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 noncovalent 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.

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 (S) 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 (T).

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

The formation of CO from CO monomolozonide is a three-step process with the isomer dependent last step leading either to c,c-CO epoxide or d,d-CO oxidoannulene. The process involves the open intermediate (first O-O then C-C/C-C bonds broken), oxidoannulene-like structure intermediate (new C-O/C-O bond formed) and finally the oxide product. On the formation of c,c-CO isomer, the final release of O is followed by the restoration of C-C bond, which stabilizes the product.

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 Cd ions produces a library of enlarged chiral mixed imines coordinated with metal cations among which the hexanuclear Cd complex of 6 + 3 + 3 imine was isolated and characterized.

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 πσ* 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 πσ* state is partial ejection of σ* electrons outside the molecule, even beyond the NH group, at the Franck-Condon point.

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.

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.

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.

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.

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.

Modifying the fullerene surface using endohedral noble gas atoms: density functional theory based molecular dynamics study of C70O3.

We have performed a series of ab initio molecular orbital and molecular dynamics calculations to ascertain the influence of an endohedral noble gas atom on the reactivity of the surface of the model system C(70)O(3). Our simulations show that the minimum energy pathways for the ozone ring-opening reaction are influenced by the presence of the endohedral atom. The effect is isomer dependent, with the enthalpy of the reaction increasing for a,b-C(70)O(3) and decreasing for e,e-C(70)O(3) when doped with the heavy noble gas atoms Xe and Rn.

Dimethylalkoxygallanes: monomeric versus dimeric gas-phase structures.

The molecular structures of the vapors produced on heating dimethylalkoxygallanes of the type [Me(2)Ga(OR)](2) have been determined by gas electron diffraction and ab initio molecular orbital calculations. In the solid state [Me(2)Ga(OCH(2)CH(2)NMe(2))](2) (1) and [Me(2)Ga(OCH(2)CH(2)OMe)](2) (2) adopt dimeric structures, although only the monomeric forms [Me(2)Ga(OCH(2)CH(2)NMe(2))] (1a) and [Me(2)Ga(OCH(2)CH(2)OMe)] (2a) were observed in the gas phase. For comparison the structure of the vapor produced on heating [Me(2)Ga(O(t)Bu)](2) (3) was also studied by gas electron diffraction.

Photochemistry of formaldoxime−nitrous acid complexes in an argon matrix: identification of formaldoxime nitrite.

We have studied the structure and photochemistry of the formaldoxime−nitrous acid system (CH2NOH−HONO) by help of FTIR matrix isolation spectroscopy and ab initio methods. The MP2/6-311++G(2d,2p) calculations show stability of six isomeric CH2NOH···HONO complexes. The FTIR spectra evidence formation of two hydrogen bonded complexes in an argon matrix whose structures are determined by comparison of the experimental spectra with the calculated ones for the six stable complexes.

C(70) oxides and ozonides and the mechanism of ozonolysis on the fullerene surface. A theoretical study.

A series of ab initio calculations have been carried out to determine why the a,b- and c,c-isomers are the most commonly observed mono-oxides of C(70) in ozonolysis reactions, when existing calculations in the literature report that these structures are not the most stable conformations. We show that the a,b- and c,c-isomers are the two most stable structures on the C(70)O(3) potential energy surface, which suggests that the reaction pathway toward oxide formation must proceed via the corresponding ozonide structure. From our calculations, we offer a mechanism for the thermally induced dissociation of C(70)O(3) that share the first two steps with the general mechanism for ozonolysis of alkenes proposed by Criegee.

Photo-induced hydrogen exchange reaction between methanol and glyoxal: formation of hydroxyketene.

We study the structure and photochemistry of the glyoxal-methanol system (G-MeOH) by means of FTIR matrix isolation spectroscopy and ab initio calculations. The FTIR spectra show that the non-hydrogen-bonded complex, G-MeOH-1, is present in an inert environment of solid argon. MP2/aug-cc-pVDZ calculations indicate that G-MeOH-1 is the most stable complex among the five optimized structures.

On three-electron bonds and hydrogen bonds in the open-shell complexes [H2X2]+ for X = F, Cl, and Br.

The [H2X2]+ (X = Cl, Br) formula could refer to two possible stable structures, namely, the hydrogen-bonded complex and the three-electron-bonded one. In contrary to the results published by other authors, we claim that for the F-type structures the hydrogen-bonded form is the only possible one and the [HFFH]+ complex is an artifact as its wave function is unstable. For all analyzed molecules, the IR anharmonic spectra have been simulated, which enabled a deeper analysis of other authors' published results of IR low-temperature matrix experiments.

The hydroperoxy radical as a hydrogen bond acceptor. HOO-HCl complexes--Ab initio study.

Protonacceptor properties of the HOO radical were investigated previously by means of ab initio as well as topological Atoms in Molecules (AIM) and Electron Localization Function (ELF) methods. It was pointed out that in the radical there are three nonequivalent positions most susceptible to protonation, and on this basis three structures of possible hydrogen bonded complexes were proposed. Results reported in the present article concern all possible 1:1 complexes formed by HCl and HOO molecules, and fully confirm suppositions given on the basis of the above-mentioned investigations.