Importance of the Electron Correlation and Dispersion Corrections in Calculations Involving Enamines, Hemiaminals, and Aminals. Comparison of B3LYP, M06-2X, MP2, and CCSD Results with Experimental Data

Mechanisms of acid generation from ionic photoacid generators for extreme ultraviolet and electron beam lithography

Photoacid generators (PAGs) are important components of chemically amplified resists. The properties of PAGs directly affect the sensitivity of photoresists, line edge roughness, and resolution. Understanding the photoacid generation process in extreme ultraviolet (EUV) and electron beam (EB) lithography is helpful for photoresist design. However, the microscopic mechanisms remain largely unclear and the large variety in the molecular structure of PAGs presents a challenge to overcome. In this work, we investigate the microscopic processes of photoacid production of ionic PAGs for EUV and EB lithography. The PAG dissociation pathway is found to depend on the molecular structure and conformations. The processes of photoacid production and by-product generation are also revealed. The results contribute to a better understanding of the photochemical reactions in EUV and EB lithography, providing insights into the molecular design of novel PAGs and photoresists.

A Holistic View of the Interactions between Electron-Deficient Systems: Clustering of Beryllium and Magnesium Hydrides and Halides

In the search for common bonding patterns in pure and mixed clusters of beryllium and magnesium derivatives, the most stable dimers and trimers involving BeX2 and MgX2 (X = H, F, Cl) have been studied in the gas phase using B3LYP and M06-2X DFT methods and the G4 ab initio composite procedure. To obtain some insight into their structure, stability, and bonding characteristics, we have used two different energy decomposition formalisms, namely MBIE and LMO-EDA, in parallel with the analysis of the electron density with the help of QTAIM, ELF, NCIPLOT, and AdNDP approaches. Some interesting differences are already observed in the dimers, where the stability sequence observed for the hydrides differs entirely from that of the fluorides and chlorides. Trimers also show some peculiarities associated with the presence of compact trigonal cyclic structures that compete in stability with the more conventional hexagonal and linear forms. As observed for dimers, the stability of the trimers changes significantly from hydrides to fluorides or chlorides. Although some of these clusters were previously explored in the literature, the novelty of this work is to provide a holistic approach to the entire series of compounds by using chemical bonding tools, allowing us to understand the stability trends in detail and providing insights for a significant number of new, unexplored structures.

Enantiodetermining processes in the synthesis of alanine, serine, and isovaline

In this study, quantum chemical calculations were used to explore the synthesis of three chiral α-amino acids, specifically alanine, serine, and isovaline, from reactants found in interstellar space. Our focus is on the crucial step in the synthesis pathway that determines the chirality of the amino acids. The results indicate that in the case of alanine, the determination of enantiomer is primarily influenced by the direction of the collision of molecules or functional groups, which leads to the formation of a chirality center in a crucial intermediate. However, contrary to chemical expectations, the enantiodetermining/enantioselection step for serine and isovaline synthesis occurs prior to the creation of a chirality center.

Pyrazinyl and pyridinyl bis-azomethines formation: an experimental and computational study

Formation of bis-azomethines from hydrazine and heterocyclic aromatic carbaldehydes, namely pyridine-2-carbaldehyde and pyrazine-2-carbaldehyde, is studied using density functional theory. The theoretical investigation is correlated with experimental results obtained by means of NMR spectroscopy. The presence of bis-hemiaminal intermediates is evidenced by NMR spectra while surprisingly stable hemiaminal intermediate was isolated experimentally. Water, methanol and acetic acid were outlined to play a crucial role as active catalysts of elementary steps of the reaction mechanisms. The possible reaction sequences, i.e. addition-dehydration-addition-dehydration or addition-addition-dehydration-dehydration are investigated and discussed. Also, alternative mechanistic path via ionic mechanism was proposed for the formation of hemiaminals.

Hemiacetal-based dynamic systems: a new mechanistic insight

The formation of hemiacetals from pyrazine trifluoromethylketone as a model receptor and four simple alcohols was studied by using quantum chemical calculations and NMR spectroscopy. Free energy profiles for four types of mechanistic pathways were calculated and discussed with respect to kinetic and thermodynamic measurements. We show that hemiacetal formation is facilitated by an assisted proton transfer process via a pseudo eight-membered transition state which brings the theory and experiment into close agreement. Also, a newly proposed mechanistic pathway for hemiacetal formation via a five-membered transition state leading to zwitterionic intermediates is discussed. Direct proton transfer in a pseudo four-membered transition state can be ruled out due to the high energy of transition states with respect to other mechanistic pathways. We also show that in the case of hemiacetals, water and alcohol molecules cannot account sufficiently for the H-transfer process via six-membered transition states.

Dispersion, Rehybridization, and Pentacoordination: Keys to Understand Clustering of Boron and Aluminum Hydrides and Halides

The structure, stability, and bonding characteristics of dimers and trimers involving BX₃ and AlX₃ (X = H, F, Cl) in the gas phase, many of them explored for the first time, were investigated using different DFT (B3LYP, B3LYP/D3BJ, and M06-2X) and ab initio (MP2 and G4) methods together with different energy decomposition formalisms, namely, many-body interaction-energy and localized molecular orbital energy decomposition analysis. The electron density of the clusters investigated was analyzed with QTAIM, electron localization function, NCIPLOT, and adaptive natural density partitioning approaches. Our results for triel hydride dimers and Al₂X₆ (X = F, Cl) clusters are in good agreement with previous studies in the literature, but in contrast with the general accepted idea that B₂F₆ and B₂Cl₆ do not exist, we have found that they are predicted to be weakly bound systems if dispersion interactions are conveniently accounted for in the theoretical schemes used. Dispersion interactions are also dominant in both homo- and heterotrimers involving boron halide monomers. Surprisingly, B₃F₉ and B₃Cl₉ C_3v cyclic trimers, in spite of exhibiting rather strong B-X (X = F, Cl) interactions, were found to be unstable with respect to the isolated monomers due to the high energetic cost of the rehybridization of the B atom, which is larger than the two- and three-body stabilization contributions when the cyclic is formed. Another important feature is the enhanced stability of both homo- and heterotrimers in which Al is the central atom because Al is systematically pentacoordinated, whereas this is not the case when the central atom is B, which is only tri- or tetra-coordinated.

Potential Energy Surfaces Sampled in Cremer-Pople Coordinates and Represented by Common Force Field Functionals for Small Cyclic Molecules

The complex conformations of the cyclic moieties impact the physical and chemical properties of molecules. In this work, we chose 22 molecules of four-, five-, and six-membered rings and performed a thorough conformational sampling using Cremer-Pople coordinates. With consideration of symmetries, we obtained a total of 1504 conformational structures for four-membered, 5576 for five-membered, and 13509 for six-membered rings. All well-known and many less well-known conformers for each molecule were identified. We represented the potential energy surfaces (PESs) by fitting the data to common analytical force field (FF) functional forms. We found that the general features of PESs can be described by the essential FF functional forms; however, the accuracy of representation can be improved remarkably by including the torsion-bond and torsion-angle coupling terms. The best fit yields R-squared (R²) values close to 1.0 and mean absolute errors in energy less than 0.3 kcal/mol.

Designing Excess Electron Compounds by Substituting Alkali Metals to a Small and Versatile Tetracyclic Framework: A Theoretical Perspective

Organic compound-based nonlinear optical (NLO) materials have sparked a lot of attention due to their multitude of applications and shorter optical response times than those of inorganic NLO materials. In the present investigation, we designed exo-exo-tetracyclo[6.2.1.1^3,6.0^2,7]dodecane (TCD) derivatives, which were obtained by replacing H atoms of methylene bridge carbon with alkali metals (Li, Na, and K). It was observed that upon the substitution of alkali metals at bridging CH₂ carbon, absorption within the visible region occurred. Moving from 1 to 7 derivatives, the maximum absorption wavelength of the complexes exhibited a red shift. The designed molecules showed a high degree of intramolecular charge transfer (ICT) and excess electrons in nature, which were responsible for rapid optical response time and significant large molecular (hyper)polarizability. Calculated trends also inferred that the crucial transition energy decreased in order that also played a key role in the higher nonlinear optical response. Furthermore, to examine the effect of the structure/property relationship on the nonlinear optical properties of these investigated compounds (1-7), we calculated the density of state (DOS), transition density matrix (TDM), and frontier molecular orbitals (FMOs). The largest first static hyperpolarizability (β_tot) of TCD derivative 7 was 72059 au, which was 43 times greater than that of the prototype p-nitroaniline (β_tot = 1675 au).

Best-Practice DFT Protocols for Basic Molecular Computational Chemistry

Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share of these quantum-chemical calculations applies density functional theory (DFT) evaluated in atomic-orbital basis sets. This work provides best-practice guidance on the numerous methodological and technical aspects of DFT calculations in three parts: Firstly, we set the stage and introduce a step-by-step decision tree to choose a computational protocol that models the experiment as closely as possible. Secondly, we present a recommendation matrix to guide the choice of functional and basis set depending on the task at hand. A particular focus is on achieving an optimal balance between accuracy, robustness, and efficiency through multi-level approaches. Finally, we discuss selected representative examples to illustrate the recommended protocols and the effect of methodological choices.

Computational Study of the Stability of Pyrrolidine-Derived Iminium Ions: Exchange Equilibria between Iminium Ions and Carbonyl Compounds

The tendency of carbonyl compounds to form iminium ions by reaction with pyrrolidine or chiral pyrrolidine derivatives (in other words, the relative stability to hydrolysis of these iminium ions) has been computationally examined, mainly using the M06-2X/6-311+G(d,p) method. We have thus obtained the equilibrium positions for R-CH=O + CH₂=CH-CH=N⁺R₂* → R-CH=N⁺R₂* + CH₂=CH-CH=O reactions and for related exchanges. In these exchanges, there is a transfer of a secondary amine between two carbonyl compounds. Their relative energies may be used to predict which iminium species can be predominantly formed when two or more carbonyl groups are present in a reaction medium. In the catalytic Michael additions of nucleophiles to iminium ions arising from conjugated enals, dienals, and trienals, if the formation of the new Nu-C bond is favorable, the chances of amino-catalyzed reactions to efficiently proceed, with high conversions, depend on the calculated energy values for these exchange equilibria, where the iminium tetrafluoroborates of the adducts (final iminium intermediates) must be more prone to hydrolysis than the initial iminium tetrafluoroborates. The density functional theory (DFT) calculations indicate that the MacMillan catalysts and related oxazolidinones are especially suitable in this regard.

Enhanced tumour penetration and prolonged circulation in blood of polyzwitterion-drug conjugates with cell-membrane affinity

Effective anticancer nanomedicines need to exhibit prolonged circulation in blood, to extravasate and accumulate in tumours, and to be taken up by tumour cells. These contrasting criteria for persistent circulation and cell-membrane affinity have often led to complex nanoparticle designs with hampered clinical translatability. Here, we show that conjugates of small-molecule anticancer drugs with the polyzwitterion poly(2-(N-oxide-N,N-diethylamino)ethyl methacrylate) have long blood-circulation half-lives and bind reversibly to cell membranes, owing to the negligible interaction of the polyzwitterion with proteins and its weak interaction with phospholipids. Adsorption of the polyzwitterion-drug conjugates to tumour endothelial cells and then to cancer cells favoured their transcytosis-mediated extravasation into tumour interstitium and infiltration into tumours, and led to the eradication of large tumours and patient-derived tumour xenografts in mice. The simplicity and potency of the polyzwitterion-drug conjugates should facilitate the design of translational anticancer nanomedicines.

Computational Study of the Addition of Methanethiol to 40+ Michael Acceptors as a Model for the Bioconjugation of Cysteines

A long series of Michael acceptors are studied computationally as potential alternatives to the maleimides that are used in most antibody-drug conjugates to link Cys of mAbs with cytotoxic drugs. The products of the reaction of methanethiol (CH3SH/MeSH, as a simple model of Cys) with N-methylated ethynesulfonamide, 2-ethynylpyridinium ion, propynamide, and methyl ethynephosphonamidate (that is, with HC≡C-EWG) are predicted by the M06-2X/6-311+G(d,p) method to be thermodynamically more stable, in relation to their precursors, than that of MeSH with N-methylmaleimide and, in general, with H2C═CH-EWG; calculations with AcCysOMe and tBuSH are also included. However, for the addition of the anion (MeS-), which is the reactive species, the order changes and N-methylated 2-vinylpyridinium ion, 2,3-butadienamide, and maleimide may give more easily the anionic adducts than several activated triple bonds; moreover, the calculated ΔG⧧ values increase following the order HC≡C-SO2NHMe, N-methylmaleimide, HC≡C-PO(OMe)NHMe, and HC≡C-CONHMe. In other words, MeS- is predicted to react more rapidly with maleimides than with ethynephosphonamidates and with propynamides, in agreement with the experimental results. New mechanistic details are disclosed regarding the advantageous use of some amides, especially of ethynesulfonamides, which, however, are more prone to double additions and exchange reactions.

Benzene-1,3-diol derivatives as the inhibitors of butyrylcholinesterase: An emergent target of Alzheimer’s disease

Molecular docking is a powerful and significant approach for the identification of lead molecules on the basis of virtual screening. With it a large number of compounds can be tested and based on the scoring function and ranking, the conclusion can be made about how the selected compounds can inhibit the targeted protein/receptor. Considering the importance of selective inhibitors of cholinesterase in the treatment of Alzheimer disease, this research is focused on the determination of the mechanism of binding interactions of few benzene-1,3-diol derivatives within the active site of both acetyl-choline-sterase (AChE) and butyrylcholinesterase (BChE). All the selective ligands were found to have a greater binding affinity with the BChE when compared to that of AChE, by an average value of ~?28.4 and ~?12.5 kJ/mol, respectively. The results suggested that the identified inhibitors can be used as the lead com-pounds for the development of novel inhibitors of the targeted enzymes against some specific diseases, thus opening the possibility of new therapeutic strategies.

Physical organic studies and dynamic covalent chemistry of picolyl heterocyclic amino aminals

A dynamic covalent system of the picolyl heterocyclic amino aminals has been studied. The aminals are characterized as a metastable species and easily switch to other forms via external stimuli. The solvent, temperature, acid-base and substituent effects have been examined to evaluate the dynamic covalent system. The results reveal that a more polar solvent, a lower temperature, basic conditions and an electron-withdrawing moiety contribute to the stabilities of aminals. The existence of the n → π* interaction between acetonitrile and the C[double bond, length as m-dash]N moiety makes the N-pyrimidyl imine (4c and 4d) yield higher in CD3CN. In a similar fashion, all aminals tend to convert to the corresponding hemiaminal ethers in a methanol environment. According to these findings, we successfully synthesized the following species: (a) N-2-picolylpyrimidin-2-amine 6c obtained by reduction using acetonitrile as the specific solvent; (b) a picolyl aromatic amino aminal 3e prepared from 2-pyridinecarboxaldehyde and the electron withdrawing 2-methoxy-5-nitroaniline.

NMR and Computational Studies on the Reactions of Enamines with Nitroalkenes That May Pass through Cyclobutanes

The addition of aldehyde enamines to nitroalkenes affords cyclobutanes in all solvents, with all of the pyrrolidine and proline derivatives tested by us and with all of the substrates we have examined. Depending on the temperature, concentration of water, solvent polarity, and other factors, the opening and hydrolysis of such a four-membered ring may take place rapidly or last for several days, producing the final Michael-like adducts (4-nitrobutanals). Thirteen new cyclobutanes have now been characterized by NMR spectroscopy. As could be expected, s-trans-enamine conformers give rise to all-trans-(4S)-4-nitrocyclobutylpyrrolidines, while s-cis-enamine conformers afford all-trans-(4R)-4-nitrocyclobutylpyrrolidines. These four-membered rings can isomerize to adduct enamines, which should be hydrolyzed via their iminium ions. MP2 and M06-2X calculations predict that one iminium ion is more stable than the other iminium species, so that protonation of the adduct enamines can be quite stereoselective; in the presence of water, the so-called syn adducts (e.g., OCH-*CHR-*CHPh-CH₂NO₂, with R and Ph syn) eventually become the major products. Why one syn adduct is obtained with aldehydes, whereas cyclic ketones (the predicted ring-fused cyclobutanes of which isomerize to their enamines more easily) produce the other syn adduct, is also explained by means of molecular orbital calculations. Nitro-Michael reactions of aldehyde enamines that "stop" at the nitrocyclobutane stage and final enamine stage do not work catalytically, as known, but those of cyclic ketone enamines that do not work stop at the final enamine stage (if their hydrolysis to the corresponding nitroethylketones is less favorable than expected). These and other facts are accounted for, and the proposals of the groups led by Seebach and Hayashi, Blackmond, and Pihko and Papai are reconciled.

Theoretical Calculation of the Thermodynamic Properties of 20 Amino Acid Ionic Liquids

The thermodynamic properties of gas-phase amino acid ionic liquids (AAILs) containing 20 amino acids ([AA]^-) and 1-ethyl-3-methylimidazolium ([Emim]⁺) are studied using a combination of the ab initio method, molecular dynamics simulations, Born-Haber (BH) cycle analysis, and isodesmic reactions. The M06-2X/TZVP method is used to explore the structure and dissociation enthalpies of [Emim][AA] by considering dispersion interaction, and the MP2/Aug-cc-pVTZ method is used to correct these enthalpies. The vaporization enthalpies of all 20 AAILs are calculated by molecular dynamics simulations, and the gas-phase formation enthalpies (Δ_f H) of the 20 [AA]^- anions and [Emim]⁺ cation are calculated by the density functional theory/M06-2X method and isodesmic reaction approaches. To obtain the Δ_f H of the AAILs, interconnections in the corresponding BH cycles are evaluated. A systematic study of the 20 [Emim][AA] ion pairs provides some initial factors contributing to the thermodynamic properties of AAILs: including length of the alkyl chain, interatomic electronic effects, steric repulsion from the cyclic group, and H-bonds formed by functional groups. Generally speaking, the results of this work provide insights into the structure-property relationships of not only ILs but also any ionic or molecular substance.

Spectroscopic and molecular structure (monomeric and dimeric model) investigation of Febuxostat: A combined experimental and theoretical study

Febuxostat (FXT) is a urate-lowering drug and xanthine oxidase inhibitor which is used for the treatment of hyperuricemia and gout caused by increased levels of uric acid in the blood (hyperuricemia). The present study aims to provide deeper knowledge of the structural, vibrational spectroscopic and physiochemical properties of FXT based on monomeric and dimeric model with the aid of combination of experimental and computational methods. The conformational analysis of form Q has been done to predict the possible structure of unknown form A. Vibrational spectra of form A and Q has been compared to get an idea of hydrogen bonding interactions of form A. A computational study of FXT has been executed at different level (B3LYP, M06-2X, WB97XD) of theory and 6-31 G (d, p) basis set for dimeric model to elucidate the nature of intermolecular hydrogen bond. The red shift observed in the stretching modes of OH, CO groups and blue shift in stretching mode of CN group in experimental as well as in theoretical spectra explains the involvement of these groups in intermolecular hydrogen bonding. NBO analysis shows that change in electron density (ED) in the lone pair orbital to σ* antibonding orbital (LP1 (N39) → σ* (O3-H38)) with maximum value of E(2) energy confirms the presence of hydrogen bond (N39⋯H38-O3) leading to dimer formation. Study of topological parameters was executed for dimer using Bader's atoms in molecules (AIM) theory predicting the partially covalent nature of hydrogen bonds present in the molecule. The study of molecular electrostatic potential surface (MEPS) map ascertains that the CO, CN group are prone to electrophilic attack and OH group is active towards nucleophilic attack. The lower energy band gap and higher value of softness of dimeric model of FXT indicates its more reactivity, polarisability than monomeric model. The local reactivity descriptors predict the order of reactive sites towards electrophilic, nucleophilic and radical attack. An investigation made to determine the ligand protein interaction of FXT through docking with different molecular targets reveals the inhibitive as well as antibacterial nature of FXT.

Exploring the effect of confinement on water clusters in carbon nanotubes

Using armchair-type single-walled carbon nanotubes (SWCNTs) of different sizes as model compounds for lignite, the effect of water molecule confinement on the water-holding capacity of lignite pores was investigated. Results indicated that the water-holding capacity of pores with diameters of <10 nm was eight times larger than that of pores with diameters of 100 nm. The configuration of the cluster of water molecules in each SWCNT and the binding energy between each SWCNT and the water molecules within it were calculated by means of density functional theory using a hybrid functional: M06-2X/6-311+G**, 6-31G*. The results prove that the configurations of the water molecules in the SWCNTs are very different to their configuration in the unconfined state. In vacuum, the cluster of three water molecules adopted a trimer configuration, while they presented a linear configuration in the 6.78 Å SWCNT. Similarly, in vacuum, the cluster of five water molecules formed a five-membered ring, while they favored a linear configuration in the 6.78 Å SWCNT, a zigzag configuration in the 8.14 Å SWCNT, and a trimer + 1 + 1 configuration (i.e., a trimer plus two isolated water molecules) in the 9.49 Å, 10.85 Å, and 13.75 Å SWCNTs. There was found to be a degree of competition between the coupling energy of the water molecules with the SWCNT and the hydrogen bonding among the water molecules. When the diameter of the SWCNT was >1 nm, the hydrogen bonding among the water molecules dominated, while the coupling energy of the water molecules with the SWCNT amounted to only 30-40% of the total interaction energy of the water molecules. Graphical Abstract Computed equilibrium structures of five water molecules confined in SWCNTs with diameters of 6.78 Å, 8.14 Å, 9.49 Å, 10.85 Å, and 13.75 Å, and in vacuum.

A theoretical study of the Duff reaction: insights into its selectivity

The selectivity-determining step of the Duff ortho-formylation was studied using DFT calculations; a hydrogen bond establishes the position where the formylation will take place.