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Lithium bonding in lithium 2-pyridyl-N-oxide acetate has been investigated using classic Car–Parrinello molecular dynamics (CPMD) and the path integral approach [path integrals molecular dynamics (PIMD)]. The simulations have been performed in 300 K. Structures, energies, and lithium trajectories have been determined. The CPMD results show that the lithium atom is generally equidistant between heavy atoms in the (O...Li...O) bridge. Applying quantum effects through the PIMD leads to similar conclusion. The theoretical lithium 2-pyridyl-N-oxide acetate infrared spectrum has also been determined using the CPMD calculations. This shows very good agreement with available experimental results and reproduces well the broad low-frequency band observed experimentally. In order to gain deeper understanding of the nature of the lithium bonding topological analysis of the electron localization function has been applied. [ABSTRACT FROM AUTHOR]

We have studied the double proton transfer (DPT) reaction in the cyclic dimer of chloroacetic acid using both classical and path integral Car-Parrinello molecular dynamics. We also attempt to quantify the errors in the potential energy surface that arise from the use of a pure density functional. In the classical dynamics a clear reaction mechanism can be identified, where asynchronized DPT arises due to coupling between the O–H stretching oscillator and several low energy intermolecular vibrational modes. This mechanism is considerably altered when quantum tunneling is permitted in the simulation. The introduction of path integrals leads to considerable changes in the thermally averaged molecular geometry, leading to shorter and more centered hydrogen bond linkages. [ABSTRACT FROM AUTHOR]

The presented results attempt to approximate the proper structure of the radical formed as a result of the oxidation of 1,2,3‐propanetriol. To fulfil the aim unstable radical originated in 1,2,3‐propanetriol was trapped by PBN. Resulted spin adduct was measured using EPR spectroscopy and the isotropic hyperfine coupling constants aiso(14N) and aiso(1H) were obtained by simulation of the EPR spectrum. The next step consisted of conducting a comparative analysis of EPR parameters, based on the calculations conducted at the DFT and MP2 methods level in open‐shell formalism including solvent effects. For comparison, calculations were also carried out at the level of combined methods (UB3LYP/QCISD and UMP2/QCISD) in terms of the ONIOM formalism. Comparison of the experimental EPR data of the isotropic hyperfine coupling constants aiso(14N) and aiso(1H) with the calculated parameters indicate that oxidation of 1,2,3‐propanetriol leads to a carbon centred radical where unpaired electron is situated on the second (middle) carbon of 1,2,3‐propanetriol. What is important, this conclusion could be made regardless of the chosen calculation method. However, it could be stated that for calculation of the isotropic hyperfine coupling constants aiso(14N) and aiso(1H) of PBN/gly• adducts, UMP2 polarisable conductor calculation model with two ethanol molecules is explicitly defined. Radical formed during oxidation of glycerol (1,2,3‐propanetriol):‐is carbon centred‐has unpaired electron situated on the middle carbon‐is best described by UMP2 CPCM with two ethanol molecules‐the combined DFT/QCISD method also gives results similar to the experimental ones. [ABSTRACT FROM AUTHOR]

Car‐Parrinello and path integrals molecular dynamics (CPMD and PIMD) simulations were carried out for the 10π‐electron aromatic systems: 2‐hydroxy‐2,4,6‐cycloheptatrien‐1‐one, commonly known as Tropolone (I) and 2‐hydroxy‐2,4,6‐cycloheptatriene‐1‐thione, called Thiotropolone (II) in vacuo and in the solid state. The extremely fast proton transfer (FPT) and "prototropy" tautomerism in the keto‐enol (thione‐enethiol) systems have been analyzed on the basis of CPMD and PIMD methods level. Comparisons of two‐dimensional (2D) free‐energy landscapes of reaction coordinate δ‐parameter and RO...O or RO...S distances shows that the OH... tautomer to be more favorable in the Thiotropolone. The hydrogen between the oxygen and the sulfur atoms adopts a starkly asymmetrical position in the double potential well. The values of the energy barriers for the FPT were calculated and suggested a strong hydrogen bond with low barrier for FPT mechanism. These studies and the 2D average index of π‐delocalization 〈λ〉 landscape of time evolutions of RO1...O2 and RC7O2 or RC7S1 distances for the both crystals indicate that hydrogen bonds in the crystals of Tropolone (I) and Thiotropolone (II) have characteristic properties for the type of bonding model resonance‐assisted hydrogen bonds and also low‐barrier hydrogen bonds. In the crystal of the Thiotropolone (II), we found the hydrogen bond OH...S existing without the equilibrium of the two tautomers whereas in the crystal of the Tropolone (I) has been confirmed the hydrogen bond OH...O existing with the equilibrium of the two tautomers. It was also found the significant differences in frequency, speed, and the image of the FPT in the studied crystals. © 2018 Wiley Periodicals, Inc. Hydrogen bond is the most important of all directional intermolecular interactions. Hydrogen bonded systems play also a very important role in many physical, chemical and biological processes. The extremely fast proton transfer (FPT) and 'prototropy' tautomerism in the keto‐enol (thione‐enethiol) 10ϕ‐electron aromatic systems have been analyzed on the basis of CPMD and PIMD methods level for the 2‐hydroxy‐2,4,6‐cycloheptatrien‐1‐one, commonly known as Tropolone (I) and 2‐hydroxy‐2,4,6‐cycloheptatriene‐1‐thione, called Thiotropolone (II) in vacuo and in the solid state. [ABSTRACT FROM AUTHOR]

The local electronic structure of the Mg–Mg and Ca–Ca bonds have been investigated in the model dimeric magnesium(I) and calcium(I) molecules: [C 10 H 18 Mg 2 N 4 ], and [C 10 H 18 Ca 2 N 4 ] using the topological analysis of Electron Localisation Function (ELF). The wave function has been approximated by the DFT method and PBE, B3LYP, M052X, M062X, ωB97XD, CAM-B3LYP, LC-ωPBE and B2PLYP functionals. The investigated bonds are covalent, and are represented by disynaptic bonding attractors V(Mg,Mg) and V(Ca,Ca). The basin population of the Ca–Ca bond (1.84–1.89e) is about 0.1e smaller than population of the Mg–Mg bond (1.95–1.98e). The results of ELF-analysis support classical Lewis representation of the 2c–2e bonds (single bond). The topological analysis of electron density field, ρ(r) shows that both the Mg–Mg and Ca–Ca bonds are characterised by the non-nuclear attractor (NNA) and pseudo-basin localised in midpoint of the bond. However, in the case of the Ca–Ca bond its localisation depends on the used functional. The median ELF-basin population of the Mg–Mg bond (1.96e) is about 2.5 larger than the population (0.79e) of pseudo-atomic basin associated with NNA of the ρ(r) field. The analysis performed for the nitrogen – magnesium and nitrogen–calcium bonds showed the dative bonds N → Mg and N → Ca with very large values of the polarity index, p NMg , p NCa , 0.96 and median ELF-basin population 3.40e. [ABSTRACT FROM AUTHOR]

The Claisen rearrangement of allyl phenyl ether to 6-(prop-2-en-1-yl) cyclohexa-2,4-dien-1-one has been studied by means of Bonding Evolution Theory (BET), which combines the topological analysis of the electron localization function (ELF) and catastrophe theory. The reaction can be presented as consisting of 10 main steps separated by fold and cusp catastrophes. The description of the mechanism of C–O bond breaking is complicated and depends on the DFT method used. It proceeds through a heterolytic cleavage (B3LYP, M052x) with the formation of the V3(O) non-bonding basin in step II (M052x) or with electron density resonating between oxygen and carbon atoms in step II (B3LYP). The C–C bond between the allyl group and the phenol ring is formed after the TS in step VIII. The reaction is terminated by the formation of two localized C=C bonds in the phenyl ring in steps IX and X. The localization of Vi=1,2(C,C) basins – typical of localized double bonds – in the phenyl ring proves the process of dearomatisation. The electronic structure of the transition structure distinguishes the non-bonding electron density concentrated in the vicinity of the C2 atom, represented by the V(C2) basin, with a population of 0.28e. This basin is a “bridgehead” for the “construction” of the C–C bond between the phenyl ring and the allyl group. [ABSTRACT FROM AUTHOR]

The molecular structure, conformational preferences, topological and vibrational analysis of allicin has been investigated at two different approaches. Calculations have been carried out on static (DFT and MP2) levels with an assortment of Dunning's basis sets and dynamic CPMD simulations. In this both case within the isolated molecule approximation. The results point out that at least twenty different conformers coexist on the PES as confirmed by the flexible character of this molecule. The topological analysis of ELF showed very similar nature of the S S and S O bonds. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed. [ABSTRACT FROM AUTHOR]

In this paper are presented the resultsof theoretical studiesof the structure in proton motion in a very short O···Oand two weak N–H···O intramolecular hydrogenbonds in the nitromalonamide crystal. The dynamics of proton motionin hydrogen bonds were investigated in the NVT ensemble at 298 K usingthe Car–Parrinello and the path integral molecular dynamics.A very large delocalization of proton in the slightly asymmetricalsingle well of free energy potential of O–H···Ointramolecular hydrogen bond was noted especially in the path integralsimulation where quantum effects are taken into account. This hydrogenbond is very strong with the estimated energy of hydrogen bond ca.−27 kcal/mol. The nature of intra- and intermolecular interactionswas studied by means of quantum theory of atoms in molecules. Theinfrared spectra were calculated and compared with available experimentaldata. CPMD vibrational results appear to be in good agreement withthe experimental ones. [ABSTRACT FROM AUTHOR]

In the paper are described studies of the double proton transfer (DPT) processes in the cyclic dimer of acetic acid in the gas phase using Car-Parrinello (CPMD) and path integral molecular dynamics (PIMD). Structures, energies and proton trajectories have been determined. The results show the double proton transfer in 450 K. In the classical dynamics (CPMD) a clear process mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. The DPT mechanism is also asynchronic when quantum tunneling has been allowed in the simulation. It has been found that the calculated values of barrier height for the proton transfer depends very strongly on the used approaches. Barrier received from the free-energy profile at the CPMD level is around 4.5 kcal mol whereas at the PIMD level is reduced to 1 kcal mol. The nature of bonding in acetic acid dimer and rearrangement of electron density due to the proton movement has been also studied by the topological analysis of Electron Localization Function and Electron Localizability Indicator function. [ABSTRACT FROM AUTHOR]

The double proton transfer process in the cyclic dimer of propionic acid in the gas phase was studied using a path integral molecular dynamics method. Structures, energies and proton trajectories were determined. Very large amplitude motions of the skeleton of a propionic acid molecule were observed during the simulations, and almost free rotation of the CH group around the C-C bond. A double-well symmetric potential with a very small energy barrier was determined from the free energy profile for the proton motions. Infrared spectra for different isotopomers were calculated, and comparative vibrational analysis was performed. The vibrational results from CPMD appear to be in qualitative agreement with the experimental ones. [ABSTRACT FROM AUTHOR]

Abstract: Theoretical studies of the structure and proton motion in the intramolecular O–H…O hydrogen bonds in 2-acetyl-1,8-dihydroxy-3,6-dimethylnapthlane were carried out at the DFT and molecular dynamics levels. Geometry optimization at the PBE1PBE/6-311++G(2d,2p) level demonstrate the existence of two tautomers on the potential energy surface. Dynamics of proton motion in intramolecular hydrogen bonds was investigated in vacuo at 100K using Car–Parrinello and path integral molecular dynamics. For the strong intramolecular hydrogen bond very large delocalization of bridging proton is noted, especially in the path integral simulation where quantum effects are taken into account. No tautomerism was found for this intramolecular hydrogen bond. [ABSTRACT FROM AUTHOR]

Abstract: Results of topological analysis of the electron density in the frameworks of the Bader’s theory of Atoms-in-Molecules (AIM) and analysis of the Becke and Edgecombe Electron Localization Function (ELF) on fluorine- and sulphur-substituted polyacetylenes are reported. AIM method indicates the presence of additional interaction between atoms in side chains. The lack of valence, disynaptic attractor basins V(F,F′) and V(S,S′) in ELF analysis support the conclusions of AIM about closed-shell type of F–F and S–S interactions. [Copyright &y& Elsevier]

Abstract: Theoretical studies of the structure and proton motion in the intramolecular N–H⋯N hydrogen bond in 6-nitro-2,3-dipyrrol-2-ylquinoxaline anion were carried out at the DFT, MP2 and molecular dynamics levels. Geometry optimization at the 6-311++G(2d,2p) level demonstrate existence of two tautomers on the potential energy surface. The difference in energy between both tautomers is equals 1.62 (1.42)kcal/mol. Dynamics of proton motion in the N–H⋯N hydrogen bond was investigated in vacuum at 233K using Car–Parrinello and path integral molecular dynamics. Very large delocalization of bridging proton is noted especially in path integral simulation. DFT calculated the coupling constant across the hydrogen bond equals 16.5Hz is in good agreement with experimental value. [Copyright &y& Elsevier]

Abstract: Acetic acid monomer, dimer and its deuterated analogue have been studied using ab initio Car–Parrinello molecular dynamics (CPMD). Full geometry optimization has been carried out in the gas phase in order to obtain minimum structures and hydrogen bonding properties. The results show a good agreement with the available experimental data. Infrared spectrum has been calculated and comparative vibrational analysis has been performed. CPMD vibrational results appear to be in a qualitative agreement with the experimental ones. [Copyright &y& Elsevier]

Hybrid organic–inorganic iodides based on Bi(III) and Sb(III) provide integrated functionalities through the combination of high dielectric constants, semiconducting properties and ferroic phases. Here, we report a pyrrolidinium-based bismuth (1) and antimony (2) iodides of (NC4H10)3[M2I9] (M: Bi(III), Sb(III)) formula which are ferroelastic at room temperature. The narrow band gaps (~2.12 eV for 1 and 2.19 eV for 2) and DOS calculations indicate the semiconducting characteristics of both materials. The crystal structure consists of discrete, face-sharing bioctahedra [M2I9]3− and disordered pyrrolidinium amines providing charge balance and acting as spacers between inorganic moieties. At room temperature, 1 and 2 accommodate orthorhombic Cmcm symmetry. 1 displays a complex temperature-induced polymorphism. It is stable up to 525 K and undergoes a sequence of low-temperature phase transitions (PTs) at 221/222 K (I ↔ II) and 189/190 K (II ↔ III) and at 131 K (IV→III), associated with the ordering of pyrrolidinium cations and resulting in Cmcm symmetry breaking. 2 undergoes only one PT at T = 215 K. The dielectric studies disclose a relaxation process in the kilohertz frequency region, assigned to the dynamics of organic cations, described well by the Cole–Cole relation. A combination of single-crystal X-ray diffraction, synchrotron powder diffraction, spin–lattice relaxation time of 1H NMR, dielectric and calorimetric studies is used to determine the structural phase diagram, cation dynamics and electric properties of (NC4H10)3[M2I9]. [ABSTRACT FROM AUTHOR]

Reaction of 1,2‐di(tetrazol‐2‐yl)ethane (ebtz) with Fe(BF4)2⋅6 H2O in different nitriles yields one‐dimensional coordination polymers [Fe(ebtz)2(RCN)2](BF4)2⋅nRCN (n=2 for R=CH3 (1) and n=0 for R=C2H5 (2) C3H7 (3), C3H5 (4), CH2Cl (5)) exhibiting spin crossover (SCO). SCO in 1 and 3–5 is complete and occurs above 160 K. In 2, it is shifted to lower temperatures and is accompanied by wide hysteresis (T1/2↓=78 K, T1/2↑=123 K) and proceeds extremely slowly. Isothermal (80 K) time‐resolved single‐crystal X‐ray diffraction studies revealed a complex nature for the HS→LS transition in 2. An initial, slow stage is associated with shrinkage of polymeric chains and with reduction of volume at 77 % (in relation to the difference between cell volumes VHS−VLS) whereas only 16 % of iron(II) ions change spin state. In the second stage, an abrupt SCO occurs, associated with breathing of the crystal lattice along the direction of the Fe–nitrile bonds, while the nitriles reorient. HS→LS switching triggered by light (808 nm) reveals the coupling of spin state and nitrile orientation. The importance of this coupling was confirmed by studies of [Fe(ebtz)2(C2H5CN/C3H7CN)2](BF4)2 mixed crystals (2 a, 2 b), showing a shift of T1/2 to higher values and narrowing of the hysteresis loop concomitant with an increase of the fraction of butyronitrile. This increase reduces the capability of nitrile molecules to reorient. Density functional theory (DFT) studies of models of 1–5 suggest a particular possibility of 2 to adopt a low (140–145°) value of its Fe‐N‐C(propionitrile) angle. [ABSTRACT FROM AUTHOR]

Bis(diisobutylammonium) octabromodiantimonate(iii), [(i-C4H9)2NH2]2Sb2Br8, has been synthesized. The differential scanning calorimetric measurements indicate a reversible, first-order phase transition at 222/229 K (cooling/heating). The single crystal X-ray diffraction studies reveal that the phase transition is isomorphous and is accompanied by a huge distortion of the crystal lattice. By comparison of the crystal structures of [(i-C4H9)2NH2]2Sb2Br8 and [(i-C4H9)2NH2]2Sb2Cl8, an analogous mechanism of the phase transition of the former is proposed. The change of the electronic structure of the complex during the phase transition was analyzed by UV-vis spectroscopy. A low-frequency dielectric relaxation process appears over phase I (below the room temperature) and corresponds to the dynamics of dipolar diisobutylammonium cations. The detailed analysis of the molecular motions of the organic cations studied by means of proton magnetic resonance (1H NMR) in a wide temperature range indicates a leading role of the methyl groups in the relaxation mechanism. A variable-temperature investigation of the infrared spectra of [(i-C4H9)2NH2]2Sb2Br8 confirms, in turn, the influence of the diisobutylammonium cation dynamics on the molecular mechanism of the structural transformation at 229 K. [ABSTRACT FROM AUTHOR]

Bis(diisobutylammonium) octabromodiantimonate(iii), [(i-C4H9)2NH2]2Sb2Br8, has been synthesized. The differential scanning calorimetric measurements indicate a reversible, first-order phase transition at 222/229 K (cooling/heating). The single crystal X-ray diffraction studies reveal that the phase transition is isomorphous and is accompanied by a huge distortion of the crystal lattice. By comparison of the crystal structures of [(i-C4H9)2NH2]2Sb2Br8 and [(i-C4H9)2NH2]2Sb2Cl8, an analogous mechanism of the phase transition of the former is proposed. The change of the electronic structure of the complex during the phase transition was analyzed by UV-vis spectroscopy. A low-frequency dielectric relaxation process appears over phase I (below the room temperature) and corresponds to the dynamics of dipolar diisobutylammonium cations. The detailed analysis of the molecular motions of the organic cations studied by means of proton magnetic resonance (1H NMR) in a wide temperature range indicates a leading role of the methyl groups in the relaxation mechanism. A variable-temperature investigation of the infrared spectra of [(i-C4H9)2NH2]2Sb2Br8 confirms, in turn, the influence of the diisobutylammonium cation dynamics on the molecular mechanism of the structural transformation at 229 K. [ABSTRACT FROM AUTHOR]