Covalent Organic Frameworks in Computational Design of Second-Harmonic Generation Materials: Role of Tetrel Atoms and Their Interactions.

Modern approaches to the design of nonlinear optical materials often rely on computational techniques. Here, we discuss the effects of the variation in the center tetrel atoms, Tt = C, Si, or Ge, in a series of covalent organic frameworks of the COF-102 family. The effects of halogen substitution, Hal = Cl, Br, or I on intramolecular tetrel bonding are also discussed.

Unexpected polarization properties of sub-nanosized magnesium clusters.

The isotropic electrostatic polarizability (IEP) of sub-nanosized magnesium clusters Mg-Mg was studied in an extensive set comprising 1237 structurally unique isomers. These isomers were found in the course of the global search for the potential energy surface minima of the magnesium clusters at the BP86/6-31G(d) level. The calculation of the polarizability at the same DFT level reveals an unexpected property of the IEP: the linear correlation between the polarizability of the most favorable isomers (and only them) and the cluster nuclearity .

How Many Isomers Do Metallic Clusters Have? Case of Magnesium Clusters of up to 55 Atoms.

About 9000 structures of magnesium clusters Mg ( = 2-13) generated via different methods were optimized at the DFT levels in order to estimate the number of all possible stable structures that can exist for the given cluster size (∼820,000 PES points were explored in total). It was found that the number of possible cluster isomers quickly grows with a number of atoms ; however, it is significantly lower than the number of possible nonisomorphic graph structures, which can be drawn for the given At the DFT potential energy surface, we found only 543 local minima corresponding to the isomers of Mg-Mg. The number of isomers obtained in the DFT optimizations grows with approximately as , whereas the values extrapolated to the infinite generation process grow as .

Pseudocyclic Form of 4-Hydroxypyrrolidine-2-carboxanilide Podands with Trioxyethylene Chain: Modeling, Conformational Search, and NMR Analysis.

The 4-hydroxypyrrolidine-2-carboxanilide podand salt demonstrates catalytic activity in asymmetric Biginelli reaction. The systematic search for prevalent conformational state of the cation was carried out by computer simulations in combination with one- and two-dimensional NMR experiments. For that purpose, we proposed a novel algorithm for the generation and selection of conformers based on molecular dynamics and clustering in the space of principal components.

Three-Photon Spectroscopy of Porphyrins.

Recent advances in laser technology have made three-photon (3P) microscopy a real possibility, raising interest in the phenomenon of 3P absorption (3PA). Understanding 3PA of organic chromophores is especially important in view of those imaging applications that rely on exogenous probes, whose optical properties can be manipulated and optimized. Here, we present measurements and theoretical analysis of the degenerate 3PA spectra of several phosphorescent metalloporphyrins, which are used in the construction of biological oxygen probes.

High accuracy machine learning identification of fentanyl-relevant molecular compound classification via constituent functional group analysis.

Fentanyl is an anesthetic with a high bioavailability and is the leading cause of drug overdose death in the U.S. Fentanyl and its derivatives have a low lethal dose and street drugs which contain such compounds may lead to death of the user and simultaneously pose hazards for first responders.

Molecular Dynamics of Combustion Reactions in Supercritical Carbon Dioxide. 6. Computational Kinetics of Reactions between Hydrogen Atom and Oxygen Molecule H + O ⇌ HO + O and H + O ⇌ HO.

Reactions of the hydrogen atom and the oxygen molecule are among the most important ones in the hydrogen and hydrocarbon oxidation mechanisms, including combustion in a supercritical CO (sCO) environment, known as oxy-combustion or the Allam cycle. Development of these energy technologies requires understanding of chemical kinetics of H + O ⇌ HO + O and H + O ⇌ HO in high pressures and concentrations of CO. Here, we combine quantum treatment of the reaction system by the transition state theory with classical molecular dynamics simulation and the multistate empirical valence bonding method to treat environmental effects.

Electronic Nature of Neutral and Charged Two-Photon Absorbing Squaraines for Fluorescence Bioimaging Application.

The electronic properties of neutral 2,4-bis(4-bis(2-hydroxyethyl) amino-2-hydroxy-6-(2-(2-(2-methoxyethoxy)ethoxy)ethoxy)phenyl)squaraine () and charged 2-((3-octadecylbenzothiazol-2(3)-ylidene)methyl)-3-oxo-4-((3-(4-(pyridinium-1-yl)butyl)benzo-thiazol-3-ium-2-yl)methylene)cyclobut-1-enolate iodide () squaraine derivatives were analyzed based on comprehensive linear photophysical, photochemical, nonlinear optical studies (including two-photon absorption (2PA) and femtosecond transient absorption spectroscopy measurements), and quantum chemical calculations. The steady-state absorption, fluorescence, and excitation anisotropy spectra of these new squaraines revealed the values and mutual orientations of the main transition dipoles of and in solvents of different polarity, while their role in specific nonlinear optical properties was shown. The degenerate 2PA spectra of and exhibited similar shapes, with maximum cross sections of ∼300-400 GM, which were determined by the open aperture -scan method over a broad spectral range.

Molecular Dynamics of Combustion Reactions in Supercritical Carbon Dioxide. Part 5: Computational Study of Ethane Dissociation and Recombination Reactions CH ⇌ CH + CH.

Fossil fuel oxy-combustion is an emerging technology where the habitual nitrogen diluent is replaced by high-pressure supercritical CO (sCO), which increases the efficiency of energy conversion. In this study, the chemical kinetics of the combustion reaction CH ⇌ CH + CH in the sCO environment is predicted at 30-1000 atm and 1000-2000 K. We adopt a multiscale approach, where the reactive complex is treated quantum mechanically in rigid rotor/harmonic oscillator approximation, while environment effects at different densities are taken into account by the potential of mean force, produced with classical molecular dynamics (MD).

Theoretical Calculation of Reaction Rates and Combustion Kinetic Modeling Study of Triethyl Phosphate (TEP).

Triethyl phosphate (TEP) is an organophosphorus compound used as a simulant for highly toxic nerve agents such as sarin GB. A high temperature decomposition pathway during TEP pyrolysis has been proposed previously and takes place via seven concerted elimination reactions. A computational study to investigate the kinetics of these seven reactions was carried out at the CBS-QB3 level of theory.

Oxyphor 2P: A High-Performance Probe for Deep-Tissue Longitudinal Oxygen Imaging.

Quantitative imaging of oxygen distributions in tissue can provide invaluable information about metabolism in normal and diseased states. Two-photon phosphorescence lifetime microscopy (2PLM) has been developed to perform measurements of oxygen in vivo with micron-scale resolution in 3D; however, the method's potential has not yet been fully realized due to the limitations of current phosphorescent probe technology. Here, we report a new sensor, Oxyphor 2P, that enables oxygen microscopy twice as deep (up to 600 μm below the tissue surface) and with ∼60 times higher speed than previously possible.

Molecular dynamics of combustion reactions in supercritical carbon dioxide. Part 4: boxed MD study of formyl radical dissociation and recombination.

Fossil fuel oxy-combustion is an emergent technology where habitual nitrogen diluent is replaced by high pressure (supercritical) carbon dioxide. The supercritical state of CO increases the efficiency of the energy conversion and the absence of nitrogen from the reaction mixture reduces pollution by NO. However, the effects of a supercritical environment on elementary reactions kinetics are not well understood at present.

Catalytic Effect of Carbon Dioxide on Reaction OH + CO → H + CO in Supercritical Environment: Master Equation Study.

We investigated the reaction rates of OH + CO → H + CO in supercritical CO environment with and without additional CO molecule included in reactive complex. Ab initio potential energy surfaces previously reported a lower activation barrier and hence a catalytic effect of additional CO molecule. Here we solve the steady-state unimolecular master equations based on the Rice-Ramsperger-Kassel-Marcus theory (RRKM) and compare the rates for the two mechanisms.

Shock Tube/Laser Absorption and Kinetic Modeling Study of Triethyl Phosphate Combustion.

Pyrolysis and oxidation of triethyl phosphate (TEP) were performed in the reflected shock region at temperatures of 1462-1673 K and 1213-1508 K, respectively, and at pressures near 1.3 atm. CO concentration time histories during the experiments were measured using laser absorption spectroscopy at 4580.

Theoretical study of chromophores for biological sensing: Understanding the mechanism of rhodol based multi-chromophoric systems.

Development of two-photon fluorescent probes can aid in visualizing the cellular environment. Multi-chromophore systems display complex manifolds of electronic transitions, enabling their use for optical sensing applications. Time-Dependent Density Functional Theory (TDDFT) methods allow for accurate predictions of the optical properties.

Molecular Dynamics Study of Combustion Reactions in Supercritical Environment. Part 3: Boxed MD Study of CH + HO → CHO + OH Reaction Kinetics.

The kinetics of reaction CH + HO → CHO + OH in supercritical carbon dioxide media at pressures from 0.3 to 1000 atm in the temperature range (600-1600) K was studied using boxed molecular dynamics simulations at QM/MM theory level with periodical boundary conditions. The mechanism of this process includes two consecutive steps: formation and decomposition of CHOOH intermediate.

Molecular Dynamics Study of Combustion Reactions in a Supercritical Environment. Part 2: Boxed MD Study of CO + OH → CO + H Reaction Kinetics.

Oxy-fuel combustion technology holds a great promise in both increasing the efficiency of the energy conversion and reducing environmental impact. However, effects of the higher pressures and replacement of the nitrogen with carbon dioxide diluent are not well understood at present. The title reaction is one of the most important processes in combustion.

Stabilizing g-States in Centrosymmetric Tetrapyrroles: Two-Photon-Absorbing Porphyrins with Bright Phosphorescence.

Using time-dependent density functional theory (TDDFT) and sum-overstates (SOS) formalism, we predicted significant stabilization of 2P-active g-states in a compact fully symmetric porphyrin, in which all four pyrrolic fragments are fused with phathalimide residues via the β-carbon positions. The synthesis of a soluble, nonaggregating meso-unsubstituted tetraarylphthalimidoporphyrin (TAPIP) was then developed, and the spectroscopic measurements confirmed that a strongly 2P-active state in this porphyrin is stabilized below the B (Soret) state level. Single-crystal X-ray analysis revealed near-ideally planar geometry of the TAPIP macrocycle, while its tetra-meso-arylated analogue (meso-ArTAPIP) was found to be highly saddled.

Quantum Chemical Study of CH + O Combustion Reaction System: Catalytic Effects of Additional CO Molecule.

The supercritical carbon dioxide diluent is used to control the temperature and to increase the efficiency in oxycombustion fossil fuel energy technology. It may affect the rates of combustion by altering mechanisms of chemical reactions, compared to the ones at low CO concentrations. Here, we investigate potential energy surfaces of the four elementary reactions in the CH + O reactive system in the presence of one CO molecule.

First principles crystal engineering of nonlinear optical materials. I. Prototypical case of urea.

The crystalline materials with nonlinear optical (NLO) properties are critically important for several technological applications, including nanophotonic and second harmonic generation devices. Urea is often considered to be a standard NLO material, due to the combination of non-centrosymmetric crystal packing and capacity for intramolecular charge transfer. Various approaches to crystal engineering of non-centrosymmetric molecular materials were reported in the literature.

Quantum Chemical Study of Supercritical Carbon Dioxide Effects on Combustion Kinetics.

In oxy-fuel combustion, the pure oxygen (O), diluted with CO is used as oxidant instead air. Hence, the combustion products (CO and HO) are free from pollution by nitrogen oxides. Moreover, high pressures result in the near-liquid density of CO at supercritical state (sCO).

Two-Photon Absorbing Phosphorescent Metalloporphyrins: Effects of π-Extension and Peripheral Substitution.

The ability to form triplet excited states upon two-photon excitation is important for several applications of metalloporphyrins, including two-photon phosphorescence lifetime microscopy (2PLM) and two-photon photodynamic therapy (PDT). Here we analyzed one-photon (1P) and degenerate two-photon (2P) absorption properties of several phosphorescent Pt (II) porphyrins, focusing on the effects of aromatic π-extension and peripheral substitution on triplet emissivity and two-photon absorption (2PA). Our 2PA measurements for the first time made use of direct time-resolved detection of phosphorescence, having the ability to efficiently reject laser background through microsecond time gating.

Potential Energy Surfaces for the Reactions of HO Radical with CHO and HO in CO Environment.

We report on potential energies for the transition state, reactant, and product complexes along the reaction pathways for hydrogen transfer reactions to hydroperoxyl radical from formaldehyde HCO + HO → HCO + HO and another hydroperoxyl radical 2HO → HO + O in the presence of one carbon dioxide molecule. Both covalently bonded intermediates and weak intermolecular complexes are identified and characterized. We found that reactions that involve covalent intermediates have substantially higher activation barriers and are not likely to play a role in hydrogen transfer kinetics.

Report on the sixth blind test of organic crystal structure prediction methods.

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations.

Chemical Reaction CO+OH(•) → CO2+H(•) Autocatalyzed by Carbon Dioxide: Quantum Chemical Study of the Potential Energy Surfaces.

The supercritical carbon dioxide medium, used to increase efficiency in oxy combustion fossil energy technology, may drastically alter both rates and mechanisms of chemical reactions. Here we investigate potential energy surface of the second most important combustion reaction with quantum chemistry methods. Two types of effects are reported: formation of the covalent intermediates and formation of van der Waals complexes by spectator CO2 molecule.