Role of Solvent and Noncovalent Interactions in Alkaline Reactivity of Strained and Strain-Free Macrocyclic Disulfides.

This study employs ab initio molecular dynamics simulations to investigate  the impact of solvent and non-bonded interactions on the structure-reactivity relationship of both strain-free and strained macrocyclic disulfides. Our findings reveal that interactions  with water as a solvent significantly influence the minimum energy geometry structures  of both conformers of the studied macrocycle.  In particular, our simulations identify short contacts, specifically S···π-aromatic interactions,  which suppress reactivity for the strained isomer by obstructing the reaction cone at the minimum free energy.   Surprisingly, the free energy barriers for the disulfide reaction with a simple nucleophile (OH- anion) remain very similar,  despite one conformer having a markedly more strained disulfide bond than the other. Enhanced molecular dynamics simulations in explicit solution  elucidate this apparent contradiction by revealing different solvent exposures of the two sulfur atoms in the macrocycles.

Photoinduced Double Proton Transfer in the Glyoxal-Methanol Complex Revisited: The Role of the Excited States.

Under irradiation in the visible range, the glyoxal-methanol complex in a cryogenic argon matrix undergoes a double proton transfer (DPT) reaction through which the glyoxal molecule isomerizes into hydroxyketene. In this work, we employ electronic structure simulations in order to shed more light on the underlying mechanism. Rewardingly, we find that the lowest singlet excited state (S1) of the complex acts as a gateway to two previously unknown isomerization pathways, of which one takes place entirely in the singlet manifold and the other also involves the lowest triplet state (T1). Both of these pathways are fully compatible with the available experimental data, implying that either or both are operative under experimental conditions. In either pathway, the methanol molecule acts as a proton shuttle between the proton-donating and proton-accepting sites of glyoxal, resulting in a dramatic lowering of the potential energy barrier to isomerization with respect to the case of isolated glyoxal. The occurrence of DPT in the singlet manifold is demonstrated directly with the use of nonadiabatic molecular dynamics simulations at the spin-flip time-dependent density functional theory level.

The mechanism of the ozonolysis on the surface of C70 fullerene: the electron localizability indicator study.

The formation of C70O from C70O3 monomolozonide is a three-step process with the isomer dependent last step leading either to c,c-C70O epoxide or d,d-C70O oxidoannulene. The process involves the open intermediate (first O-O then Cc-Cc/Cd-Cd bonds broken), oxidoannulene-like structure intermediate (new Cc-O/Cd-O bond formed) and finally the oxide product. On the formation of c,c-C70O isomer, the final release of O2 is followed by the restoration of Cc-Cc bond, which stabilizes the product. Neither Cd-Cd bond is restored nor the total energy essentially lowered upon d,d-C70O formation. At all steps of the studied process, the four CC bonds adjacent to Cc-Cc or Cd-Cd bond, respectively, play a crucial role donating or withdrawing the necessary electron density. C70(O)O2 products, with O2 bridging one of the bonds adjacent to the parent Cc-Cc/Cd-Cd one, may compete with the oxide products. The OO bond in such structures is weak as suggested by its low electron population. For both c,c-C70O3 and d,d-C70O3, the shape of the potential energy surfaces (0 K) and the related, reported earlier, room temperature-free energy surfaces differ. Graphical abstract.

Mixed Macrocycles Derived from 2,6-Diformylpyridine and Opposite Enantiomers of trans-1,2-Diaminocyclopentane and trans-1,2-Diaminocyclohexane.

The condensation reaction of 2,6-diformylpyridine with an equimolar mixture of opposite enantiomers of trans-1,2-diaminocyclopentane and trans-1,2-diaminocyclohexane using a dynamic combinatorial chemistry approach has been examined. In nonmetal-templated reactions, depending on reaction conditions, mixed 2 + 1 + 1 macrocyclic imine or bigger mixed 4 + 2 + 2 imine macrocycle are formed selectively. The 2 + 1 + 1 imine used as a precursor in the templated by CdII ions produces a library of enlarged chiral mixed imines coordinated with metal cations among which the hexanuclear CdII complex of 6 + 3 + 3 imine was isolated and characterized. All macrocyclic imine compounds have been reduced to the corresponding macrocyclic amines, which have been further transformed into their hydrochlorides. Each macrocyclic compound has been obtained as two enantiomers. For imine macrocycles and for the hydrochloride derivatives of macrocyclic amines, their X-ray crystal structures have been determined. In particular, the crystals of protonated 4 + 2 + 2 macrocyclic amine, which contains two types of diastereomeric cations differing in terms of inverted twists of pyridine moieties, and hexanuclear CdII complex of 6 + 3 + 3 imine, which gives a deeper insight into the expansion reaction, have been investigated. A heterochiral self-sorting of 2 + 2 and 2 + 1 + 1 macrocyclic imines has been confirmed by a competition reaction of 2,6-diformylpyridine, racemic trans-1,2-diaminocyclopentane, and racemic trans-1,2-diaminocyclohexane and theoretical calculations.

Hydrogen detachment driven by a repulsive 1πσ* state - an electron localization function study of 3-amino-1,2,4-triazole.

Electron localization function analysis reveals the details of a charge induced hydrogen detachment mechanism of 3-amino-1,2,4-triazole, identified recently to be responsible for phototautomerization of the molecule. In this process vertical excitation to the 1πσ* state is followed by the barrier-less migration of a H atom along the N-H bond toward the conical intersection with the S0 ground state. The most striking feature revealed for the 1πσ* state is partial ejection of σ* electrons outside the molecule, even beyond the NH group, at the Franck-Condon point. Further gradual spatial localization of the electron around the proton moving along the N-H stretching coordinate gives a plausible explanation for the repulsive character of the 1πσ* potential energy surface with the proton wading through the region of space where some negative charge is accumulated ('a virtual acceptor'), dragging some electron density. This mechanism resembles the one postulated for the hydrogen transfer from a donor molecule (D-H) to an acceptor one (A) in a class of vertically excited molecules with a preexisting inter- or intramolecular D-HA motif, even though the acceptor molecule is absent. The present analysis demonstrates also that the bond evolution and changes in the electron density along the excited state reaction path can be effectively studied with the use of an electron localization function.

Mechanism Underlying the Nucleobase-Distinguishing Ability of Benzopyridopyrimidine (BPP).

Benzopyridopyrimidine (BPP) is a fluorescent nucleobase analogue capable of forming base pairs with adenine (A) and guanine (G) at different sites. When incorporated into oligodeoxynucleotides, it is capable of differentiating between the two purine nucleobases by virtue of the fact that its fluorescence is largely quenched when it is base-paired to guanine, whereas base-pairing to adenine causes only a slight reduction of the fluorescence quantum yield. In the present article, the photophysics of BPP is investigated through computer simulations. BPP is found to be a good charge acceptor, as demonstrated by its positive and appreciably large electron affinity. The selective quenching process is attributed to charge transfer (CT) from the purine nucleobase, which is predicted to be efficient in the BPP-G base pair, but essentially inoperative in the BPP-A base pair. The CT process owes its high selectivity to a combination of two factors: the ionization potential of guanine is lower than that of adenine, and less obviously, the site occupied by guanine enables a greater stabilization of the CT state through electrostatic interactions than the one occupied by adenine. The case of BPP illustrates that molecular recognition via hydrogen bonding can enhance the selectivity of photoinduced CT processes.

Donor-Acceptor Complexes between Ammonia and Sulfur Trioxide: An FTIR and Computational Study.

The complexes of ammonia with sulfur trioxide have been studied using FTIR matrix isolation spectroscopy and DFT/B3LYP calculations with the aug-cc-pVTZ basis set. The NH3/SO3/Ar matrixes were prepared in two different ways. In one set of experiments the matrix was prepared by the simultaneous deposition of the NH3/Ar mixture and SO3 vapor from the thermal decomposition of K2S2O7. In the second set of experiments thermolysis products of sulfamic acid were trapped in an argon matrix. Both methods of matrix preparation led to the formation of the H3N·SO3 electron donor-acceptor complex that was characterized earlier. In the matrixes comprising thermolysis products of sulfamic acid, in addition to H3N·SO3, the H3N-SO3···NH3 complex (II(D)) was also identified. The identity of the complex was confirmed by comparison of the experimental and theoretical spectra of H3N-SO3···NH3 and D3N-SO3···ND3. The performed calculations show that in H3N-SO3···NH3 the two N atoms and the S atom are collinear; the two S-N bonds are nonequivalent, one is much shorter (2.230 Å) than the other one (2.852 Å). In the AIM topological analysis, the interaction energy decomposition and topological properties of the electron localizability indicator (ELI-D) allowed us to categorize the stronger N-S bond in the II(D) complex as a dative bond and to assume that the fragile N-S bond is a consequence of a weak electron-donor-acceptor interaction. The calculations indicate that the identified II(D) complex corresponds to a local minimum on the PES of the NH3/SO3 system of 2:1 stoichiometry. The (NH3)2SO3 complex, II(HB), corresponding to a global minimum is 7.95 kcal mol(-1) more stable than the II(D) complex. The reason that the II(D) complex is present in the matrix but not the II(HB) complex is discussed.

Isomers of the acetic acid-water complex trapped in an argon matrix.

The complexes of acetic acid (AcOH) with water have been studied using FTIR matrix isolation spectroscopy and DFT/B3LYP, DFT/B3LYP-D, and MP2 calculations with the aug-cc-pVTZ basis set. The AcOH/H2O/Ar matrices were prepared in two different ways. In one set of experiments, the vapor above a solid AcOH sample, cooled to 203 K, was diluted with H2O/Ar mixture in the vacuum chamber of the cryostat, and the mixture was solidified on the target. In the second set of experiments, the matrix was prepared by simultaneous deposition of AcOH/Ar and H2O/Ar mixtures at room temperature. The first method of matrix preparation strongly favors the formation of the "acyclic" higher energy AcOH-H2O complex I(B) compared to the second one. Warming of matrices containing the higher energy complex, I(B), from 11 to 39 K, results in the decrease of I(B) concentration and formation of the lowest energy cyclic complex I(A). The calculations indicate that I(B) is formed by an O-H···O hydrogen bond between the carbonyl oxygen and a water O-H group and, additionally, by a weak interaction between one of the methyl group hydrogen atoms and the water oxygen atom. The cyclic complex I(A) has a six-membered ring involving two O-H···O bonds. An activation energy of 0.94, 1.71, and 1.38 kcal mol(-1) was calculated for the I(B) → I(A) rearrangement at the B3LYP, B3LYP-D, and MP2 levels of theory, respectively. Van't Hoff plots for the association of H2O and AcOH leading to formation of the complexes I(A) and I(B) are presented and discussed. Evidence is also given for the formation of the AcOH-(H2O)2 and (AcOH)2-H2O complexes in the matrices. A potential atmospheric impact of the enhanced formation of the higher energy I(B) complex at low temperatures is discussed.

OH-induced oxidative cleavage of dimethyl disulfide in the presence of NO.

We report the results of the theoretical study of (•)OH-induced oxidative cleavage of dimethyl disulfide (DMDS) and the experimental study of the CH3SSCH3 + (•)OH reaction in the presence of (•)NO. Infrared low temperature argon matrix studies combined with ab initio calculations allowed us to identify cis-CH3SONO, which evidences the formation of the CH3SO(•) and CH3SH molecules in the course of the CH3SSCH3 + (•)OH reaction. Ab initio/quantum chemical topology calculations revealed details of the oxidative cleavage of dimethyl disulfide, which is a complex multistep process involving an alteration of S-O and S-S covalent bonds as well as a hydrogen atom transfer. The ability of delocalization of the unpaired electron density by sulfur atoms and a formation of a hydrogen bond by CH3SO(•) and CH3SH are the factors which seem to explain antiradical properties of DMDS.

Hybrid QM/QM simulations of photochemical reactions in the molecular crystal N-salicylidene-2-chloroaniline.

In this paper, we report the application of the QM/QM hybrid simulation technique to the photoisomerisation reactions of anils (i.e., Schiff bases of salicylaldehyde with aniline derivatives) in the solid state, on the example of the photochromic polymorph of N-salicylidene-2-chloroaniline. By propagating molecular dynamics on a potential energy surface constructed using a combination of time-dependent DFT and ground-state DFT calculations, two reaction pathways of the cis-enol isomer were observed, which occur with approximately equal probability. In the first pathway, the photoexcited molecule undergoes an intramolecular proton transfer reaction on average 25 fs after photoexcitation. It then persists in the cis-keto form for a few hundred femtoseconds before undergoing a pedal motion through which it reaches an S1/S0 conical intersection. This pathway, whose existence has previously been proposed in the literature to rationalize the feasibility of the photoisomerisation reaction in the confined environment of the crystal lattice, is predicted to lead to the formation of the trans-keto form. The second pathway is nonreactive and is analogous to a previously characterised radiationless de-excitation pathway of the isolated molecule. The cis-enol to trans-keto photoisomerisation is reversible. Following the photoexcitation of a trans-keto molecule, it persists in a largely unchanged geometry for a period of time ranging from a few hundred femtoseconds to over a picosecond, and subsequently undergoes a pedal motion in the same direction as the one involved in the cis-enol to trans-keto photoisomerisation, leading to the cis-keto isomer through another S1/S0 conical intersection.