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Tubulin self-association is a critical process in microtubule dynamics. The early intermediate structures, energetics, and their regulation by fluxes of chemical energy, associated with guanosine triphosphate (GTP) hydrolysis, are poorly understood. We reconstituted an in vitro minimal model system, mimicking the key elements of the nontemplated tubulin assembly. To resolve the distribution of GTP- and guanosine diphosphate (GDP)-tubulin structures, at low temperatures (∼10 °C) and below the critical concentration for the microtubule assembly, we analyzed in-line size-exclusion chromatography-small-angle X-ray scattering (SEC-SAXS) chromatograms of GTP- and GDP-tubulin solutions. Both solutions rapidly attained steady state. The SEC-SAXS data were consistent with an isodesmic thermodynamic model of longitudinal tubulin self-association into 1D oligomers, terminated by the formation of tubulin single rings. The analysis showed that free dimers coexisted with tetramers and hexamers. Tubulin monomers and lateral association between dimers were not detected. The dimer-dimer longitudinal self-association standard Helmholtz free energies were -14.2 ± 0.4 kBT (-8.0 ± 0.2 kcal mol-1) and -13.1 ± 0.5 kBT (-7.4 ± 0.3 kcal mol-1) for GDP- and GTP-tubulin, respectively. We then determined the mass fractions of dimers, tetramers, and hexamers as a function of the total tubulin concentration. A small fraction of stable tubulin single rings, with a radius of 19.2 ± 0.2 nm, was detected in the GDP-tubulin solution. In the GTP-tubulin solution, this fraction was significantly lower. Cryo-TEM images and SEC-multiangle light-scattering analysis corroborated these findings. Our analyses provide an accurate structure-stability description of cold tubulin solutions.

Despite the synthesis and structural characterization of closo-hydroborate dianions, [Bn Hn ]2- (n=6-12) more than 50 years ago, some ambiguity remains about the structure of [B8 H8 ]2- . Although the solid-state structure of [B8 H8 ]2- was established by single-crystal X-ray studies in 1969, fast rearrangements in solution at accessible temperatures prevented its detailed characterization. We therefore stabilized a derivative of [B8 H8 ]2- by using Cp2 MBH3 and structurally characterized two new octaborane analogues, [(Cp2 MBH3 )2 B8 H6 ] (Cp=η5 -C5 H5 ; M=Zr (1-Zr) and Hf (1-Hf)), so that the dynamics of the B8 skeleton were arrested. The solid-state structures of both 1-Zr and 1-Hf comprise a dodecahedron core protected by {Cp2 MBH3 } moieties on both sides of the cluster. Spectroscopic characterization (11 B NMR) validates the intactness of the B8 dodecahedron core in solution as well. Theoretical calculations establish that the two exo-{Cp2 MBH3 } fragments provide structural and electronic structural stability to the B8 core and its intact dodecahedral dianionic nature. Furthermore, we propose isodesmic equations for the formation of higher analogues of the Bn core (n>8) guarded by different group 4 transition metals. Our analysis suggests that, as we move to higher polyhedra (n>10), the formation becomes unfavourable irrespective of metal.

To evaluate the physical and chemical degradation of monoclonal antibodies in the presence of Zn2+. A full length IgG1 monoclonal antibody (mAb1) was formulated with various amounts of Zn2+. The resulting mixture was incubated for several weeks at room temperature and analyzed using a variety of biochemical techniques to look for various physical (e.g. aggregation) and chemical (e.g. fragmentation) degradation pathways. mAb1 of the IgG1 subclass undergoes aggregation in the presence of Zn2+ in a concentration dependent manner. Up to hexamers were characterized using SEC-MALS. No fragmentation was noticed in the presence of Zn2+ as opposed to that found in our previous report when IgG1 mAbs were incubated in the presence of Cu2+ ions. Site directed mutagenesis indicated the involvement of Fc histidine (His 310) in Zn2+ mediated aggregation. A novel metal ion mediated isodesmic aggregation mechanism was found in IgG1 class of monoclonal antibodies. Histidine residues in the Fc region were determined to be the binding site and implicated in Zn2+ mediated aggregation.

The effective charges on hydrogen and carbon atoms and the Fukui functions for the electrophilic and radical attacks for the hydrogen atoms of the chair and boat conformations of cyclohexanone were calculated using the density functional theory (DFT) with the hybrid functionals: B3LYP in the 6-311g++(d,p) basis set; X3LYP in the 6-311g++(d,p) and D95++(d,p) basis sets; and pbe1pbe in the D95++(d,p) basis set, and by the MP2 method in the 6-311g++(d,p) basis set. For these conformations, the transition states were localized; the length of the broken CH bond in the transition state was determined; and the activation energies, activation entropies, and enthalpies of the elementary reactions of the tert-butylperoxyl ((СН3)3СOO•) radical with all types of CH bonds of cyclohexanone were calculated. The relative reactivity of the CH bonds of cyclohexanone in reactions with ((СН3)3СOO•); the local electrophilicity indices of the carbon-centered radicals formed from cyclohexanone after elimination of the hydrogen atom; and the energy difference (ΔЕSOMO) between the single-occupied molecular orbitals of these carbon-centered radicals and the (СН3)3СOO• radical were calculated. The CH bond dissociation energies of cyclohexanone were calculated by the DFT B3LYP 6-311g++(d,p), CBS-QB3, and G3MP2B3 methods using the isodesmic reactions technique. The factors governing the CH bond reactivity of cyclohexanone in reactions with the (СН3)3СOO• radical were considered. The increased reactivity of CH bonds of cyclohexanone in the 2, 6 (α) positions was shown to be due to the low bond dissociation energy, high electron-donor capacity of hydrogen atoms, smaller length of the broken CH bond in the transition state, and small ΔЕSOMO value. The lower reactivity of CH bonds at positions 3, 5 (β), and 4 (γ) is determined by the higher bond dissociation energies, decreased electron density due to the inductive effect of the carbonyl group, nucleophilicity of the carbon-centered radicals, greater length of the broken CH bonds in the transition state, and larger ΔЕSOMO value. The difference in the reactivity of CH bonds at positions 3, 5 (β), and 4 (γ) is determined by these factors, but not by the difference in the dissociation energies of these bonds. The reactivity of CH bonds in the boat conformation is higher than that in the chair conformation in the reactions with the (СН3)3СOO• radical.

Background: Redox active metal cations, such as Cu2 +, have been related to induce amyloid plaques formation and oxidative stress, which are two of the key events in the development of Alzheimer’s disease (AD) and others metal promoted neurodegenerative diseases. In these oxidative events, standard reduction potential (SRP) is an important property especially relevant in the reactive oxygen species formation. Objective: The SRP is not usually considered for the selection of drug candidates in anti-AD treatments. In this work, we present a computational protocol for the selection of multifunctional ligands with suitable metal chelating, pharmacokinetics, and redox properties. Methods: The filtering process is based on quantum chemical calculations and the use of in silico tools. Calculations of SRP were performed by using the M06-2X density functional and the isodesmic approach. Then, a virtual screening technique (VS) was used for similar structure search. Results: Protocol application allowed the assessment of chelating, drug likeness, and redox properties of copper ligands. Those molecules showing the best features were selected as molecular scaffolds for a VS procedure in order to obtain related compounds. After applying this process, we present a list of candidates with suitable properties to prevent the redox reactions mediated by copper(II) ion. Conclusion: The protocol incorporates SRP in the filtering stage and can be effectively used to obtain a set of potential drug candidates for AD treatments.

The correlation between molecular structure and mechanism of supramolecular polymerizations is a topic of great interest, with a special focus on the pathway complexity of porphyrin assemblies. Their cooperative polymerization typically yields highly ordered, long 1D polymers and is driven by a combination of π‐stacking due to solvophobic effects and hydrogen bonding interactions. Subtle changes in molecular structure, however, have significant influence on the cooperativity factor and yield different aggregate types (J‐ versus H‐aggregates) of different lengths. In this study, the influence of amide connectivity on the self‐assembly behavior of porphyrin‐based supramolecular monomers was investigated. While in nonpolar solvents, C=O centered monomers readily assemble into helical supramolecular polymers via a cooperative mechanism, their NH centered counterparts form short, non‐helical J‐type aggregates via an isodesmic pathway. A combination of spectroscopy and density functional theory modelling sheds light on the molecular origins causing this stunning difference in assembly properties and demonstrates the importance of molecular connectivity in the design of supramolecular systems. Finally, their mutual interference in copolymerization experiments is presented., Amide connectivity in the molecular design of porphyrin supramolecular monomers strongly impacts the assembly behavior in nonpolar solvents. While C=O centered monomers aggregate cooperatively into long, 1D supramolecular fibers, their NH‐centered counterparts only form isodesmic J‐aggregates. With a combination of spectroscopy and density functional modelling, the authors shed light on the molecular origins of these differences in properties.

The so-called protobranching phenomenon, that is the greater stability of branched alkanes with respect to their linear isomers, represents an interesting challenge for approaches based on density functional theory (DFT), since it requires a balanced description of several electronic effects, including (intramolecular) dispersion forces. Here, we investigate this problem using a protocol recently developed based on double-hybrid functionals and a small basis set, DH-SVPD, suited for noncovalent interactions. The energies of bond separation reactions (BSR), defined on the basis of an isodesmic principle, are taken as reference properties for the evaluation of 15 DFT approaches. The obtained results show that error lower than the so-called “chemical accuracy” (

Structures, thermochemical properties, bond energies, and internal rotation potentials of acetic acid hydrazide (CH3CONHNH2), acetamide (CH3CONH2), and N-methyl acetamide (CH3CONHCH3), and their radicals corresponding to the loss of hydrogen atom, have been studied. Gas-phase standard enthalpies of formation and bond energies were calculated using the DFT methods B3LYP/6-31G(d,p), B3LYP/6-31G(2d,2p) and the composite CBS-QB3 methods employing a series of work reactions further to improve the accuracy of the ΔHf°(298 K). Molecular structures, vibration frequencies, and internal rotor potentials were calculated at the DFT level. The parent molecules’ standard formation enthalpies of CH3–C=ONHNH2, CH3–C=ONH2, and CH3–C=ONHCH3 were evaluated as −27.08, −57.40, and −56.48 kcal mol−1, respectively, from the CBS–QB3 calculations. Structures, internal rotor potentials, and C–H and N–H bond dissociation energies are reported. The DFT and the CBS-QB3 enthalpy values show close agreement, and this accord is attributed to the use of isodesmic work reactions for the analysis. The agreement also suggests this combination of the B3LYP/work reaction approach is acceptable for larger molecules. Internal rotor potentials for the amides are high, ranging from 16 to 22 kcal mol−1.

The density functional theory (DFT) calculations are carried out to assay the effects of nitrogen atoms on the stability and reactivity of singlet (s) and triplet (t) forms of novel silylenes with one, two, and three silylene centers (1s-18s and 1t-18t, receptively) at B3LYP/6-311 + + G** level of theory. Every one of the 36 silylenes scrutinized appears as minimum on its energy surface, for showing no negative force constant. All of our silylenes have singlets ground state and the highest stability belongs to silylene 2 (ΔEs−t = 44.71.95 kcal/mol). This clearly demonstrates the effect of intermolecular interactions ( $$\sigma$$ (C(E and G)−H(exo))→LP*Si). The aim of the present work was to consider the influence of nitrogen substituents on the stability (ΔEs−t), band gap (ΔEHOMO−LUMO), nucleophilicity (N), electrophilicity (ω), and isodesmic reactions. Finally, our investigation offers new insights into the chemistry of novel bicyclic silylenes that can be applied as cumulated multi-dentate ligands. We have compared and contrasted the substituent effects on the stability and reactivity of singlet (s) and triplet (t) forms of novel silylenes with one, two, and three silylene centers (1s-18s and 1t-18t, receptively) at B3LYP/6-311 + + G** level of theory. All novel silylenes show singlet ground state and the highest stability belongs to silylene 2 (ΔEs−t = 44.71.95 kcal/mol). This stability can be related to its intermolecular interactions. The nonbonding electrons at the nitrogens (E or G) of silylenes 3s, 5s, 6s, 7s, 8s, 9s, 11s, 14s and 15s appear to have a tendency to interact with the empty p orbital of the silylene center and form a σ-bond.

Reversible self-association (RSA) remains a challenge in the development of therapeutic monoclonal antibodies (mAbs). We recently analyzed the energetics of RSA for five IgG mAbs (designated as A-E) under matched conditions and using orthogonal methods. Here we examine the thermodynamics of RSA for two of the mAbs that showed the strongest evidence of RSA (mAbs C and E) to identify underlying mechanisms. Concentration-dependent dynamic light scattering and sedimentation velocity (SV) studies were carried out for each mAb over a range of temperatures. Because self-association was weak, the SV data were globally analyzed via direct boundary fitting to identify best-fit models, accurately determine interaction energetics, and account for the confounding effects of thermodynamic and hydrodynamic nonideality. mAb C undergoes isodesmic self-association at all temperatures examined, with the energetics indicative of an enthalpically-driven reaction offset by a significant entropic penalty. By contrast, mAb E undergoes monomer-dimer self-association, with the reaction being entropically-driven and comprised of only a small enthalpic contribution. Classical interpretations implicate van der Waals interactions and H-bond formation for mAb C RSA, and electrostatic interactions for mAb E. However, noting that RSA is likely coupled to additional equilibria, we also discuss the limitations of such interpretations.

Various 1,2,5-oxadiazole-1,2,3,4-tetrazole-based high-energy materials were designed and their properties investigated. Their heat of formation, detonation properties, and thermal stability were calculated on the basis of isodesmic reactions, Kamlet-Jacobs equation, and bond dissociation energy, respectively. The results showed that all designed compounds possess high positive heat of formation, and the –N=N–/–N3 substituents were found to be the most effective for improving the heat of formation. The trend of changes in density, detonation pressure, and detonation velocity was almost identical in all compounds, which suggests that density was key to the determination of detonation properties. In view of bond dissociation energy, the –CN/–NH2 substituents improved the thermal stability of the designed compounds, while the other substituents/bridges decreased the stability to some extent. Considering the detonation properties and thermal stability, six compounds (C7, D3, D7, F7, G7, and H7) were selected as potential high-energy materials because they exhibited higher detonation properties and thermal stability than 1,3,5-trinitro-1,3,5-triazinane (RDX). Finally, electronic structures (such as distribution of frontier molecular orbitals and electrostatic potential) of the selected compounds were simulated to obtain detailed information about the electronic structures of the screened compounds.

Enhanced thermodynamic stability is a fundamental characteristic of aromatic molecules, yet most previous studies of aromatic stabilization energy (ASE) have been limited to small rings with up to 18 π-electrons. Here we demonstrate that ASE can be detected experimentally in π-conjugated porphyrin nanorings with Hückel circuits of 76-108 π-electrons. This conclusion is supported by analyzing redox potentials to calculate the energy change for isodesmic reactions that convert an aromatic ring to an antiaromatic ring or vice versa. It is also supported by analyzing the energy barriers to conformational equilibria that disrupt aromaticity in the transition state. Both types of experiment indicate that cationic porphyrin nanorings display ASEs of 1-5 kJ mol-1. Density functional theory calculations reproduce the results for both types of experiment and predict ASEs in the range of 1-16 kJ mol-1. The experimental ASEs in porphyrin nanorings are compared with an experimental ASE of [18]annulene of ∼11 kJ mol-1, deduced from analysis of the energy barriers to conformational equilibria in [16], [18], and [20]annulene. Calculated energies of isodesmic reactions give an ASE of ∼37 kJ mol-1 in [18]annulene. This work contributes to a fundamental understanding of aromaticity in large macrocycles.

Circularly polarized luminescence (CPL) materials have potential applications in three-dimensional (3D) displays, quantum encryption, and optical sensors. The development of single-component CPL materials with polymorphic assembly and handedness inversion remains a significant challenge. Herein, we present the access of such materials by controlling the underlying assembly pathway of well-designed chiral emitters. A pair of enantiomeric platinum complexes (R)-1 and (S)-1 decorated with a chiral α-methylbenzyl isocyanide ligand were prepared. By using the mixed-solvent (THF/n-hexane, THF=tetrahydrofuran) or high-concentration condition, these complexes were found to assemble via a cooperative or isodesmic pathway with significantly enhanced yellow or red emission, respectively. The aggregate samples obtained via these conditions show efficient CPL (dissymmery factor ∣glum∣>0.02, emission quantum yield Φ>20%). Interestingly, different assembly pathway leads to helical nanoribbons or nanofibers with opposite handedness from the complex with the same molecular chirality. This has been unambiguously and consistently manifested by circular dichroism and CPL spectral analysis and transmission electron, scanning electron, and atomic force microscope studies. This work demonstrates an appealing example of constructing polymorphic helical architectures with highly efficient CPL and inverted handedness thanks to the excellent assembly and emission of platinum complexes.

In this study, density functional theory (DFT) was employed to predict thermochemical and energetic properties for single-walled carbon nanotubes (SWCNTs) decorated with one and more nitroaromatic substituents. Heat of sublimation and crystal density of these molecules were estimated on the basis of molecular surface properties calculated by electrostatic potential (ESP) analysis. Heats of formation in gas and solid phases were calculated using isodesmic approach. These data were used to measure velocity, pressure, and heat of detonation based on valid theoretical equations. Results show that crystal density of these molecules is close to TNT and their heat of formation is much larger. The calculated velocity and pressure of detonation for these molecules are approximately 4–6 km/s and 20–123 kbar, respectively; which are in the range of high explosives. However, their performance is lower than TNT. The detonation performance of these molecules increases as the number of nitroaromatic substituents increases.

The DLPNO-CCSD(T1)/CBS and G4 methods combined with isogyric, isodesmic, and homodesmotic working reactions were applied to calculate gas-phase enthalpies of formation for thirty-three C–H–N–O compounds with well-established experimental values. Unlike the G4 method, the DLPNO calculations, even together with isogyric reactions with small reference species, reproduce the experimental enthalpies of formation within chemical accuracy (≈ 4 kJ/mol). For more than half of the compounds, a better accuracy, within 2 kJ/mol, was achieved. These results make the DLPNO-CCSD(T1)/CBS method a promising tool for accurate prediction of enthalpy of formation of medium-sized organic compounds. Being convinced of its reliability, the DLPNO-CCSD(T1)/CBS method was also used to estimate the enthalpies of formation for some challenging compounds with conflicting values reported in the literature (glycerol, nitromethane, nitrobenzene, 1-aminoadamantane, piperazine, and others).

We have examined the use of systematic bond-separation reactions and purposely constructed chemistry-preserving isodesmic reactions for the thermochemical calculation of aromatic hydrocarbon species. The bond-separation approach yields somewhat disappointing accuracy even when the reaction energies are obtained with generally robust composite and double-hybrid (DH) density functional theory (DFT) methods. In contrast, for the purposely constructed reactions, we find a dramatic improvement in the accuracy for energies calculated with all methods examined. Notably, for medium-sized aromatic hydrocarbons, we find that an effective approach for formulating a well-balanced reaction is to split the target species into two halves with an aromatic overlapping region. Overall, the G4(MP2)-XK, MPW2PLYP, MN15, PBE, and DC-DFTB3 methods are reasonable within their respective classes of methods for the calculation of bond-separation as well as chemistry-preserving isodesmic reactions. We have further computed per-carbon atomization energy (AE) for a series of D6h benzene-type molecules, and thus obtained a formula for extrapolation to the graphene limit [AEn = 711.5 × (1 − 1/n0.640) kJ mol−1, where n = number of carbons]. It suggests that nano-graphene with a length larger than 10 nm would resemble properties of bulk graphene, and conversely, downsizing a nano-graphene beyond this point may lead to considerably altered properties from the bulk.

The standard state enthalpy of formation and the enthalpy of sublimation are essential thermochemical parameters determining the performance and application prospects of energetic materials (EM). Direct experimental measurements of these properties are complicated by low volatility and high heat release in bomb calorimetry experiments. As a result, the uncertainties in the reported enthalpies of formation for a number of even well-known CHNO-containing compounds might amount up to tens kJ mol-1, while for some novel high-nitrogen molecules they reach even hundreds of kJ mol-1. The present study reports a facile approach to determining the solid-state formation enthalpies comprised of complementary high-level quantum chemical calculations of the gas-phase thermochemistry and advanced thermal analysis techniques yielding sublimation enthalpies. The thermogravimetric procedure for the measurement of sublimation enthalpy was modified by using low external pressures (down to 0.2 Pa). This allows for observing sublimation/vaporization instead of thermal decomposition of the compounds studied. Extensive benchmarking on nonenergetic and energetic compounds reveals the average and maximal absolute errors of the sublimation enthalpies of 3.3 and 11.0 kJ mol-1, respectively. The comparison of the results with those obtained from the widely used Trouton-Williams empirical equation shows that the latter underestimates the sublimation enthalpy up to 140 kJ mol-1. Therefore, we performed a reparametrization of the latter equation with simple chemical descriptors that reduces the mean error down to 30 kJ mol-1. Highly accurate multi-level procedures W2-F12 and/or W1-F12 in conjunction with the atomization energy approach were used to calculate theoretically the gas-phase formation enthalpies. In several cases, the DLPNO-CCSD(T) enthalpies of isodesmic reactions were also employed to obtain the gas-phase thermochemistry for medium-sized important EMs. Combining the obtained thermochemical properties, we determined the solid-state enthalpies of formation for nearly 60 species containing various important explosophoric groups, from common nitroaromatics, nitroethers, and nitramines to novel nitrogen-rich heterocyclic species (e.g., the derivatives of pyrazole, tetrazole, furoxan, etc.). The large-scale benchmarking against the available experimental solid-state enthalpies of formation yielded the maximal inaccuracy of the proposed method of 25 kJ mol-1.

Controlled supramolecular polymerization has emerged as an active research area in the last decade. Recent contributions have revealed that their dynamic self-assembly into different molecular packings is strongly influenced by kinetic effects. However, the examples reported are very limited and the understanding of pathway complexity by molecular design remains elusive. In this work, two supramolecular monomers 1 and 2 by coupling BODIPY with a class of newly designed pyrazole-based motifs were designed. The flexible ethylene linker together with the presence of benzamide groups bring about intramolecular hydrogen-bonding (H-bonding) interactions between pyrazole N as the H-bonding acceptor and the adjacent amide. Our results unveiled two distinct pathways during self-assembly. Namely, a metastable J-aggregate is formed through an isodesmic model, while the thermodynamically stable H-aggregate obeys the cooperative mechanism. The detailed transformation of 1J-agg into 1H-agg, as well as the individual formation mechanisms of 1J-agg and 1H-agg have been investigated by various spectroscopic techniques. Encouraged by the drastic emission changes of monomers and aggregates, luminescence temperature sensing has been demonstrated as a proof of concept.

Structures and thermochemical properties of these species were determined by the gaussian M-062x/6-31 + g (d, p) calculation enthalpies of formation for 19 fluorinated ethanol and some radicals were calculated with a popular Ab initio and density functional theory methods: The gaussian M-062x/6-31 + g (d, p) via several series of isodesmic reactions. Entropies (S298°K in Cal·Mol-1 K-1) were estimated using the M-062x/6-31 + g (d, p) computed frequencies and geometries. Contributions of entropy, S298°K, and heat capacities, Cp(T) due to vibration, translation, and external rotation of the molecules were calculated based on the vibration frequencies and structures obtained from the M-062x/6-31 + g (d, p) Density Functional Method. Potential barriers are calculated using M-062x/6-31 + g (d, p) density functional method and are used to calculate rotor contributions to entropy and heat capacity using integration over energy levels of rotational potential. Rotational barriers were determined and hindered internal rotational contributions for S298° - 1500°K, and Cp (T) were calculated using the rigid rotor harmonic oscillator approximation, with direct integration over energy levels of the intramolecular rotation potential energy curves. Thermochemical properties of fluorinated alcohols are needed for understanding their stability and reactions in the environment and in thermal process

DFT calculations in combination with appropriate isodesmic reactions are employed to assess topological effects of nitrogens on thermodynamic parameters of novel mono-, di-, tri-, tetra-, and pentaaza-7-boratricyclo[1,1,1,01,7,07,3,07,5]hexa-2-silylenes (1–20). Despite the enormous steric strain involved in their cubic structures, all our scrutinized singlet and triplet silylenes (1s-20s vs. 1t-20t, respectively) appear as minima on their energy surfaces, for showing singlet ground states. The highest stability (ΔEs−t) is achieved by 1,3,5-triaza-7-boratricyclo[1,1,1,01,7,07,3,07,5]hexa-2-silylene (11), where all the three nitrogens are bonded to the central boron atom. All of our silylenes show the same trend for their calculated ΔEs−t and band gap (ΔEHOMO−LUMO). Isodesmic reactions are employed to compare and contrast nucleophilicity (N), electrophilicity (ω), and heat of hydrogenation (ΔEH) for our 40 silylenes (1s-20s vs. 1t-20t). In fact, we introduce a novel generation of tridimensional silylenes which have the intrinsic potential of expanding the existing boundaries of semiconductors, cumulated multi-dentate ligands, etc..

A series of derivatives of uracil were designed through substituting the hydrogen atoms by nitro groups to look for high-energy-density compounds. To explore the thermal stabilities, the heats of formation (HOF) are calculated at the G3MP2 using the isodesmic reaction accompanied with the atomization reaction. Furthermore, the determinate factors of the stability are also discussed in detail. The bond dissociation energy (BDE) were calculated at the same level through homolytic cleavage reaction accompanied with the energy gaps (Eg). Based on our calculations, excellent stabilities are confirmed not only thermally but also kinetically. To confirm the possibility as high-energy-density compounds, the detonation characters including detonation pressure, detonation velocity, molecular density, and explosive heats are predicted by using the Kamlet-Jacobs equation. Finally, two molecules (C2 and C3) are evaluated as the candidates of high-energy-density materials. It is expected that our works can benefit the further research about title molecules.

A prerequisite for the generation of detailed fundamental kinetic models is the availability of accurate thermodynamic properties. To address the scarcity of accurate experimental data, theoretical calculations can be used. The accuracy of these quantum chemistry methods for determination of thermodynamic properties can be improved by making use of empirical correction methods, such as the isodesmic bond additivity correction (BAC) method. In this work, ab initio calculations for a set of 371 molecules have been performed to determine a new set of BACs for the CBS-QB3 level of theory. For each of these molecules also accurate experimental data, that is with an experimental uncertainty less than 3 kJ mol(-1), is available. This broad dataset of hydrocarbons and heteroatomic compounds contains (non)cyclic molecules with a wide range of functional groups consisting of hydrogen, carbon, oxygen, nitrogen, and sulfur. The new set of 26 BAC parameters is obtained via linear regression analysis, minimizing the differences between experimental and corrected CBS-QB3 values. The CBS-QB3 method combined with BACs succeeds in approximating the experimental standard enthalpy of formation at 298 K with an accuracy of 4 kJ mol(-1) for almost all species. The BACs reduce the mean absolute deviation for the complete dataset from 5.65 to 2.37 kJ mol(-1), corresponding to a decrease of the root mean square deviation from 6.95 to 3.00 kJ mol(-1).

Following our quest for stable group 14 divalents, novel N-heterocyclic plumbylenes (NHPbs), composed of 2,4,6-cycloheptatriene-2,7-diazaplumbylene (1), benzannulated with one (2), two (3, 4), and three benzene rings (5), are compared and contrasted at the density functional theory level. Results indicate that in going from 1 to 5, the absolute values of singlet-triplet energy gap (ΔEs-t) and band gap (ΔEH-L) increase, while nucleophilicity (N), electrophilicity (ω), and chemical potential (μ) decrease. The most benzannulated structure, ([a,c,e]tribenzo)cyclohepta-2,7-diazaplumbylene (5), turns out as the most stable plumbylene for showing the most negative ΔEs-t of − 194.94 kcal/mol. Furthermore, 5 shows the highest ΔEH-L (− 2.75 eV), with the lowest N (1.31 eV), ω (8.20 eV), μ (− 7.15 eV), and charge of (+ 0.736) on Pb atom. Isodesmic reactions of 1-5 with common transition metal halides, MX2, give forty new metal complexes of 1M-X-5M-X, where M = Pt and Pd, while X = F, Cl, Br, and I. Their complexation energies (ΔECom) indicate that 1-5 are rather stronger ligands with Pt than Pd. Bader’s atoms in molecules (AIM) and NBO analyses show the partial covalent and partial electrostatic nature of Pb-M bonds.

Transfer C–H borylation is an isodesmic approach to the borylation reaction using B–C-containing molecules as boron sources. In this work, we report that 2-mercaptothiazole and other analogues are ...

Prediction of the standard enthalpy of formation ΔfH0298 of boron nitride nanocone BNNCs structures with disclination angles 60°, 120°, and 180°is recommended to be performed by the isodesmic reaction approach. NH3, BH3, and N2H4 were selected as key reference compounds. In order to calculate ΔfH0298 of nanocones, we must first calculate the enthalpies of nanocone rings at their apexes. For this purpose, ΔfH0298 values of 40 different structures, such as boron, nitrogen, and hydrogen compounds, have been calculated by combining Gaussian-4 G4 theory calculations with the isodesmic and other balanced reactions approach. At each stage of the calculations, the previously estimated enthalpies of formation of nanocones were used as reference points for new molecules in the isodesmic and other balanced reactions. The results of enthalpies of formation of reference compounds were then used as reference values to estimate the enthalpy of formation of rings of BNNCs at their apexes. Finally, enthalpies of formation of BNNCs with disclination angles of 60°, 120°, and 180°and cone heights of 1-5 Å, 3-7 Å, and 4-8 Å were calculated. The results show that the reactions are highly exothermic. An increase in cone height causes the enthalpy of formation of boron nitride nanocone structures to become more negative.

Tubulin nucleation, microtubule assembly, stability, and dynamics depend on fluxes of chemical energy, controlled by hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP), and nucleotide exchange reactions. In this paper, we determined how tubulin self-association in glycerol-free assembly buffers affects the rate of GTP hydrolysis and the thermodynamics of nucleotide exchange. In the absence of tubulin, GTP hydrolysis was negligible. In the presence of tubulin, below the critical conditions for microtubule assembly, no GTP hydrolysis was observed, even though tubulin 1D curved oligomers and single rings were formed, suggesting that GTP hydrolysis was not involved in their formation. Under conditions permitting spontaneous tubulin nucleation and microtubule assembly, GTP hydrolysis was detected and followed pseudo-first-order kinetics, limited by the rate of tubulin nucleation and microtubule assembly. By simultaneously determining the concentrations of tubulin-free and tubulin-bound GTP and GDP at steady-state, we investigated the nucleotide exchange reaction under conditions where GTP hydrolysis was negligible. The exchange reaction strongly depended on the molar ratio between tubulin-free GDP and GTP and the total tubulin concentration. To analyze these data, we used a thermodynamic model of isodesmic tubulin self-association, terminated by the formation of tubulin single-rings, to calculate the distribution of tubulin single rings, 1D oligomers, and free dimers, and thereby the molar fractions of tubulin dimers with exposed and buried nucleotide exchangeable sites (E-sites). Our data suggest that the exchange reaction occurred to a different extent on tubulin dimers with buried E-sites than on dimers with exposed E-sites.

Standard enthalpies of formation (ΔfH°298), standard entropies (S°(T)), and heat capacities (Cp(T)) are calculated for dimethyl and ethyl methyl fluorinated ethers, both the parent and related radical species. The parent and radical species are utilized to determine carbon–hydrogen, carbon–fluorine, carbon–carbon, and carbon–oxygen bond dissociation energies (C–H, C–F, C–C, and C–O BDEs). The ΔfH°298 and BDEs are calculated using a variety of error-canceling isogyric and/or isodesmic reactions at the MN15/cc-pVTZ, CBS-QB3, and CBS-APNO levels of theory. ΔfH°298 calculations from the MN15 functional for these ether species are shown to have consistency with the CBS-QB3 and CBS-APNO composite methods with our recommended ideal gas phase ΔfH°298 values from the average of these two composite methods. C–F BDE values are shown to range overall between 111 and 128 kcal mol–1, the C–H BDEs are in the 93–106 kcal mol–1 range, the C–O BDEs are in the 83–107 kcal mol–1 range, and the C–C BDEs are in the 88–101 kcal...

A new class of bent amphiphilic alkynylplatinum(II) terpyridine complexes was found to adopt different modes of molecular stacking to give diverse nanostructures. In chlorinated solvents, the complexes aggregate in the presence of water droplets and assist in the formation of porous networks, while in DMSO solutions, they self-assemble to give fibrous nanostructures. The complexes would adopt a head-to-tail tetragonal stacking arrangement, as revealed by X-ray crystallographic studies, computational studies and powder X-ray diffraction (PXRD) studies. Their self-assembly follows a cooperative growth mechanism in DMSO and an isodesmic growth mechanism in DMSO–H2O mixture. The balance between hydrophobic and hydrophilic components of the complex system, in conjunction with the nuclearity and the positioning of the substituents, are found to govern the mode of molecular stacking and the fabrication of precise functional nanostructures. This class of complexes serve as versatile building blocks to construct orderly packed molecular materials and functional materials in a well-controlled manner.

The utilization of anions to induce the formation of self-assembled supramolecular polymers in solution is an undeveloped area of host-guest chemistry. We report in this manuscript a comparative study of two tripodal anion receptors by hydrogen or halogen bonding interactions to form self-assembled supramolecular structures induced by the presence of anions. DOSY NMR and DLS experiments provided evidence for the formation of supramolecular structures in solution in both halogen and hydrogen bond donors with H2PO4- anions. The nucleation and elongation constants obtained using the thermodynamic model indicate that the polymers grow following an isodesmic mechanism. Emission studies demonstrate that only the formation of the supramolecular polymer between the halogen bond donor receptor and H2PO4- anions results in the appearance of the excimer emission band.

Reported here is the synthesis, characterization, and isodesmic supramolecular polymerization of [3.3]paracyclophane-5,8,14,17-tetracarboxamide ([3.3]pCpTA). The self-assembling monomer, a bridge-expanded homolog of [2.2]paracyclophane-4,7,12,15-tetracarboxamide ([2.2]pCpTA), forms homochiral assemblies in nonpolar solution and the solid state through double-helical intermolecular and transannular hydrogen bonding. The additional methylene unit in the [3.3]paracyclophane bridge results in a weakened supramolecular assembly for [3.3]pCpTA compared to [2.2]pCpTA in solution. Likely origins of the change in assembly strength, revealed through X-ray crystallography, computational analysis, and solution-phase spectroscopy, are an increase in (a) the intramolecular and intermolecular deck-to-deck spacing compared to [2.2]paracyclophane resulting from larger amide dihedral angles accompanying transannular hydrogen bonding in the [3.3]paracyclophane and (b) monomer entropy associated with the scissoring motion of the [3.3]paracyclophane bridge.

β-lactam antibiotics, which are used to treat infectious diseases, are currently the most widely used class of antibiotics. This study focused on the chemical reactivity of five- and six-membered ring systems attached to the β-lactam ring. The ring strain energy (RSE), force constant (FC) of amide (C-N), acylation transition states and second-order perturbation stabilization energies of 13 basic structural units of β-lactam derivatives were computed using the M06-2X and G3/B3LYP multistep method. In the ring strain calculations, an isodesmic reaction scheme was used to obtain the total energies. RSE is relatively greater in the five-(1a-2c) compared to the six-membered ring systems except for 4b, which gives a RSE that is comparable to five-membered ring lactams. These variations were also observed in the calculated inter-atomic amide bond distances (C-N), which is why the six-membered ring lactams C-N bond are more rigid than those with five-membered ring lactams. The calculated ΔG# values from the acylation reaction of the lactams (involving the S-H group of the cysteine active residue from L,D transpeptidase 2) revealed a faster rate of C-N cleavage in the five-membered ring lactams especially in the 1-2 derivatives (17.58 kcal mol-1 ). This observation is also reflected in the calculated amide bond force constant (1.26 mDyn/A) indicating a weaker bond strength, suggesting that electronic factors (electron delocalization) play more of a role on reactivity of the β-lactam ring, than ring strain.

The thermochemical network of 91 isodesmic and other balanced reactions was used to adjust simultaneously the enthalpies of formation of 14 urea compounds. The experimental enthalpies of formation of these compounds were treated as unknowns in the least-squares minimization of deviations between the theoretically predicted enthalpies of reaction and experimental values. A result of a least-squares fit confirms the accuracy of experimental enthalpies of formation of 8 ureas, whereas the experimental measurements for 6 urea compounds require re-examination. The gas-phase standard enthalpies of formation of 8 ureas were used as a consistent basis to obtain values for other 15 ureas through isodesmic reactions. To estimate the enthalpies of formation in crystalline state, the sublimation enthalpies were predicted using the molecular electrostatic potential model.

The nematic (chromonic N) and isotropic phases formed by aqueous solutions of a perylene dye are investigated by x-ray diffraction and visible light absorption spectroscopy. X-ray diffracti...

International audience; The synthesis of two series of N-annulated perylene bisimides (PBIs), compounds 1 and 2, is reported, and their self-assembling features are thoroughly investigated by a complete set of spectroscopic measurements and theoretical calculations. The study corroborates the enormous influence that the distance between the PBI core and the peripheral groups exerts on the chiroptical properties and the supramolecular polymerization mechanism. Compounds 1, with the peripheral groups separated from the central PBI core by two methylenes and an ester group, form J-type supramolecular polymers in a cooperative manner but exhibit negligible chiroptical properties. The lack of clear helicity, due to the staircase arrangement of the self-assembling units in the aggregate, justifies these features. In contrast, attaching the peripheral groups directly to the N-annulated PBI core drastically changes the self-assembling properties of compounds 2, which form H-type aggregates following an isodesmic mechanism. These H-type aggregates show a strong aggregation-caused quenching (ACQ) effect that leads to nonemissive aggregates. Chiral (S)-2 and (R)-2 experience an efficient transfer of asymmetry to afford P- and M-type aggregates, respectively, although no amplification of asymmetry is achieved in majority rules or "sergeants-and-soldiers" experiments. A solvent-controlled stereomutation is observed for chiral (S)-2 and (R)-2, which form helical supramolecular polymers of different handedness depending on the solvent (methylcyclohexane or toluene). The stereomutation is accounted for by considering the two possible conformations of the terminal phenyl groups, eclipsed or staggered, which lead to linear or helical self-assemblies, respectively, with different relative stabilities depending on the solvent.

The supramolecular polymerization of 2,11-dithia[3.3]paracyclophanes through self-complementary intermolecular and transannular amide hydrogen bonding is presented. An n → π* interaction between the amide hydrogen bonding units and the central bridging atom results from the single-point exchange of a carbon atom for a sulfur atom. This orbital donor-acceptor interaction can be strengthened by oxidizing the sulfide to a sulfone which acts to shorten the donor···acceptor distance and increase orbital overlap. Experimental signatures of the increased n → π* interaction include larger isodesmic polymerization elongation constants in solution, changes in characteristic bond stretching frequencies, and geometric/structural changes evaluated by X-ray crystallography. The experimental data are supported by extensive computational investigations of both assembling and nonassembling 2,11-dithia[3.3]paracyclophanes as well as a rationally designed model system to confirm the role of stereoelectronic effects on supramolecular polymer assembly.