The wave nature of the protonic conductivity mechanism in the active site of carboanhydrase

Quantum-chemical calculations were performed for the (NH₃)₃Zn²⁺...(H₂O)_n...NH₃ (n = 3–11) molecular complex to model the proton transfer system of the carboanhydrase enzyme. H-bond proton transfer along the chain connecting the donor and acceptor groups was shown to be concerted vibrational motion of all protons in the chain. A wave of H-bond deformations was related to the moving proton. The displacement of H-bond protons in the transition state of the proton transfer reaction with respect to their equilibrium positions corresponded to a structure that could be defined as a proton wave. The length of this wave found as the distance between H-bond contraction (O-H bond elongation) maxima was ～8 Å. Charge transfer from the donor to the acceptor occurred according to the mechanism of the concerted jump of H-bond protons as the wave reached the chain end. The barrier to transfer was independent of the number of chain links and equaled 10 kcal/mol.     

The Structure of Nickel(Ii) and Copper(Ii) Complexes with 1,4,8,11-Tetraazacyclotetradecanein Aqueous Solution as Studied by the X-Ray Diffraction Method

The structure of 1,4,8,11-tetraazacyclotetradecane (cyclam) complexes with nickel(II) and copper(II) ions in aqueous solution has been determined by the x-ray diffraction method at 25°C. The [Ni-(cyclam)]²⁺ complex has a square-planar structure with four nitrogen atoms of the cyclam, and the Ni-N bond length has been determined to be 198 pm. Upon the addition of ammonia, the color of the nickel(II)-cyclam solution turns to deep purple and the [Ni(NH₃)₂(cyclam)]²⁺ complex is formed. The complex has a regular octahedral structure with an additional two NH₃ molecules along the axis vertical of the cyclam plane, and the Ni-N (NH₃ and cyclam) bond lengths are 209 pm. The copper(II)-cyclam complex in the aqueous solution is a distorted octahedron with two water molecules along the elongated axis. The axial Cu—O and equatorial Cu—N bond lengths are 277 and 210 pm, respectively.     

Periodicity in proton conduction along a H‐bonded chain. Application to biomolecules

Molecular complexes are constructed to simulate proton transfer channels of the influenza A virus and of the active site of carbonic anhydrase. These complexes consist of proton donor and acceptor groups connected by a chain of water molecules. Quantum chemical calculations on the methylimidazole(H⁺)? H₂O? CH₃COO^? model of the M2 virus channel indicate free translational motion of the water molecule between donor and acceptor, as well as concerted transfer of both H‐bond protons. The proton transfer barrier does not depend on the position of the bridged water molecule and varies linearly with the difference of electrostatic potentials between the donor and acceptor. When the water chain is elongated, and with various donor and acceptor models, periodicity appears in the H‐bond lengths and the progression of proton transfer in each link. This “wave” is shown to propagate along the chain, as it is driven by the displacement of a single proton. One can thereby estimate the velocity of the proton wave and proton conduction time. Computations are performed to examine the influence of immersing the system within a polarizable medium. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Computational studies on electron and proton transfer in phenol‐imidazole‐base triads

The electron and proton transfer in phenol‐imidazole‐base systems (base = NH₂^? or OH^?) were investigated by density‐functional theory calculations. In particular, the role of bridge imidazole on the electron and proton transfer was discussed in comparison with the phenol‐base systems (base = imidazole, H₂O, NH₃, OH^?, and NH₂^?). In the gas phase phenol‐imidazole‐base system, the hydrogen bonding between the phenol and the imidazole is classified as short strong hydrogen bonding, whereas that between the imidazole and the base is a conventional hydrogen bonding. The n value in spⁿ hybridization of the oxygen and carbon atoms of the phenolic CO sigma bond was found to be closely related to the CO bond length. From the potential energy surfaces without and with zero point energy correction, it can be concluded that the separated electron and proton transfer mechanism is suitable for the gas‐phase phenol‐imidazole‐base triads, in which the low‐barrier hydrogen bond is found and the delocalized phenolic proton can move freely in the single‐well potential. For the gas‐phase oxidized systems and all of the triads in water solvent, the homogeneous proton‐coupled electron transfer mechanism prevails. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Cooperative interactions of hydrogen bonds in proton-transfer processes involving water molecules. Simulation of biochemical systems

Quantum-chemical calculations of molecular complexes simulating the proton channel of influenza A virus and the proton-transfer system of the active site of carboanhydrase enzyme were performed. These complexes comprise a proton-donor and a proton-acceptor groups bridged by a chain of water molecules. Calculations of the methylimidazole (H⁺)-H₂O-CH₃COO^? complex as a model of influenza M₂ virus revealed free translation motion of the water molecule between the donor and acceptor, as well as concerted proton transfer in both H bonds. The barrier for proton transfer is independent of the position of the bridging water molecule and varies linearly with the difference in the electrostatic potentials between the donor and acceptor. With elongation of the H-bond bridge between the donor and acceptor groups, the H-bond lengths and proton shifts in the chain links vary periodically. This process can be defined as an H-bond deformation wave (proton wave). It was shown that motion of one proton along the H bond is associated with vibrational motion of protons in other links, which results in wave propagation along the chain. The calculation results allowed the rate of the proton wave and the time of proton transfer from the donor to acceptor to be estimated.     

A theoretical structural analysis of the factors that affect 1JNH, 1hJNH and 2hJNN in N–H···N hydrogen‐bonded complexes

Calculations of ¹ J_NH, ^1h J_NH and ^2h J_NN spin–spin coupling constants of 27 complexes presenting N–H·N hydrogen bonds have allowed to analyze these through hydrogen‐bond coupling as a function of the hybridization of both nitrogen atoms and the charge (+1, 0, ? 1) of the complex. The main conclusions are that the hybridization of N atom of the hydrogen bond donor is much more important than that of the hydrogen bond acceptor. Positive and negative charges (cationic and anionic complexes) exert opposite effects while the effect of the transition states ‘proton‐in‐the‐middle’ is considerable. Copyright © 2008 John Wiley & Sons, Ltd.     

Proton dissociation and transfer in hydrated phosphoric acid clusters

The dynamics and mechanisms of proton dissociation and transfer in hydrated phosphoric acid (H₃PO₄) clusters under excess proton conditions were studied based on the concept of presolvation using the H₃PO₄–H₃O⁺–nH₂O complexes (n = 1–3) as the model systems and ab initio calculations and Born–Oppenheimer molecular dynamics (BOMD) simulations at the RIMP2/TZVP level as model calculations. The static results showed that the smallest, most stable intermediate complex for proton dissociation (n = 1) is formed in a low local‐dielectric constant environment (e.g., ε = 1), whereas proton transfer from the first to the second hydration shell is driven by fluctuations in the number of water molecules in a high local‐dielectric constant environment (e.g., ε = 78) through the Zundel complex in a linear H‐bond chain (n = 3). The two‐dimensional potential energy surfaces (2D‐PES) of the intermediate complex (n = 1) suggested three characteristic vibrational and ¹H NMR frequencies associated with a proton moving on the oscillatory shuttling and structural diffusion paths, which can be used to monitor the dynamics of proton dissociation in the H‐bond clusters. The BOMD simulations over the temperature range of 298–430 K validated the proposed proton dissociation and transfer mechanisms by showing that good agreement between the theoretical and experimental data can be achieved with the proposed rate‐determining processes. The theoretical results suggest the roles played by the polar solvent and iterate that insights into the dynamics and mechanisms of proton transfer in the protonated H‐bond clusters can be obtained from intermediate complexes provided that an appropriate presolvation model is selected and that all of the important rate‐determining processes are included in the model calculations. © 2015 Wiley Periodicals, Inc.     

An analysis of the structure of fullerene C70 by quantum-chemical methods

Hartree-Fock and density functional theory calculations showed that the B, C, D, and E fullerene C₇₀ cycles were not coplanar. The interrelation between acoplanarity and pyramidality of atoms was studied. The bond lengths, valence and torsion angles, and charges and chemical shifts of fullerene C₇₀ atoms were jointly analyzed. Most attention was given to the acoplanarity of hexagons E in the aromatic belt.     

Remarkable shifts of Csp2-H and O-H stretching frequencies and stability of complexes of formic acid with formaldehydes and thioformaldehydes

Thirty-six stable complexes of formic acid with formaldehydes and thioformaldehydes were determined on the potential energy surface, in which the XCHO···HCOOH complexes are found to be more stable than the XCHS···HCOOH counterparts, with X = H, F, Cl, Br, CH₃, NH₂. All complexes are stabilized by hydrogen bonds, and their contribution to the total stabilization energy of the complexes increases in going from C-H···S to C-H···O to O-H···S and finally to O-H···O. Remarkably, a significant blueshift of C_sp2-H bond by 81–96 cm⁻¹ in the C_sp2-H···O hydrogen bond has hardly ever been reported, and a considerable redshift of O-H stretching frequency by 206–544 cm⁻¹ in the O-H···O/S hydrogen bonds is also predicted. The obtained results in our present work and previous literatures support that a distance contraction and a stretching frequency blueshift of C-H bond involving hydrogen bond depend mainly on its polarity and gas phase basicity of proton acceptor, besides the rearrangement of electron density due to complex formation. Markedly, we suggest the ratio of deprotonation enthalpy to proton affinity (R _c) as an indicator to prospect for classification of hydrogen bonds. The symmetry adapted perturbation theory results show a larger role of attractive electrostatic term in XO-n as compared to that in XS-n and the electrostatic interaction is overwhelming dispersion or induction counterparts in stabilizing XO-n and XS-n , with n = 1, 2, 3. © 2019 Wiley Periodicals, Inc.     

Electronic structure,geometry, and stability of organic cations,dications, and donor-acceptor complexes

Geometric, electronic, and energy characteristics of the complexes formed in the CF₄ ·nAIF₃ (n = I or 2) and CBr₄ ·nAIBr₃ (n = 1, 2, or 4) systems have been determined by the semiempirical AM I method. Besides the donor-acceptor complexes, the CBr₃ ⁺...AIBr₄ ^–, CBr₃ ⁺...Al₂Br₇ ^–, CBr2²⁺...(AlBr₄ ^–)₂, and CBr₂ ²⁺...(Al₂Br₇ ^–)₂ ionic complexes can be formed in the CBr₄ ·nAlBr₃ systems. In the cations and dications of polyhalomethanes (when Hal = Cl, Br, or l) in both the free and bound (included in ionic complexes) states, carbon atoms carry negative charges, the C-Hal bonds are substantially shortened, and the positive charges are located on one-coordinate halogen atoms. These cations and dications can be considered as halenium ions that differ from halenium salts with dicoordinate halogen atoms. In the cationic and dicationic complexes of the CBr₄ ·nAlBr₃ systems, the maximum positive charges on the Br atoms are 0.39 and 0.94, respectively. Fluorine-containing cations and dications have structures similar to those of carbenium ions, whereas in the CF₄ ·nAIF₃ systems (n = l or 2), only donor-acceptor complexes are formed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya. No. 3, pp. 554–560, March, 1996.     

Theoretical investigation of the structure and properties of H2B=NH2...Mn+, HB≡NH...Mn+, and Borazine...Mn+ complexes (M = Alkaline and Earth Alkaline Metals)

The nature of H₂B=NH₂...M ⁿ⁺, HB=NH...M ⁿ⁺, and Borazine...M ⁿ⁺ interactions were studied with ab-initio calculations. The interaction energies were calculated at B3LYP/6-31G(d, p) level. The calculations suggest that the size and charge of cation are two influential factors that affect the nature of interaction. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analysis of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies.     

Scalar-relativistic 5f-in-core pseudopotentials and core-polarization potentials for trivalent actinides: calibration calculations for Ac<Superscript>3+</Superscript>, Cm<Superscript>3+</Superscript> and Lr<Superscript>3+</Superscript> complexes

The performance of recently proposed 5f-in-core pseudopotentials for the trivalent actinides was investigated in calculations for model complexes An³⁺L ⁿ⁻ for three selected actinides (An³⁺ = Ac³⁺, Cm³⁺, Lr³⁺) and eight simple ligands with atoms from the first three periods of the table of elements (L ⁿ⁻ = F⁻, Cl⁻, OH⁻, SH⁻, CO, NH₂⁻, H₂O, H₂S, NH₃). Results of Hartree-Fock and Coupled Cluster with singles, doubles and perturbative triples calculations using basis sets of quadruple-zeta quality are compared to corresponding reference data obtained with scalar-relativistic energy-adjusted 5f-in-valence small-core pseudopotentials. The inclusion of core-polarization potentials in the 5f-in-core pseudopotential calculations and corrections of the basis set superposition error by the counterpoise correction leads to very good agreement between the 5f-in-valence and 5f-in-core pseudopotential results for bond lengths, bond angles and binding energies. Results from 5f-in-core pseudopotential calculations using different density functionals also show reasonable agreement with the more rigorous Coupled Cluster results. It is argued that the An 5f rather than the An f population is a useful criterion for the applicability of a specific An 5f-in-core pseudopotential.     

Nature of the Chemical Bond and the Mutual Influence of Ligands in Co(III) Dioximinates

The results of MWG calculations of the electronic structures of real Co(III) complexes [Co(HD)₂L¹L²] ⁿ were used to analyze the electron density distribution and to determine the charges on atoms and configurations, where nis the charge of the complex and HD is the acid residue of dimethylglyoxime (H₂D); L¹= NH₃at L²= NH₃, Cl^–, Br^–, or I^–and L¹= L²= Cl^–; and L¹= H₂O or NO^– ₂at L²= NO^– ₂, with self-consistency over all atoms of the system and over d, s, and pconfigurations of cobalt. The mutual influence of the ligands (trans- and cis-) was shown to be determined by the atomic charges and bond orders on the axial coordinate and in the equatorial plane of the complex. The following order of the trans-effect was proposed: I^–> Br^–> Cl^–> NO^– ₂> NH₃> H₂O. The effects of the electronic factors on distorsion and conformational processes in the complexes were discussed.     

Disruptive influence of the host cage C60 on the guest He–H+ bond and bonding in H3+

Although a helium atom prefers to stay at the centre of a fullerene (C₆₀) cage and a proton binds with one of the carbon atoms from inside, DFT(MN15)/cc-pVTZ and DLPNO-MP2/def2-TZVP calculations show that the helium atom and the proton in HeH⁺ prefer to stay away from the centre of the cage, weakening the He–H⁺ covalent bond considerably. Both the helium atom and the proton exhibit noncovalent interactions with the carbon atoms of two pentagons at the opposite ends of the fullerene cage. Our calculations also show that a linear arrangement of H₃⁺ (inside C₆₀), pointing towards the centres of two pentagons opposite to each other, with the proton breaking away from H_2, is energetically more favored over the equilateral triangle geometry of free H₃⁺.     

Electronic and Steric Structure of the Methanofullerene C61(CO2Me)[P(O)(OMe)2]. A Density Functional Study

The asymmetric addend in the methanofullerene C₆₁(CO₂Me)[P(O)(OMe)₂] polarizes and divides the fullerene shell into four nonequivalent fragments. According to DFT/PBE calculations, the most stable conformers of the methanofullerene C₆₁(CO₂Me)[P(O)(OMe)₂] involve Coulomb interactions of the phosphoryl oxygen with one of the fullerene carbon atoms, which produces polarization of the corresponding fragment and asymmetry in bond lengths and atomic charges in the fullerene shell. Alternation and attenuation of changes in bond lengths along the conjugation branches was revealed.     

Computational study of structures and proton transfer in hydrogen‐bonded ammonia complexes using semiempirical valence‐bond approach

In this study, the seGVB method was implemented for the N H bonding system, specifically for hydrogen‐bonded ammonia complexes, and the model well reproduces the MP2 geometries and energetics. A comparison between the ammonia dimer and water dimer is given from the viewpoint of valance‐bond structures in terms of the calculated bond energies and pair–pair interactions. The linear hydrogen bond is found to be stronger than the bent bonds in both cases, with the difference in energy between the linear and cyclic structures being comparable in both cases although the NH bonds are generally weaker. The energy decomposition clearly demonstrates that the changes in electronic energy are quite different in the two cases due to the presence of an additional lone pair on the water molecule, and it is this effect which leads to the net stabilization of the cyclic structure for the ammonia dimer. Proton‐transfer profiles for hydrogen‐bonded ammonia complexes [NH₂ H NH₂]⁻ and [NH₃ H NH₃]⁺ were calculated. The barrier for proton transfer in [NH₃ H NH₃]⁺ is larger than that in [NH₂ H NH₂]⁻, but smaller than that in the protonated water dimer. The different bonding structures substantially affect the barrier to proton transfer, even though they are isoelectronic systems. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 357–367, 1999     

Strong effect of methyl group on the strength of ionic hydrogen bond between C2H2 and H3O+

The effect of methyl group on the strength of the ionic hydrogen bond between C₂H₂ and H₃O⁺ has been studied with quantum chemical calculations at the UMP2/6‐311++G(d,p) level. The presence of a methyl group in the proton acceptor results in an energetic increase of 6.02 kcal/mol, increased by about 39%, whereas that in the proton donor leads to an energetic decrease of 2.18 kcal/mol, decreased by 14%. The charge analyses indicate that the methyl group in the proton acceptor is electron‐donating and that in the proton donor is electron‐withdrawing. The former plays a positive contribution to the formation of ionic hydrogen bond and the latter plays a negative contribution to the formation of ionic hydrogen bond. The weakening effect of solvent on the role of methyl group in the ionic hydrogen bond has also been studied at the UB3LYP/6‐311++G(d,p) level. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Small heterocyclics as hydrogen bond acceptors and donors: the case of the C2H3XS···NH3 complexes (X = H, F and CH3)

B3LYP/6-311++G(d,p) calculations were employed in order to examine the molecular parameters of the C₂H₃XS···NH₃ heterocyclic hydrogen-bonded complexes with X = H, F and CH₃. Intermolecular criteria were taken into account when studying the formation of these hydrogen-bonded complexes, such as geometry analysis, charge density quantification and interpretation of the harmonic vibrational spectrum, in which case the appearance of red-shift and blue-shift effects was discussed. It was assumed from the outset that many hydrogen bond types may exist in these systems, and these were investigated using the results of topological integrations from the quantum theory of atoms in molecules (QTAIM) and intermolecular charge transfer calculations using the ChelpG scheme. The proton donor/acceptor behavior of C₂H₃XS was interpreted in terms of hydrogen bond energies, whose values were corrected using the basis sets superposition error (BSSE) and zero point energy (ZPE). Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

1,2,4-三氮杂苯-(H2O)n复合物氢键相互作用的密度泛函理论研究

用密度泛函理论方法在B3LYP/6-31++G**水平上对1,2,4-三氮杂苯-(H₂O)_n (n＝1, 2, 3)氢键复合物的基态进行了结构优化和能量计算, 结果表明复合物之间存在较强的氢键作用, 所有稳定复合物结构中形成一个N…H—O氢键并终止于弱O…H—C氢键的氢键水链的构型最稳定. 同时, 用含时密度泛函理论方法(TD-DFT)在TD-B3LYP/6-31++G**水平上计算了1,2,4-三氮杂苯单体及其氢键复合物的单重态第一¹(n, π^*)垂直激发能.     

Intra- and intermolecular hydrogen bonding in formohydroxamic acid complexes with water and ammonia: infrared matrix isolation and theoretical study

The complexes of formohydroxamic acid with water and ammonia have been studied using FTIR matrix isolation spectroscopy and MP2 calculations with a 6-311++G(2d,2p) basis set. The analysis of the experimental spectra of the HCONHOH/H₂O(NH₃)/Ar matrixes indicates formation of strongly hydrogen-bonded complexes in which the NH group of formohydroxamic acid acts as a proton donor toward the oxygen atom of water or the nitrogen atom of ammonia. The NH stretching vibration of formohydroxamic acid exhibits 150 cm⁻¹ red shift in the complex with water and 443 cm⁻¹ red shift in the complex with ammonia as compared to the NH stretch of the HCONHOH monomer. The theoretical calculations indicate stability of five isomers for the water complex and three isomers for the ammonia complex. The most stable are the cyclic structures in which the water or ammonia molecules are inserted within the intramolecular hydrogen bond of the formohydroxamic acid molecule and act as proton donors for the CO group and proton acceptors for the OH group of the formohydroxamic acid molecule. In spite of their stability the cyclic structures have not been observed in the matrixes which indicates high energy barrier for their formation, the reaction of complex formation is under kinetic and not thermodynamic control.