Theoretical investigation (DFT and MP2) of the intermolecular proton transfer in the supersystems uracil-(H2O) n and uracil-(CH3OH) n (n = 1, 2)

Twelve binary and eight ternary H-bonded systems between uracil and water/methanol were investigated at the B3LYP and MP2 theoretical levels using 6 − 31 + G(d) basis functions. The binary and ternary systems that contain the hydroxo-uracil tautomer H-bonded with water and methanol were found to be the most stable complexes. The calculated energy barriers of the intermolecular proton exchange showed that the methanol molecule provokes larger reduction of the energy barrier of the intermolecular proton exchange reactions than the water molecule. Correspondence: Vassil B. Delchev, Department of Physical Chemistry, University of Plovdiv, Plovdiv, Bulgaria     

Structure of adducts of the intermolecular interaction of dimethylpyrazole and diphenylformamidine with hydrogen halides in the solution

The structure of adducts forming in the solution due to the interaction of bifunctional azo compounds (dimethylpyrazole (DMP) and diphenylformamidine (DPFA)) with hydrogen halides (HF, HCl, and HBr) is found from the data of the IR absorption spectra and quantum chemical calculations. It is shown that in the interaction with HCl or HBr proton donors, proton transfer via the hydrogen bond to the basic N atom of the azo compound occurs with the formation of an NH⁺…Hal⁻ ionic pair. Strong evidences of proton transfer and the anion-cation pair formation are not found for the DMP-_F structure, and complexes with the molecular N…HF hydrogen bond are the dominant structures. Geometric parameters of the formed structures are calculated. The formation of trimers, containing two molecules of the azo compound and one HHal molecule, with an increase in the nitrogenous base concentration is experimentally proved, and the trimer structure is determined.     

Simulation of proton migration pathways in phenolsulfonic acid-based membranes by B3LYP/6-31G** DFT calculations

Geometrical and energetic characteristics of clusters simulating crystal hydrates of phenolsulfonic acid (PSA) and its complexes with poly(vinyl alcohol) (PVA) and the pathways of proton transport therein were determined using the DFT (B3LYP) theory with the 6-31G** basis set. In the formation of proton-conducting PVA—PSA-based membranes, it is energetically favorable to have at least one water molecule in close proximity of the SO₃H fragment. In water-free media, the proton migration along the SO₃H group is hindered by a barrier of 30–34 kcal mol⁻¹. In the presense of water, the proton conductivity follows the relay mechanism with the activation barrier of 5–8 kcal mol⁻¹, which is close to the experimetally observed barrier of 4–6 kcal mol⁻¹. Thus, the relay mechanism of proton transfer in a sulfonic acid—water complex is energetically the most favorable. The most energetically favorable isomer is the one with the PSA and PVA fragments H-bonded through a water molecule. The deficiency of water causes the PVA OH protons to be involved in hydrogen bonding as well. The role of PVA is to align the acid molecules and participate in the relay proton transfer. Introduction of an aldehyde into the membrane results in significant improvement of its physical properties. The aldehyde reacts with the hydroxyl groups of PVA. At high humidity, one may expect little effect of the degree of cross-linking on the proton mobility.     

Theoretical study of environmental effects on proton transfer reaction through the peptide bond in a model system

This study considered the possibility of proton transfer reactions through the peptide bond under different environments using the dipeptide and the 12-mer polyglycine α-helix models, in which diglycine is substituted by the 12-mer polyglycine helix. Ab initio molecular orbital calculations were carried out at the B3LYP/6-31+G(d) level of theory. To evaluate the free energies in solution, calculations of the solvation energies were performed using PCM. The correction functions on the calculated solvation energies were provided to reproduce experimental pKa values. The proton transfer reactions through the peptide bond are concluded to be possible in the protein for a wide range of proton acceptors. His complex has two free energy minima along a putative proton transfer pathway in spite of one minimum in the other complexes. The α-helix is estimated to suppress the proton transfer reactions through the peptide bond at the termini of the helix, although it is possible to proceed when the proton affinity of the acceptor is low. Contribution to the Mark S. Gordon 65th Birthday Festschrift Issue.     

Anion-molecular interaction through CH3 groups: Model ab initio studies

3-21G, 6–31G and 6–31 +G calculations have been performed on Cr…H₃CCl and LiCl…H₃CCl complexes with two different configurations each. Optimized geometries, stabilization energies, CH force constants and harmonic vibrational frequencies for CH₃Cl and its complexes are reported. Comparison of the calculated frequency shifts of CH-stretching bands of CH₃C1, on complexation, with experimental results of related systems indicate that the interaction of Cl^- with CH₃ group takes place in a linear manner with the CH bond. A lower frequency shift for LiCl…H₃CX with reference to the C1^-…H₃CX complexes is explained on the basis of the reduction of the basicity of Cl^- ion in the presence of counter ion in the former complex considered.     

Synthesis and optical behaviour of hydrogen-bonded liquid crystals based on a chiral pyridine derivative

Three series of cholesteryl-containing supramolecular hydrogen-bonded (H-bonded) liquid crystal (LC) complexes with different number of fluoro-substituent were synthesised and characterised. Cholesteryl isonicotinate as proton acceptor and 4-n-alkoxybenzoic acids with or without fluoro-substituent as proton donor had been mixed in tetrahydrofuran to obtain H-bonded LC complexes. The effect of lateral substitution and the length of terminal chain in the H-bonded precursors on the formation of the supramolecular complexes had been examined. It was found that the introduction of fluoro substituent on the induced mesogens could widen the molecular width and thus reduce the molecular aspect ratio of the complexes, therefore it could lead to compress the formation of the LCs. However, the fluoro substituent played a positive role in enhancing the intermolecular interactions and stabilising the H-bond structure of the complexes. The influence of terminal length on the mesogenic behaviours is also discussed. On increasing the spacer length, the clear point and the thermal range of induced mesophase-like cholesteric phase decreased, and an induced chiral smectic phase began to appear in some complexes with long terminal tails.     

An SCF and CI Study of the 1,3 Shift in the HX?CHY⇌XCH?YH Isoelectronic Series: X,YCH2, NH,and O

Ab initio molecular orbital calculations at SCF level with the 3-21G, 6-31G, and 6-31G** basis sets and CI level with the 6-31G basis set have been carried out for an isoelectronic series HX? CH?Y and X?CH? YH, where X, Y can be CH₂, NH, and O. Optimized structures (3-21G and 6-31G**) for both tautomers and the 1,3 hydrogen shift transition states are reported. The relative stabilities of the isomers and the barriers of the 1,3 shift are discussed in terms of proton affinities and bond orders. It is shown that both the relative stabilities of the tautomers and the relative barrier heights can be explained qualitatively using simple proton affinity arguments and that the barrier heights are quantitatively related to bond orders.     

Controlling Light-Induced Proton Transfer from the GFP Chromophore

Green Fluorescent Protein (GFP) is known to undergo excited-state proton transfer (ESPT). Formation of a short H-bond favors ultrafast ESPT in GFP-like proteins, such as the GFP S65T/H148D mutant, but the detailed mechanism and its quantum nature remain to be resolved. Here we study in vacuo, light-induced proton transfer from the GFP chromophore in hydrogen-bonded complexes with two anionic proton acceptors, I⁻ and deprotonated trichloroacetic acid (TCA⁻). We address the role of the strong H-bond and the quantum mechanical proton-density distribution in the excited state, which determines the proton-transfer probability. Our study shows that chemical modifications to the molecular network drastically change the proton-transfer probability and it can become strongly wavelength dependent. The proton-transfer branching ratio is found to be 60 % for the TCA complex and 10 % for the iodide complex, being highly dependent on the photon energy in the latter case. Using high-level ab initio calculations, we show that light-induced proton transfer takes place in S₁, revealing intrinsic photoacid properties of the isolated GFP chromophore in strongly bound H-bonded complexes. ESPT is found to be very sensitive to the topography of the highly anharmonic potential in S₁, depending on the quantum-density distribution upon vibrational excitation. We also show that the S₁ potential-energy surface, and hence excited-state proton transfer, can be controlled by altering the chromophore microenvironment.     

Dynamic and electrooptical properties of FH…F and FH…N hydrogen bridges

The dynamic and electrooptical parameters of the hydrogen bridges in (HF)₂, FH…FCD₃, FH…NCH, and FH…NCCH₃ complexes were calculated by the MINDO/3 method. Relationships between these parameters have been found. These parameters for the F−H…Y bridges mainly coincide with the relationships previously established for the hydrogen O−H…Y bridges. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1067–1069, May, 1997.     

Calculation of proton transfers in hydrogen bonding interactions with semi-empirical MNDO/H

A method for calculating proton transfer enthalpies by a proper modification of the recent H-bonding version of MNDO is presented. This method perceives the proton as being both “bonded” and “hydrogen bonded” to the two electronegative atoms involved in the hydrogen bond: as it moves from one potential minimum at X-H---Y to the other at X---H-Y, a hydrogen bonding function is attached to the proportion of the distance that is to be traversed. The method is applied to two proton transfers within anionic oxygen H-bonded complexes and is shown to reduce the previously calculated barriers which were too high. Gas phase results for the single step of proton transfer over a barrier are required to evaluate the results obtained by this method.     

H-bonded network rearrangements in the S0, S1 and D0 states of neutral and cationic p-cresol(H2O)(NH3) complexes

The H-bonded network rearrangements in the S(0), S(1) and D(0) states of the neutral and cationic p-CreOH(H(2)O)(NH(3)) complexes were studied experimentally by means of (1 + 1)/(1 + 1') REMPI (Resonantly Enhanced MultiPhoton Ionization) and time resolved LIF (Laser Induced Fluorescence) spectroscopies combined with DFT (Density Functional Theory) calculations at the B3LYP/6-311G++(d,p) level. A comparison of the rearrangement process of the H-bonded network in the three states is given. Two cyclic H-bonded isomers were found on the S(0) potential energy surface and the results indicate that the rearrangement in this state is unlikely at the temperature of the supersonic expansion due to the presence of a high-energy barrier (7503 cm(-1)). On the other hand, the re-determination of the S(1) excited state lifetimes confirms that neither the H-bonded rearrangement nor the excited state hydrogen transfer (ESHT) reaction takes place in the S(1) state at the excitation energies of this work. Thus, it is concluded that the absorption of the second photon to reach the D(0) state takes place from the S(1) state of the cyclic-(OH-OH(2)-NH(3)) isomer. A preferential evaporation of H(2)O upon vertical ionization of the cyclic-(OH-OH(2)-NH(3)) isomer is observed which is consistent with a statistical redistribution of the internal energy. Nevertheless, our theoretical calculations suggest that initial excitation of the H-bonded network rearrangement modes may also play a role to leave the H(2)O molecule as a terminal moiety in a chain-(OH-NH(3)-OH(2))(+) isomer. The reaction pathway for the solvent rearrangement involves a double proton transfer process with a very low energy barrier (575 cm(-1)) that is overcome at the vertical ionization energy of the complex.     

氢键链质子接受能力对质子转移反应影响的理论研究

采用密度泛函B3LYP方法,6-311+g(d,p)基组,对甲酸与质子性溶剂分子形成的HCOOH-S_1-S_2(S_1和S_2分别为H_2O和NHF2)复合物在气相时发生的基态三质子转移反应过程进行了理论研究.4个甲酸复合物HCOOH-H_2O-H_2O,HCOOH-NHF2-NHF2,HCOOH-H_2O-NHF2及HCOOH-NHF2-H_2O中发生的三质子转移反应都是以异步协同质子迁移方式进行的.甲酸复合物中的氢键链组成和连接方式对基态三质子转移反应能垒有显著影响.HCOOH-S_1-S_2复合物中氢键链的质子接受能力可以表示为a×β1+b×β2(a+b=1).当a=0.45,b=0.55时,HCOOH-S_1-S_2中氢键链的质子接受能力和HCOOH-S_1-S_2复合物中的质子转移反应能垒成线性关系.氢键链的质子接收能力越强,反应能垒越低.     

Pathways of the reactions of nucleophilic addition of H2O and HF molecules to formaldehyde in the gas phase and in the complex with formic acid:ab initio calculations

The gradient pathways of the reactions of nucleophilic addition of H₂O and HF molecules to formaldehyde in the gas phase and in the XH…H₂CO…HC(O)OH complex (X=OH, F) were calculated by theab initio RHF/6-31G^**, MP2(fc)/6-31G^**, and MP2(full)/6-311++G^** methods. Both reactions proceed concertedly. The formation of H-bonded bimolecular pre-reaction complexes is the initial stage of the gas-phase reactions; at the same time, no indications of the formation of stable π-complexes were found on the potential energy surfaces of systems under study. The calculated energy barriers to the gasphase reactions exceed 40 kcal mol⁻¹, while those to reactions in the complex XH…H₂CO…HC(O)OH (X=OH, F) become more than halved. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2146–2154, November, 1998.     

Self-consistent reaction field calculations on the proton transfer in ammonia-formic acid systems as a model for hydrogen bonding in amino acids in solution

The reaction field (RF ) model of solvent effects, implemented within the SCF -CNDO /2 scheme of calculation, has been applied to analyze the proton transfer in the NH₃…HCOOH system in the presence of several polarizable media. The aim of such a study was to characterize the tatutomeric equilibrium between the neutral and zwiterionic forms of H-bonded amino acids in aprotic solvents. Qualitative results concerning the energetics of this equilbrium show the stabilization of two different H-bonded complexes, corresponding to two separate minima in the free energy surface. These well known double minima potentials are found to be dependent on both the intermolecular N? O distance and the strength of the reaction field. The behavior of this model is qualitatively consistent with experimental observations of nitrogen-substituted amino acids in solution: both show, for low values of the dielectric constant, tautomeric equilibria where the H-bonded complexes appear to be more stable than the corresponding monomeric forms. The charge transfer process associated with the proton migration along the H-bond is also discussed. It is found that the amount of charge transferred increases with the N? O distance and with the RF strength, In order to test the general approach and compare it with previous work, calculations on the real monomeric systems glycine, β-alanine, and γ-amino butyric acid was also performed.     

Hydrogen bonds with pi and sigma electrons as the multicenter proton acceptors: high level ab initio calculations

Pi-electrons of acetylene and sigma-electrons of molecular hydrogen were investigated as Lewis bases in different complexes. Hence high level ab initio calculations were performed up to the MP2/6-311++G(3df,3pd) level of approximation. It was found that species analyzed possess characteristics typical for H-bonded systems. The Bader theory was additionally applied; bond paths between proton and pi-electrons of acetylene or sigma-electrons of molecular hydrogen were detected with the corresponding bond critical points attributed to the proton-acceptor interactions. Numerous correlations between topological, geometrical and energetic parameters were also found. For example, the H...pi or H...sigma interaction is stronger for the shorter corresponding distance between the proton and the middle of C[triple bond]C or H-H bond. It is connected with the greater elongation of C[triple bond]C or H-H bonds and the greater transfer of electron charge from the Lewis base to the Lewis acid.     

Theoretical Study of the Interactions between Isolated DNA Bases and Various Groups IA and IIA Metal Ions by Ab Initio Calculations

Interactions of the DNA bases adenine (A), guanine (G), cytosine (C), and thymine (T) with various metal ions (M) of groups IA and IIA of the periodic table of the elements were studied at the HF, MP2, and DFT levels of theory. The structures and thermodynamic stabilities of these species were studied at the gas phase. The calculations uphold that there exist two active sites in G and one in A, C, and T. The calculations also show that the O² atom in T is a more active site for metal ion bindings than that in C. The stability energies for G … M complexes are larger than those for A … M complexes and the stability energies for T … M complexes are larger than those for C … M complexes. As z/r ratio for the metal ion increases, the interaction energy for the complex increases systematically. Thermodynamic quantities such as ΔH, ΔG, ΔS, and ln K were determined for each complexation reaction, [Base+M ⁿ⁺ →(Base … M) ⁿ⁺]. A, G, and C complexation reactions except for C … Rb⁺ are exothermic. The situation is quite different for T complexation reactions and all except for T … Be²⁺ and T … Mg²⁺ are endothermic.     

Theoretical Study of the Interactions between Isolated <Emphasis Type="Italic">DNA</Emphasis> Bases and Various Groups IA and IIA Metal Ions by <Emphasis Type="Italic">Ab Initio</Emphasis> Calculations

Summary. Interactions of the DNA bases adenine (A), guanine (G), cytosine (C), and thymine (T) with various metal ions (M) of groups IA and IIA of the periodic table of the elements were studied at the HF, MP2, and DFT levels of theory. The structures and thermodynamic stabilities of these species were studied at the gas phase. The calculations uphold that there exist two active sites in G and one in A, C, and T. The calculations also show that the O² atom in T is a more active site for metal ion bindings than that in C. The stability energies for G … M complexes are larger than those for A … M complexes and the stability energies for T … M complexes are larger than those for C … M complexes. As z/r ratio for the metal ion increases, the interaction energy for the complex increases systematically. Thermodynamic quantities such as ΔH, ΔG, ΔS, and ln K were determined for each complexation reaction, [Base+M ⁿ⁺ →(Base … M) ⁿ⁺]. A, G, and C complexation reactions except for C … Rb⁺ are exothermic. The situation is quite different for T complexation reactions and all except for T … Be²⁺ and T … Mg²⁺ are endothermic.     

Role of steric factors in formation of O—H...M hydrogen bonds with metallocenes

Molecular mechanics calculations of geometric parameters and energies of molecular complexes with a O-H...M hydrogen bond have been performed for osmocene and decamethylosmocene with three proton donors. The results of calculations demonstrated that when rings are methylated, steric hindrances to formation of this hydrogen bond increase. This is the reason for anomalously low formation constants of H-bonded Cp ₂ ^* M molecular associates compared to CP₂M associates.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1925–1927, October, 1995.The work was supported by the Russian Foundation for Basic Research (Project No. 93-03-4610) and the International Science Foundation (Grant MP5 000).     

Energetics of proton transfer between carbon atoms (H3CH ? CH3)−

Ab initio calculations were carried out to study the potential energy surface of (H₃C? H? CH₃)^?. The 6–31G* basis set is supplemented by a set of diffuse p functions on both C and H (with a range of exponents for the latter). The binding energy of CH₄ and CH₃^? to form the (H₃CH? CH₃)^? complex is about 2 kcal/mol, much smaller than for comparable ionic H-bonded systems involving O or N atoms. Nearly half of this interaction energy is due to correlation effects, computed at second and third orders of Møller-Plesset perturbation theory. Correlation is also responsible for substantial reductions in the energy barrier to proton transfer within the complex. This barrier is computed to be 13?15 kcal/mol at the MP3 level, depending upon the exponent used for the H p functions.