specifically, we generate infrared spectra that can be employed as a benchmark for NPSs. We apply a multivariate classification to evaluate the results. We conclude that in silico methods are an alternative that provide information about the spectra of undetected substances. This information can help to identify new drugs, to increase knowledge about them, and to feed information procedures.

In silico studies of the inhibition mechanism of dengue with papain

Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and His159) complexes are analysed by Density Functional Theory (M06-2X/cc-pVDZ) method. Among the E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and Hys159) complexes, E-protein(Glu76)…Papain(Cys25) complex has the highest interaction value of -352.22 kcal/mol. Moreover, the natural bond orbital analysis also supports the above results. The 100 ns Molecular Dynamics simulation reveals that, E-protein(Ala54-Ile129)…Papain(Cys25) complex had the lowest root mean square deviation value of 1 Å compared to the E-protein(Ala54-Ile129)… Papain(Asn175 & His159) complexes. The salt bridge formation between the Asp103 and Lys110 residues are the important stabilizing factor in E-protein(Ala54-Ile129)…Papain(Cys25) complex. This result can extend our knowledge of the functional behaviour of Papain and provides structural insight to target Envelope protein as forthcoming drug targets in Dengue.

Molecular Mechanism of Viscosity Sensitivity in BODIPY Rotors and Application to Motion-Based Fluorescent Sensors

Viscosity in the intracellular microenvironment shows a significant difference in various organelles and is closely related to cellular processes. Such microviscosity in live cells is often mapped and quantified with fluorescent molecular rotors. To enable the rational design of viscosity-sensitive molecular rotors, it is critical to understand their working mechanisms. Herein, we systematically synthesized and investigated two sets of BODIPY-based molecular rotors to study the relationship between intramolecular motions and viscosity sensitivity. Through experimental and computational studies, two conformations (i.e., the planar and butterfly conformations) are found to commonly exist in BODIPY rotors. We demonstrate that the transformation energy barrier from the planar conformation to the butterfly conformation is strongly affected by the molecular structures of BODIPY rotors and plays a critical role in viscosity sensitivity. These findings enable rational structure modifications of BODIPY molecular rotors for highly effective protein detection and recognition.

A proton transfer mechanism along the PO4 anion chain in the [Zn(HPO4)(H2PO4)]2- coordination polymer

In this study, we revisit the proton transfer mechanism in [Zn(HPO4)(H2PO4)]2-, a coordination polymer possessing high proton conductivity. In a previous report [N. Phattharasupakun, J. Wutthiprom, S. Kaenket, Th. Maihom, J. Limtrakul, M. Probst, S. S. Nagarkar, S. Horike and M. Sawangphruk, Chem. Commun., 2017, 53, 11786-11789], it was hypothesized that protons could move along the ImH+ chain involving phosphate anions within the polymer structure, with energy barriers >1.3 eV. Adopting M06-2X calculations to examine the reaction pathway, we observe that it is much more favorable for H+ to move along a one-dimensional channel formed by HPO42- and H2PO4- anions. Within a unit cell, the proton hopping process can be divided into three elementary steps. For the forward proton transfer direction, the maximum energy barrier is only 0.04 eV, while that of the backward direction is 0.27 eV. Even though the barriers of the backward direction seem to outreach the barriers of the forward direction, both are still low in comparison with those reported in the literature. Moreover, we also point out the involvement of PO4 rotation during the proton transfer process. Activation energies of 0.37 eV and 0.15 eV are required for single steps of rotation of the phosphate anion. Both H+ translation (hopping) and rotation steps of PO4 anions simultaneously participate in the course of proton transfer in the coordination polymer.

Influence of DFT Functionals and Solvation Models on the Prediction of Far-Infrared Spectra of Pt-Based Anticancer Drugs: Why Do Different Complexes Require Different Levels of Theory?

Computational modeling was applied to far-infrared (FIR) spectra of Pt-based anticancer drugs to study the hydrolysis of these important molecules. Here, we present a study that investigates the influence of different factors-basis sets on non-Pt atoms, relativistic effective core potentials (RECPs) on the Pt atom, density functional theory (DFT) functionals, and solvation models-on the prediction of FIR spectra of two Pt-based anticancer drugs, cisplatin and carboplatin. Geometry optimizations and frequency calculations were performed with a range of functionals (PBE, PBE0, M06-L, and M06-2X), Dunning's correlation-consisted basis sets (VDZ, VTZ, aVDZ, and aVTZ), RECPs (VDZ-pp, VTZ-pp, aVDZ-pp, and aVTZ-pp), and solvation models (IEFPCM, CPCM, and SMD). The best combination of the basis set/DFT functional/solvation model was identified for each anticancer drug by comparing with experimentally available FIR spectra. Different combinations were established for cisplatin and carboplatin, which was rationalized by means of the partial atomic charge scheme, ChelpG, that was utilized to study the charge transfer between the Pt ion and ligands in both cisplatin and carboplatin.

Helical Assembly of Flavin Mononucleotides on Carbon Nanotubes as Multimodal Near-IR Hg(II)-Selective Probes

The development of novel methods to detect mercury is of paramount importance owing to the impact of this metal on human health and the environment. We observed that flavin mononucleotide (FMN) and its helical assembly with a single-walled carbon nanotube (SWNT) selectively bind Hg²⁺ arising from HgCl₂ and MeHgCl. Absorption spectroscopic studies show that FMN preferentially forms a 2:1 rather than a 1:1 complex with Hg²⁺ at high FMN concentrations. On the basis of the analogy to the thymine-Hg-thymine complex, it is proposed that the 2:1 complex between FMN and Hg²⁺ comprises a Hg-bridged pair of FMN groups, regardless of the presence of SWNT. Upon addition of as little as a few hundred nanomoles of Hg²⁺, both FMN and FMN-SWNT exhibit absorption and photoluminescence (PL) changes. Moreover, FMN-SWNT displays simultaneous multiple sigmoidal changes in PL of SWNT tubes having different chiral vectors. Assessment of binding affinities using the Hill equation suggests that 2:1 and 1:1 complexes form between Hg²⁺ and FMN groups on the FMN-SWNT. Theoretical calculations indicate that optical changes of the FMN-SWNT originate from Hg-mediated conformational changes occurring on the helical array of FMN on the SWNT. High-resolution transmission electron microscopy revealed that the presence of Hg²⁺ in complexes with the FMN-SWNT enables visualization of helical periodic undulation of FMN groups along SWNT without the need for staining. Circular dichroism (CD) study revealed that FMN-SWNT whose CD signal mainly originates from FMN decreases dichroic bands upon the addition of Hg²⁺ owing to the formation of a centrosymmetric FMN-Hg-FMN triad on SWNT. The binding mode specificity and multimodal changes observed in response to Hg²⁺ ions suggest that systems based on FMN-SWNT can serve as in vivo NIR beacons for the detection of various mercury derivatives.

Monitoring Mechanical, Electronic, and Catalytic Trends in a Titanium Metal Organic Framework Under the Influence of Guest-Molecule Encapsulation Using Density Functional Theory

In this study, we conduct a density functional theory investigation to study the mechanical stability of a titanium-based metal organic framework (MOF-901), which was hypothetically assumed to possess 2D characteristics. It is systematically found that the encapsulation of methanol enhances the mechanical stability of MOF-901 as the elastic tensors C_ij of MOF-901∙nMeOH are higher than the corresponding C_ij quantities reported for solvent-free MOF-901. Moreover, the 2D characteristics of MOF-901 is confirmed by verifying the negative values of C₃₃. At the same time, the band gap of MOF-901 is observed to be solvent-dependent. In its pure form, MOF-901 possesses a direct gap (E_g) of 2.07 eV, with the valence and conduction bands mainly constituted by electrons of 4-aminobenzoate linkers. Introducing methanol into MOF-901 causes distortion to the 4-aminobenzoate geometry, thereby induces electronic degeneracy to the conduction bands. Consequently, E_g is narrowed to 1.84 eV with 5.7 wt% MeOH or 1.63 eV with 11.4 wt% MeOH. Hence, it is possible to tailor the band gap of MOF-901 by controlling methanol guest, which only acquires van der Waals interaction to the framework. In addition, our theoretical prediction shows a Ti(IV) site can undergo electronic hopping to become Ti(III) under the effect of visible light (~440–443 nm). Then, Ti(III) is capable of breaking the C-Br bond in ethyl α-bromophenylacetate spontaneously, which in turn activates the polymerization of methyl methacrylate with an energy barrier of 0.30 eV.

Multireference Methods for Calculating the Dissociation Enthalpy of Tetrahedral P4 to Two P2

The potential energy surface for the thermal decomposition of P₄ → 2P₂ was computed along the C_{2 v} reaction trajectory. Single-reference methods were not suitable for describing this complex bond-breaking process, so two multiconfigurational methods, namely, multistate complete active space second-order perturbation theory (MS-CASPT2) and multiconfiguration pair-density functional theory (MC-PDFT), were used with the aim of determining the accuracy and efficiency of these methods for this process. Several active spaces and basis sets were explored. It was found that the multiconfiguration pair-density functional theory method was up to 900 times faster than multistate complete active space second-order perturbation theory while providing similar accuracy.