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1

Hydrogen bonding network emulating frequency driven source of triangular pulses

Rusev R., Angelov G., Gieva E., Hristov M., Takov T.

International Journal of Microelectronics and Computer Science

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2010

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Vol. 1, nr 3

293-298

EN

A three output microelectronic circuit functionally equivalent to a hydrogen bonding network is modeled. Proton transfer characteristics of each hydrogen bond of the network are emulated by block-elements in the microelectronic circuit with their respective l-V characteristics. These characteristics are coded in Matlab where the dynamic and static analyses are carried out. The results imply that in static mode the functionally analogous circuit operates as a current source or an amplifier. In dynamic mode the circuit behaves as a voltage driven triangular pulse signal source. The simulations show that the generated pulses at the three circuit outputs have different frequency, amplitude, and width.

2

The Influence of Waterin Different Sites on Multi-Channel Reactions of the Proton Transfer of Serinamide

Zhou X. M., Ma H. K., Zhang A. G., Ma K. S., Tang K., Zhou Z. Y.

Polish Journal of Chemistry

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2009

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Vol. 83, nr 4

555-564

EN

The multi-channel reactions of proton transfer of water-bridged serinamide have been investigated em ploy ing the B3LYP/6-311++G** level of thetheory. The reactants, transition states and products of four channels have been optimized. Further more, the validity of these transition states has been validated by the internal reaction coordinate (IRC). The activation energies, standard enthalpy and free energy change have also been calculated. From the free energy changes we conclude that the water molecule serving as a bridge facilitates the proton transferreaction.

3

Molecular Interactions and Structure of H-Bonded Complexes of Bifunctional Nitrogen-Containing Molecules

Bureiko S. F., Kucherov S. Yu., Schreiber V. M.

Polish Journal of Chemistry

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2009

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Vol. 83, nr 5

771-785

EN

The results of experimental studies and quantum chemical calculations of vibrational spectra and struc ture of H-bonded complexes formed by N-containing bases 3,5-dimethylpyrazole, diphenyltriazene and diphenylformamidine with carboxylic acids and HHal are discussed. The IR spectra of solutions in CH2Cl2 and CCl4 and low temperature NMR spectra show the existence of equilibrium between monomers and cyclic selfassociates of the mole ules studied. Under the interaction with weak carboxylic acids the complexes have molecular structure with two H-bonds NH…O=C and OH…N, and the interaction with strong acids results information of cyclic H-bonded ionic pairs with proton transfer to the N atom of the base. The proton transfer in solution was observed also for open complexes with HHal. The quantum chemical DFT calulations in harmonic and an harmonic approximations confirm the formation of cyclic complexes, while the proton transfer along the OH…N bridge was supported for the complexes with strongest ac ids. It was shown that the use of variational multidimensional an harmonic approach is the most preferable for calculations of the high-frequency XH stretch in systems where the corresponding normal mode is less characteristic and involves motions of many atoms.

4

Zjawiska dysocjacji i asocjacji towarzyszące reakcjom przeniesienia protonu między C-kwasami i zasadami organicznymi w rozpuszczalnikach aprotonowych

Nowak I., Binkowska I., Stańczyk-Dunaj M., Jarczewski A.

Wiadomości Chemiczne

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2008

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[Z] 62, 1-2

67-95

EN

The proton transfer reactions in solutions have attracted the attention of a number of laboratories for many years. These processes seem to be quite simple as they proceed without perturbation of bounding electrons and have low steric demands what enables study of their mechanism. However, many factors influences the mechanisms of these reactions. Among them and not the trifling ones, are dissociation-association effects accompanying them. The definition, behavior and reactivity of carbon acids (C-acids) depending on the type of electron withdrawing group are given [1-57]. Also the values of dissociation constants of C-acids in protic and aprotic solvents are collated in Tables 4, 5 and 7 [11, 38, 49]. The nature of products, free ions and ion pairs, of proton transfer reactions of various C-acids and strong organic bases are carefully discussed. Also their spectral characteristics are given. The equilibria and the possible routes between the substrates and the products of these reactions are also shown [58-66]. The reasons of the homoconjugation effects as a result of an association of the ionic products of the proton transfer reactions in different solvents are discussed in the context of their solvation abilities [67-86]. The formation constants of the homoconjugation complexes of amidine and guanidine bases in relation to their pK? values are quoted in Table 6 [87-95]. The nature of heteroconjugation complexes formed as the result of hydrogen bonding of different entities in the system of proton transfer reactions is discussed [96-116]. The pK? values of a number of C-acids, derivatives of nitromethane, measured in acetonitrile by potentiometric method, are given in Table 7. The pK? values of these derivatives measured in DMSO/H2O systems are compared with those obtained in acetonitrile [18, 38]. The general view of these problems is discussed and carefully reviewed.

5

Proton or Hydrogen Transfer? Charge Distribution Analysis

Waluk J.

Polish Journal of Chemistry

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2008

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Vol. 82, nr 4

947-962

EN

The meaning of terms "proton transfer" (PT) and "hydrogen transfer" (HT), commonly encountered in the literature, is not always unambiguous, especially in the case of intramolecular tautomerization processes. Depending on the used criterion, the same reaction may be classified as either PT or HT. Two criteria for distinguishing between PT and HT are discussed: (a) formal translocation of charge; (b) the reaction mechanism, in particular the coupling between the motion of the proton and the electron density redistribution. The analysis is illustrated using the values of ground and excited state partial charges calculated for three well-known examples of molecules that undergo photo-induced and/or ground state tautomerization: -hydroxyacetophenone, 2,2'-bi pyridyl- 3,3'-diol, and porphycene.

6

Crystal Structure of a Schiff Base, 2-Hydroxynaphthylidene-(8-aminoquinoline) - In Search of Two Tautomeric Forms

Lipkowski J., Fita P., Grabowska A.

Polish Journal of Chemistry

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2008

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Vol. 82, nr 10

2009-2016

EN

Crystal structure of a Schiff base, 2-hydroxynaphthylidene-(8-aminoquinoline) (HNAQ) has been determined at 4 different temperaturs in the range of 100-400 K. While spectral studies would indicate the coexistence of two different tautomeric forms in thermal equilibrium, no statistically significant structural effects have been observed as the pre umed evidence for the presence of the enol form in the solid. HNAQ crystallizes in the monoclinic space group Pc with unit cell parameters a = 10.3400(7) Capital A, b = 5.8870(19) Capital A, c = 14.2960(21) Capital A, beta = 125.844(10) graduate, V = 705.41(27) Capital A 3 and Z = 2 (at 100 K). Crystallographic data for HNAQ have been compared to previously known structures of its metalo-organic complexes. This showed only minor changes due to complexation. In all the cases the mol e cules in the crys tal are al most pla nar and the presence of the metal atom affects only the bonds in the chelate ring.

7

The Diversification of the Optical Rotation Study in the Process of Proton Transfer : Theoretical Study for Alaninamide

Zhao S. L., Kong F. Z., Zhou Z. Y., Ma H. K., Wang W. J.

Polish Journal of Chemistry

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2007

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Vol. 81, nr 10

1807-1807

EN

The tautomerism of alaninamide induced by the intramolecular proton transfer and the reaction mechanism of that has been investigated using density functional theory calculations with B3LYP hybrid functional. Six significant possible reactant conformers as well as their transition and product state of the proton transfer were optimized at 6-311++G(2d,2p) basis set level. The geometry parameters and the relative order of the activation energy for hydrogen atom transfer of all the conformers have been systematically examined in this work. Obtained relative order of the activation energy is following Ea3 > Ea1 > Ea6 > Ea4 > Ea2 > Ea5. Study of the diversification of optical rotations in process of the intramolecular proton transfer has been performed by the calculation of the specific optical rotation values at a wavelength of 589.3 nm for incident light for the conformers of both the reactants and the products, using B3LYP method of density functional theory at 6-311++G(2d,2p) and aug-cc-pvdz basis sets, respectively. The relations between the change of the dihedral angles of the conformers and the diversification in optical rotations of both the reactant and the product conformers have been studied with a conclusion that the change of helix structures in molecule conformers in the process of tautomerization leads to the change of optical rotation. The helix structures of the conformers build up the chiralmolecules with the properties of the optical rotation.

8

Assisted and Protected Effects of Methanol Molecules on Intramolecular Proton Transfer in Formamide Studied with the Density Functional Theory

Du M., Qin M., Fu A., Zhou Z.

Polish Journal of Chemistry

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2007

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Vol. 81, nr 3

369-380

EN

Methanol assisted and protected proton transfers from the amide nitrogen to carbonyl oxygen atom inmodel peptide compound formamide have been investigated employing the B3LYP/6-311++G(d,p) level of theory. In the vicinity of formamide (F) and formamidic acid (FA), three different regions are considered to form hydrogen bond with methanol. Methanol molecule only in one of them can assist the proton transfer reaction while in other two sites can protect formamide from tautomerization. Totally, 27 geometries, including nine important transition states, were optimized, and their geometric parameters have also been discussed in detail. The thermodynamic and kinetic parameters, such as tautomeric energies, equilibrium constants, barrier heights, and rate constants have been predicted, respectively. In addition, the factors influencing the thermodynamic and kinetic parameters, such as temperature dependences, and solvent effects have also been explored qualitatively. Computational results show that the lowest proton transfer barrier heights are 83.30 (61.61) kJ/mol without (with) ZPVE correction for the assistance of two methanol molecules, which are also lower than that of the water-assisted process. Nonspecific solvent effects have also been taken into account by using the IPCM model of methanol. The tautomerization energies and the barrier heights are increased for these proton transfer systems because of the bulk solvent, which imply that the tautomerization of F becomes less favorable in the polar medium.

9

tert-Butylimino-tris(dimethylamino)phosphorane as a Proton Acceptor in the System of Reaction of 1-Nitro-1-(4-nitrophenyl)alkanes in THF

Wisłocka I., Nowak I., Jarczewski A.

Polish Journal of Chemistry

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2006

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Vol. 80, nr 12

2017-2029

EN

Unexpectedly the reaction of deprotonation of carbon acids with phosphazene bases occurred very slowly. The kinetic study of the proton transfer reactions between C-acids of the series of nitroalkanes with increasing bulk of R = H, Me, Et, i-Pr substituents as 4-nitrophenylnitromethane (1), 1-nitro-1-(4-nitrophenyl)ethane (2), 1-nitro-1-(4-nitrophenyl) propane (3), 2-methyl-1-nitro-1-(4-nitrophenyl)propane (4) and the tert-butylimino-tris(dimethylamino)phosphorane (5) named P1-t-Bu phosphazene is elaborated. The reactions have been studied in THF under pseudo-first-order conditions. The product of the proton transfer reactionwith P1-t-Bu in THF appeared to be associated into ion pairs. The equilibrium constants range from >100000 to 11.8 decreasing along with growing bulk of alkyl substituent in the reacting C-acid. The second order rate constants (k2H) are rapidly declining: 9360, 2.31, 0.66, 0.09 dm3 mol–1 s–1for 1, 2, 3, and4 respectively, and could not be accounted for the small values of the enthalpies of activation HH = 6.1, 18.0, 20.7 and 11.1 kJ mol–1. The reactions show negative and relatively large values of the entropies of activation SH = –149.7, –176.5, –178.7, –227.8 J mol–1 deg–1. The primary deuterium kinetic isotope effects are large showing tendency of reverse relation towards steric hindrance of the reacting C-acids, kH/kD = 15.8, 13.6, 13.2 for 1,2, and 3, respectively. The results have been discussed in terms of the influence of steric effects brought by the bulk of alkyl substituents in the C-acid and the base on formation of the transition state. Also the influence of traces of residual water present in the reaction system has been taken into consideration.

10

Analytical Functions for the Proton Transfer in the H5O+2 Complex Immersed in a Solvent (Water, 1-Octanol)

Neagoe C., Lepadatu C.

Polish Journal of Chemistry

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2004

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Vol. 78 / nr 2

279-285

EN

The analytical functions for the energy barrier of the proton transfer in H5O2 + complex have been fitted by nonlinear regression from ab initio quantum mechanical calculations for the complex in gas phase and solvent phase (water, 1-octanol) simulated using the PCM approach. The best fitted function describing the proton transfer energy for any distance R between H3O+ and H2O and for any proton position is of the form E(R,r) = E(R/2)Erfc(z), where Erfc( z) is the complementary error function, z = [(r - 0.5R)/c]2, R is the O(H3O+)-O(H2O) distance, r is the space position of proton relative to R/2 and c a constant determined by regression for each proton transfer at a given R distance. The fitted functions are: E(R/2) = [a + b/(R/2)]2 which is the highest potential energy value for the proton situated at R/2 and c = a + bln(R/2). The energy barriers for the solvent phase are higher than those for the gas phase, because of the solute-solvent interactions considered by PCM. The energy barrier for the 1-octanol phase is somewhat lower than that for water phase, most likely due to the amphipathic character of the 1-octanol. The energy potential values for the proton transfer in solvent can be expressed as a sum of two terms corresponding to the gas phase and to solvent effects contributions.

11

Spectral Features of Unconventional Hydrogen Bonds and Proton Transfer to Transition Metal Hydrides

Epstein L., Belkova N. V., Gutsul E. I., Shubina E. S.

Polish Journal of Chemistry

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2003

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Vol. 77 / nr 11

1371-1383

EN

The spectral (low temperature IR, NMR, UV-Vis) changes accompanying the formation of the new unconventional hydrogen bonds (HB): to a metal atom and to a hydride ligand of transition metal hydrides, and allowing to distinguish the different ways of proton transfer via these types of H-bonds are summarized. The spectral and theoretical results show, that HB of the first type (M…HX)and of the second (MH…HX) type induce proton transfer respectively to the metal atom and to the hydride ligand, producing classical and nonclassical cationic hydrides. The spectral evidence of ion pairs formation stabilized by HB with anions is presented.

12

Proton of hydrogen transfer in model hydrogen bonded systems

Chojnacki H.

Bulletin of the Polish Academy of Sciences. Chemistry

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2002

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Vol. 50, No. 4

501-507

EN

The population analysis of the hydrogen bond atoms was analyzed within the different basis sets for model molecular systems for the ground and low-lying excited electronic states. The systems were considered as multireference ones and at the CAS SCF level the Mulliken, Lowdin and Hirshfeld methods were used in our investigations. It has been shown that in some cases the proton is transferred. However, there are systems where in the excited electronic states rather hydrogen atom is responsible for the tautomeric interconversion. The density functional method has also been applied for cases known to require the multireference description. It should be noted that the calculations including correlation energy within the DFT formalism, in some cases, do not properly account for the multireference character of the wavefunction.

13

Experimental and theoretical study on proton tunneling in jet-cooled 9-hydroxyphenalenone-CO2 van der Waals complex

Mori H., Furusawa J., Sekiya H.

Bulletin of the Polish Academy of Sciences. Chemistry

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2002

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Vol. 50, No. 4

451-462

EN

The fluorescence excitation, dispersed fluorescence, and hole-burning spectra of the 9-hydroxyphenalenone (9HPO)-C(2) 1:1 complex have been measured to investigate the effects of the van der Waals interaction on proton tunneling in the So state. The Si-So electronic origin is only 4 cm (-1) red-shifted with respect to that of the monomer, suggesting that proton tunneling occurs in both the So and Si states of the 9HPO-CO(2) complex, although the tunneling splittings have not been observed in the excitation spectrum. The structure of the observed complex and its tunneling potential for the So state of 9HPO have been theoretically investigated by using the reaction surface Hamiltonian method. The intermolecular interaction significantly changes the shape of two dimensional potential energy surface along the reaction coordinates, and slightly decreases the tunneling splitting in the zero-point level.

14

Proton Abstraction from 4-Nitrophenyl[bis(ethylsulphonyl)]methane with TMG, TBD and MTBD Bases in Acetonitrile

Jarczewski A., Binkowska I.

Polish Journal of Chemistry

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2001

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Vol. 75, nr 12

1895-1903

EN

4-Nitrophenyl[bis(ethylsulphonyl)]methane has been synthesized and used in kinetic studies of proton abstraction induced by 1,1,3,3-tetramethylguanidine (TMG), 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) and 7-methyI-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) bases in acetonitrile. The pK, values of this carbon acid in water and in acetonitrile solvents are 10.08 and 22.8 respectively. The electronic spectra of 4-nitrophenyl[bis(ethylsulphonyl)]methane and its anion ar well defined and temperaturę dependent. The rates of proton abstraction are large as the reaction occurs in the range of microseconds. The relaxation times were studied by spectrophotometric temperature-jump technique. The rate constants for proton transfer reaction promoted by TMG, TBD and MTBD bases in acetonitrile are: 1.39x10 5-2.1 Ix10 5; 8.8x10 6-19.2x10 6; 0.84x105-2.43x 10S [dm3 mol-1 s-1] respectively between 20-40°C. The enthalpies of activation are: deltaH# = 18.1, 28.7 and 40.0 [kJ mol-1] for TMG, TBD and MTBD respectively. The entropies of activation are all negative: deltaS# = -84.9, -13.6, -14.3 [J mol-1 deg-1] for the same sequence of bases reacting with 4-nitrophenyl[bis(ethylsulphonyl)]methane in acetonitrile solvent. The general discussion of the results obtained and their comparison with those for proton transfer reaction carried out with "normal" C-acids is given.

15

Solvation and proton transfer phenomena in phenol derivative-tertiary amine-aprotic solvent systems

Ilczyszyn M.

Bulletin of the Polish Academy of Sciences. Chemistry

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2000

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Vol. 48, No. 1

91-100

EN

Proton transfer (PT) equilibria inside hydrogen-bonded complexes of phe-nols (AH) with triethylamine and JV-methylpiperidine (B), A-H...B A - o -H-B+, dissolved in cooled (up to 113 K) aprotic solvents are analysed using H NMR results. Two categories of situations, depending on the acid and base initial concentrations, are considered: slower and faster PT for the Cg : CAg w 2 and Cg : CAu > 2 solutions, re-spectively. They are characterised by enthalpy and entropy of PT and interpreted as a result of relations between the proton transfer and solvation phenomena. In strongly cooled CB : CAH Ť 2 solutions the intra-complex proton motion is probably coupled to the motion of the solvating base molecule. This phenomenon is qualitatively described by the density function of the energy attraction between the bridging AHB proton and the solvating amine molecule. In the CB : CAH > 2 solutions this mechanism does not work probably and the hydrogen bonded ion-pairs are strongly solvated by the neighbour amine molecules.

16

Periodic Hartree-Fock studies on (HCl) infinity chain

Berski S., Latajka Z.

Polish Journal of Chemistry

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1998

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Vol. 72, nr 7S

1540-1550

EN

The infinite chain of hydrogen chloride (HCl) infinity is studies by the periodic Hartree-Fock (PHF) method using CRYSTAL 92 program. The basis sets of double zeta type containing sp- diffuse as d-and p- polarization functions are investigated. The relationship between structural and energetic parameters of (HCL) infinity and these basis sets is discussed. Furthermore, it is shown that [12s9p/6s4p] basis set of Veillard and Huzinaga, which was successfully used in stidies on HCl dimer, yields the best geometry of the infinite chain. Based on this basis set, the height of the barier for proton transfer is obtained with value of 39.6 kcal/mol. The comparison of the density of states plots (DOS) computed for (HF) infinity and (HCl) infinity indicates that computational level influences rather slightly the DOS function in case of the hydrogen chloride chain.

17

Comparison of the molecular structures of 1,5-bis(p-toluenesulphonamido)-2,4,6,8-tetranitronaphthalene and its dianion in the bispyridinium salt

Olejnik Z., Lis T., Grech E., Nowicka-Scheibe J.

Polish Journal of Chemistry

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1998

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Vol. 72, nr 7

1255-1268

EN

1,5-Bis(p-toluenesulphonamido)-2,4,6.8-tetranitronaphthalene (1,5-TSATNN) [alternative name: N,N'-(2,4,6,8-tetranitronaphthalene-1,5-diyl)-bis(p-toluenesulphonamide)] crystalized from acetic acid or pyridine with three molar equivalents of solvent. The compound with pyridine is shown to be a 1:1 adduct of bispyridinium salt. Substantial differences between molecular geometries of 1,5-TSATNN and its dianion are found. Naphthalene cores are distorted from planarity in quite different modes and the neutral and deprotonated p-tosylamide groups adopt different rotational conformations. A significant delocalization of the negative charge, observed as shortening of the S-N and N(amide)-C bonds, as well as evidence of conjugation between the amide and nitro groups are found in the dianion.