Quantum Chemical Modeling Research Articles

The first HyDRA challenge for computational vibrational spectroscopy.

Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the vacuum-isolated monohydrates of formaldehyde, tetrahydrofuran, pyridine, tetrahydrothiophene, trifluoroethanol, methyl lactate, dimethylimidazolidinone, cyclooctanone, trifluoroacetophenone and 1-phenylcyclohexane-cis-1,2-diol are provided. The results of the challenge show promising predictive properties in both purely quantum mechanical approaches as well as regression and other machine learning strategies.

FORMATION OF A DIPHENYL OXIDE FRAGMENT UNDER HETEROPHASE CONDITIONS

In the course of this work, two ways of formation of substituted diphenyl oxides were compared. They can be represented by the following transformation sets. Firstly, after the chemical sorption of phenol on the solid surface of potassium carbonate, the structure formed on the surface acts as a nucleophilic substitution reagent. Without passing into solution, it interacts with the substrate to form a complex, which further decomposes with subsequent desorption of reaction products and substituted diphenyl ether respectively. The second point of view is as follows: on the first step phenol is chemisorbed on the solid surface of potassium carbonate, and then irreversibly desorbed into solution together with a fragment of a potassium carbonate cluster in the form of a complex. Interaction with the substrate of this system in this case occurs in the liquid phase. As a research method, quantum chemical modeling of the mechanisms of the formation of diphenyloxide derivatives in the liquid phase-solid phase system (unlimited Hartree-Fock approximation, UHF and the basis set 6-31G(d,p) was used. The energy profiles of the above processes were constructed, and the values of the energy barriers of the formation of the corresponding complexes were calculated. It is shown that the formation of substituted diphenyl oxides by the interaction of a phenoxide anion on the surface of a deprotonating agent (potassium carbonate) with a substrate is more energetically advantageous than in the case of desorption of a p-nitrophenol molecule together with a fragment of a potassium carbonate cluster into a solution. Thus, the formation of substituted diphenyl oxides by the interaction of the phenoxide anion on the surface of the deprotonating agent (potassium carbonate) with the substrate is more energetically advantageous and seems more likely.

The alkoxy radical polymerization of N-vinylpyrrolidone in organic solvents: theoretical insight into the mechanism and kinetics.

Poly(N-vinylpyrrolidone) (PVP) is a polymer with many applications in cosmetic, pharmaceutical, and biomedical formulations due to its minimal toxicity. PVP can be synthesized through radical polymerization in organic solvents; this well-known industrial process is thoroughly characterized experimentally, however, quantum chemical modeling of the process is scarce: the mechanism and kinetics have not been thoroughly investigated yet. In this work, the mechanism and kinetics of the alkoxy radical polymerization of N-vinylpyrrolidone in organic solvents, namely isopropanol (IP) and toluene (TL), were successfully modeled by computational chemistry. The initiator radicals di-tert-butyl peroxide (TBO˙) and dicumyl peroxide (CMO˙) as well as the solvents isopropanol and toluene, were shown to be capable of assisting in the initiation reactions. The rate constant was influenced by the combination of initiators and solvent and the values of the rate constant of propagation were approximately 101-103 M-1 s-1. The radical polymerization of NVP with dicumyl peroxide as an initiator was comparable to that of di-tert-butyl peroxide in all of the examined organic solvents, whereas the solvents had less of an effect.

Synthesis and characterization of selenium nanoparticles stabilized with cocamidopropyl betaine

In this work, selenium nanoparticles (Se NPs) stabilized with cocamidopropyl betaine were synthesized for the first time. It was observed that Se NPs synthesized in excess of selenic acid had a negative charge with ζ-potential of −21.86 mV, and in excess of cocamidopropyl betaine—a positive charge with ξ = + 22.71 mV. The resulting Se NPs with positive and negative charges had a spherical shape with an average size of about 20–30 nm and 40–50 nm, respectively. According to the data of TEM, HAADF-TEM using EDS, IR spectroscopy and quantum chemical modeling, positively charged selenium nanoparticles have a cocamidopropylbetaine shell while the potential- forming layer of negatively charged selenium nanoparticles is formed by SeO32− ions. The influence of various ions on the sol stability of Se NPs showed that SO42− and PO43− ions had an effect on the positive Se NPs, and Ba2+ and Fe3+ ions had an effect on negative Se NPs, which corresponded with the Schulze-Hardy rule. The mechanism of coagulating action of various ions on positive and negative Se NPs was also presented. Also, influence of the active acidity of the medium on the stability of Se NPs solutions was investigated. Positive and negative sols of Se NPs had high levels of stability in the considered range of active acidity of the medium in the range of 1.21–11.98. Stability of synthesized Se NPs stability has been confirmed in real system (liquid soap). An experiment with the addition of Se NPs stabilized with cocamidopropyl betaine to liquid soap showed that the particles of dispersed phases retain their initial distributions, which revealed the stability of synthesized Se NPs.

Effect of non‐covalent interactions in 2,5‐di‐Me‐pyrazine‐di‐N‐oxide ‐ methanol – Carbon nanotube electrocatalytic system

AbstractCatalytic oxidation of methanol (MeOH) in the absence of noble metals and noble metal oxides as catalysts, and the use of metal‐free materials are inexpensive and attractive process for practical use in electrocatalysis, sensors, and in direct methanol fuel cells. In previous works, it was found that the use of single‐walled (SWCNT) or multi‐walled (MWCNT) carbon nanotube paper electrodes instead of GC increases the catalytic efficiency of organic compounds oxidation in the presence of aromatic di‐N‐oxides by several times. In this work, the effect of non‐covalent interactions on the catalytic efficiency of MeOH oxidation in the presence of 2,5‐di‐Me‐pyrazine‐di‐N‐oxide (Pyr1) in 0.1 M Bu4NClO4 solution in acetonitrile at SWCNT and MWСNT paper electrodes was studied by the methods of quantum chemical modeling, Raman spectroscopy, and using electrochemical data. New factors determined the features of mechanism of MeOH oxidation on CNT electrodes and lead to an increase in the catalytic efficiency of the electrode process in comparison with the GC electrode were established.

Investigating the Heaviest Halogen: Lessons Learned from Modeling the Electronic Structure of Astatine’s Small Molecules

We present a systematic study of electron-correlation and relativistic effects in diatomic molecular species of the heaviest halogen astatine (At) within relativistic single- and multireference coupled-cluster approaches and relativistic density functional theory. We establish revised reference ab initio data for the ground states of At2, HAt, AtAu, and AtO+ using a highly accurate relativistic effective core potential model and in-house basis sets developed for accurate modeling of molecules with large spin-orbit effects. Spin-dependent relativistic effects on chemical bonding in the ground state are comparable to the binding energy or even exceed it in At2. Electron-correlation effects near the equilibrium internuclear separation are mostly dynamical and can be adequately captured using single-reference CCSD(T). However, bond elongation in At2 and, especially, AtO+ results in rapid manifestation of its multireference character. While useful for evaluating the spin-orbit effects on the ground-state bonding and properties, the two-component density functional theory lacks predictive power, especially in combination with popular empirically adjusted exchange-correlation functionals. This drawback supports the necessity to develop new functionals for reliable quantum-chemical models of heavy-element compounds with strong relativistic effects.

New Nanosized Systems Doxorubicin-Amphiphilic Copolymers of N-Vinylpyrrolidone and (Di)methacrylates with Antitumor Activity.

Nanosized systems of DOX with antitumor activity on the base of micelle-like particles of amphiphilic thermosensitive copolymers of N-vinylpyrrolidone (VP) with triethylene glycol dimethacrylate (TEGDM), and N-vinylpyrrolidone and methacrylic acid (MAA) with TEGDM were explored. They were investigated in aqueous solutions by electron absorption spectroscopy, dynamic light scattering and cyclic voltammetry. Experimental data and quantum-chemical modeling indicated the formation of a hydrogen bond between oxygen-containing groups of monomer units of the copolymers and H-atoms of OH and NH2 groups of DOX; the energies and H-bond lengths in the considered structures were calculated. A simulation of TDDFT spectra of DOX and its complexes with the VP and TEGDM units was carried out. Electrochemical studies in PBS have demonstrated that the oxidation of encapsulated DOX appeared to be easier than that of the free one, and its reduction was somewhat more difficult. The cytotoxicity of VP-TEGDM copolymer compositions containing 1, 5 and 15 wt% DOX was studied in vitro on HeLa cells, and the values of IC50 doses were determined at 24 and 72 h of exposure. The copolymer compositions containing 5 and 15 wt% DOX accumulated actively in cell nuclei and did not cause visual changes in cell morphology.

On-off-on Control of Molecular Inversion Symmetry via Multi-stage Protonation: Elucidating Vibronic Laporte Rule.

The Laporte rule dictates that one- and two-photon absorption spectra of inversion-symmetric molecules should display alternatively forbidden electronic transitions; however, for organic fluorophores, drawing clear distinction between the symmetric- and non-inversion symmetric two-photon spectra is often obscured due to prevalent vibronic interactions. We take advantage of consecutive single- and double-protonation to break and then reconstitute inversion symmetry in a nominally symmetric diketopyrrolopyrrole, causing large changes in two-photon absorption. By performing detailed one- and two-photon titration experiments, with supporting quantum-chemical model calculations, we explain how certain low-frequency vibrational modes may lead to apparent deviations from the strict Laporte rule. As a result, the system may be indeed considered as an on-off-on inversion symmetry switch, opening new avenues for two-photon sensing applications.

Gas-Phase Computational Spectroscopy: The Challenge of the Molecular Bricks of Life.

Gas-phase molecular spectroscopy is a natural playground for accurate quantum-chemical computations. However, the molecular bricks of life (e.g., DNA bases or amino acids) are challenging systems because of the unfavorable scaling of quantum-chemical models with the molecular size (active electrons) and/or the presence of large-amplitude internal motions. From the theoretical point of view, both aspects prevent the brute-force use of very accurate but very expensive state-of-the-art quantum-chemical methodologies. From the experimental point of view, both features lead to congested gas-phase spectra, whose assignment and interpretation are not at all straightforward. Based on these premises, this review focuses on the current status and perspectives of the fully a priori prediction of the spectral signatures of medium-sized molecules (containing up to two dozen atoms) in the gas phase with special reference to rotational and vibrational spectroscopies of some representative molecular bricks of life.

Quantum chemical modeling of the thermodynamics of the formation of Au(III), Pd(II), and Pt(II) chloride complexes.

Quantitative prediction of physical properties of liquids and equilibrium constants is important for many applications. Computational methods based on either explicit or implicit solvent models can be used to approximate thermodynamics of complexation. A practical method for calculating the stability constant of d8 chlorocomplexes (PdCl42-, PtCl42-, AuCl4-) in aqueous solution has been developed by using DFT and DLPNO-CCSD with the SMD solvation model and 100 unique explicit water molecules. Stability constants have been calculated by using methods, such as DFT/PBE0-D3, DLPNO-CCSD, DLPNO-CCSD-DK, and DLPNO-CCSD(T), and basis sets, such as def2-TZVPD, def2-TZVPP, ma-def2-TZVP, ma-DKH-def2-TZVP, SARC-TZVP, and SARC-TZVPP. Calculations using DFT/PBE0-D3/def2-TZVPD and DLPNO-CCSD-DK/ma-DKH-Def2-TZVP/SARC-DKH-TZVP with SMD solvation with explicit waters are found to have errors of 2-3 logunits relative to experimental data. The best results are obtained by using 8 explicit waters for d8 aqua complexes, 14 explicit waters for d8 chlorocomplexes, and 4 explicit waters for chloride ion.

Oligomer formation from the gas-phase reactions of Criegee intermediates with hydroperoxide esters: mechanism and kinetics

Abstract. Hydroperoxide esters, formed in the reactions of carbonyl oxides (also called Criegee intermediates, CIs) with formic acid, play a crucial role in the formation of secondary organic aerosol (SOA) in the atmosphere. However, the transformation mechanism of hydroperoxide esters in the presence of stabilized Criegee intermediates (SCIs) is not well understood. Herein, the oligomerization reaction mechanisms and kinetics of distinct SCI (CH2OO, syn-CH3CHOO, anti-CH3CHOO, and (CH3)2COO) reactions, with their respective hydroperoxide esters and with hydroperoxymethyl formate (HPMF), are investigated in the gas phase using quantum chemical and kinetics modeling methods. The calculations show that the addition reactions of SCIs with hydroperoxide esters proceed through successive insertion of SCIs into hydroperoxide ester to form oligomers that involve SCIs as the repeated chain unit. The saturated vapor pressure and saturated concentration of the formed oligomers decrease monotonically as the number of SCIs is increased. The exothermicity of oligomerization reactions decreases significantly when the number of methyl substituents increases, and the exothermicity of anti-methyl substituted carbonyl oxides is obviously higher than that of syn-methyl substituted carbonyl oxides. The −OOH insertion reaction is energetically more feasible than the −CH insertion pathway in the SCI oligomerization reactions, and the barrier heights increase with increasing the number of SCIs added to the oligomer, except for syn-CH3CHOO. For the reactions of distinct SCIs with HPMF, the barrier of the −OOH insertion pathway shows a dramatic decrease when a methyl substituent occurs at the anti-position, while it reveals a significant increase when a methyl group is introduced at the syn-position and dimethyl substituent. Compared with the rate coefficients of the CH2OO + HPMF reaction, the rate coefficients increase by about 1 order of magnitude when a methyl substituent occurs at the anti-position, whereas the rate coefficients decrease by 1–2 orders of magnitude when a methyl group is introduced at the syn-position. These new findings advance our current understanding of the influence of Criegee chemistry on the formation and growth processes and the chemical compositions of SOA.

Effect of the Solvate Environment of Lithium Cations on the Resistance of the Polymer Electrolyte/Electrode Interface in a Solid-State Lithium Battery.

The effect of the composition of liquid electrolytes in the bulk and at the interface with the LiFePO4 cathode on the operation of a solid-state lithium battery with a nanocomposite polymer gel electrolyte based on polyethylene glycol diacrylate and SiO2 was studied. The self-diffusion coefficients on the 7Li, 1H, and 19F nuclei in electrolytes based on LiBF4 and LiTFSI salts in solvents (gamma-butyrolactone, dioxolane, dimethoxyethane) were measured by nuclear magnetic resonance (NMR) with a magnetic field gradient. Four compositions of the complex electrolyte system were studied by high-resolution NMR. The experimentally obtained 1H chemical shifts are compared with those theoretically calculated by quantum chemical modeling. This made it possible to suggest the solvate shell compositions that facilitate the rapid transfer of the Li+ cation at the nanocomposite electrolyte/LiFePO4 interface and ensure the stable operation of a solid-state lithium battery.

Small Heterocyclic Ligands as Anticancer Agents: QSAR with a Model G-Quadruplex.

G-quadruplexes (GQs) have become valid targets for anticancer studies in recent decades due to their multifaceted biological function. Herewith, we aim to quantify interactions of potential heterocyclic ligands (Ls) with model GQs. For seven 4-aminoquinazolines and three 2-heteroaryl perimidines, seven of this ten-membered group so far unknown, we use routine quantum chemical modeling. As shown in the literature, a preferred mode of interaction of heterocycles with cellular structures is stacking to exposable faces of G-quadruplexes. To exploit the energy of this interaction as a molecular descriptor and achieve the necessary chemical precision, we use state of the art large-scale density functional theory (DFT) calculations of stacked heterocycles to a GQ. Actually, the GQ has been simplified for the computation by stripping it off all pentose phosphate residues into a naked model of stacked guanine quartets. The described model thus becomes computable. The obtained heterocyclic ligand GQ.L stacking energies, that is, their GQ affinities, are the necessary ligand descriptors. Using the ligand biological inhibitory activities (IC50) on a human malignant melanoma A375 cell line, we obtain a good linear relationship between computed ligand stacking affinities to GQ, and experimental log (IC50) values. Based on the latter relationship, we discuss a putative mechanism of anticancer activity of heterocyclic ligands via stacking interactions with GQs and thereby controlling cell regulatory activity. This mechanism may tentatively be applied to other condensed five- and six-membered small heterocycles as well.

Structure, Thermal Properties and Proton Conductivity of the Sulfonated Polyphenylquinoxalines

This paper briefly reviews the results of scientific research on the proton conductivity of sulfonated polyphenylquinoxalines. Synthesis, structure (IR spectroscopy, SEM, quantum-chemical modeling, molecular weight distribution), moisture capacity, thermal properties, and proton conductivity of sulfonated polyphenylquinoxalines (sulfur content 2.6, 4.2, 5.5, and 7%) were studied. The relative stable configurations of sulfonated polyphenylquinoxalines with different positions of benzene rings and sulfogroups with the help of quantum chemical modeling were modeled. Sulfonation of the starting polyphenylquinoxalines was confirmed by IR spectroscopy and elemental analysis. The SEM method was used to study the surface of sulfonated polyphenylquinoxalines, and sulfonation regions were found. It was shown that sulfonated polyphenylquinoxalines contain water and are stable up to 250 °C; on further heating, the decomposition of the sulfogroups occurs. The conductivity of the obtained polymer electrolytes was studied by impedance spectroscopy, and long-term tests were carried out. It is shown that the proton conductivity at an ambient humidity of 98 rel. % reaches values 10-6-10-3 S/cm depending on the degree of sulfonation. It was shown that even after long-term storage in air (7 years), samples of sulfonated polyphenylquinoxalines with a high sulfur content of 7% at 98% air humidity have a conductivity of 8 × 10-4 S/cm.

Light-Responsive Oligothiophenes Incorporating Photochromic Torsional Switches.

We present a quaterthiophene and sexithiophene that can reversibly change their effective π-conjugation length through photoexcitation. The reported compounds make use of light-responsive molecular actuators consisting of an azobenzene attached to a bithiophene unit by both direct and linker-assisted bonding. Upon exposure to 350 nm light, the azobenzene undergoes trans-to-cis isomerization, thus mechanically inducing the oligothiophene to assume a planar conformation (extended π-conjugation). Exposure to 254 nm wavelength promotes azobenzene cis-to-trans isomerization, forcing the thiophenic backbones to twist out of planarity (confined π-conjugation). Twisted conformations are also reached by cis-to-trans thermal relaxation at a rate that increases proportionally with the conjugation length of the oligothiophene moiety. The molecular conformations of quaterthiophene and sexithiophene were characterized by using steady-state UV-vis spectroscopy, X-ray crystallography and quantum-chemical modeling. Finally, we tested the proposed light-responsive oligothiophenes in field-effect transistors to probe the photo-induced tuning of their electronic properties.

On the fluorescence enhancement of arch neuronal optogenetic reporters

The lack of a theory capable of connecting the amino acid sequence of a light-absorbing protein with its fluorescence brightness is hampering the development of tools for understanding neuronal communications. Here we demonstrate that a theory can be established by constructing quantum chemical models of a set of Archaerhodopsin reporters in their electronically excited state. We found that the experimentally observed increase in fluorescence quantum yield is proportional to the computed decrease in energy difference between the fluorescent state and a nearby photoisomerization channel leading to an exotic diradical of the protein chromophore. This finding will ultimately support the development of technologies for searching novel fluorescent rhodopsin variants and unveil electrostatic changes that make light emission brighter and brighter.

Influence of the Lithium Cation Desolvation Process at the Electrolyte/Electrode Interface on the Performance of Lithium Batteries

The article considers the effect of the solvate environment of the lithium cation in various aprotic solvents.The redox reactions of electrodes made from a polymeric condensation product of triquinoyl with 1,2,4,5-tetraaminobenzene are studied. A 1 M LiPF6 solution was used as an electrolyte, in either ethylene carbonate/dimethyl carbonate (EC/DMC) or tetraglyme. Based on the electrochemical studies and quantum chemical modeling, it was shown that the desolvation of lithium cations in the tetraglyme-based electrolyte makes it possible to obtain a capacity close to the theoretical one (up to 546 mAh g−1) and only 125 mAh g−1 for the EC/DMC electrolyte. This decrease is due to the fact that the lithium cation adds to the functional groups of the organic material with two dimethyl carbonate molecules, as well as the PF6− anion.

The photoprotection mechanism in the black–brown pigment eumelanin

The natural black-brown pigment eumelanin protects humans from high-energy UV photons by absorbing and rapidly dissipating their energy before proteins and DNA are damaged. The extremely weak fluorescence of eumelanin points toward nonradiative relaxation on the timescale of picoseconds or shorter. However, the extreme chemical and physical complexity of eumelanin masks its photoprotection mechanism. We sought to determine the electronic and structural relaxation pathways in eumelanin using three complementary ultrafast optical spectroscopy methods: fluorescence, transient absorption, and stimulated Raman spectroscopies. We show that photoexcitation of chromophores across the UV-visible spectrum rapidly generates a distribution of visible excitation energies via ultrafast internal conversion among neighboring coupled chromophores, and then all these excitations relax on a timescale of ∼4 ps without transferring their energy to other chromophores. Moreover, these picosecond dynamics are shared by the monomeric building block, 5,6-dihydroxyindole-2-carboxylic acid. Through a series of solvent and pH-dependent measurements complemented by quantum chemical modeling, we show that these ultrafast dynamics are consistent with the partial excited-state proton transfer from the catechol hydroxy groups to the solvent. The use of this multispectroscopic approach allows the minimal functional unit in eumelanin and the role of exciton coupling and excited-state proton transfer to be determined, and ultimately reveals the mechanism of photoprotection in eumelanin. This knowledge has potential for use in the design of new soft optical components and organic sunscreens.

Sub-optical-cycle light-matter energy transfer in molecular vibrational spectroscopy

The evolution of ultrafast-laser technology has steadily advanced the level of detail in studies of light-matter interactions. Here, we employ electric-field-resolved spectroscopy and quantum-chemical modelling to precisely measure and describe the complete coherent energy transfer between octave-spanning mid-infrared waveforms and vibrating molecules in aqueous solution. The sub-optical-cycle temporal resolution of our technique reveals alternating absorption and (stimulated) emission on a few-femtosecond time scale. This behaviour can only be captured when effects beyond the rotating wave approximation are considered. At a femtosecond-to-picosecond timescale, optical-phase-dependent coherent transients and the dephasing of the vibrations of resonantly excited methylsulfonylmethane (DMSO2) are observed. Ab initio modelling using density functional theory traces these dynamics back to molecular-scale sample properties, in particular vibrational frequencies and transition dipoles, as well as their fluctuation due to the motion of DMSO2 through varying solvent environments. Future extension of our study to nonlinear interrogation of higher-order susceptibilities is fathomable with state-of-the-art lasers.

Novel porphyrazine derivative – 2,3,5,7,8,10,12,13,15,17,18,20-dodecaazaporphin and its complexes with M(II) ions of 3d-elements: DFT quantum-chemical modeling

Using three different versions of the density functional theory (DFT) – B3PW91/TZVP, M06/TZVP and OPBE/TZVP chemical models, the calculation of the molecular structures of (6666) macrocyclic complexes of 3d-elements (M) with a novel (NNNN)-donor macrocyclic ligand, 2,3,5,7,8,10,12,13,15,17,18,20-dodecaazaporphin (H2L), was carried out. The values of the most important bond lengths, bond and non-bond angles in these metal complexes were presented. The standard enthalpy, entropy, and Gibbs energy of formation of these compounds were also calculated. It was noted that according to the data of the above chemical models, [MnL], [FeL], [CoL], [NiL], and [CuL] complexes with this novel ligand have a flat MN4 chelate node and a planar structure as a whole, while the [TiL], [VL], [CrL] and [ZnL] complexes have a non-coplanar MN4 chelate node. Moreover, all 6-membered rings in each of these metal chelates are identical to each other (both in terms of the sum of the bond angles included in them and in their assortment); adjoining 5-membered cycles for the majority of M are also identical to each other (non-identity is noted only in the cases M = Ti, Mn, as well as for the original 2,3,5,7,8,10,12,13,15,17,18,20-dodecaazaporphin). A good agreement was also noted between similar parameters calculated by various DFT methods, both qualitatively and quantitatively.