Theoretical studies of organometallic compounds. II. All electron and pseudopotential calculations of M(CH3)nCl4 − n (M = C,Si, Ge,Sn, Pb; n = 0–4)

The performance of effective core potentials (ECP) for the main group elements of group IV has been studied by calculating the geometries and reaction energies of isodesmic reactions for the molecules M(CH₃)_nCl_{4 ? n} (M = C, Si, Ge, Sn, Pb; n = 0–4) at the Hartree–Fock level of theory. The results are compared with data from all electron calculations and experimental results as far as available. The all electron calculations were performed with a 3-21G(d) and a 6-31G(d) basis set for Si, a (43321/4321/41) basis set for Ge, and a (433321/43321/431) basis set for Sn. For the ECP calculations the potentials developed by Hay and Wadt with a configuration (n)s^a(n)p^b and the valence basis set (21/21), extended by a set of d functions, are employed. © 1992 by John Wiley & Sons, Inc.     

Effect of loop on the stability of intramolecular triplex DNA

Conformation stabilities of intramolecular triple-helical DNAs (intra-tnplex DNAs: 5-d(TC)6-d(T)m-d(CT)6-d(C)n-d(AG)6-3',where m and n are chosen to be 4 and 3) have been examined by molecular mechanics.The four intra-triplexes (H-DNAs) are compared with the mtermolecular triplexes d(TC)6 * d ( AG)6 d(CT)6.The results revealed that loops do not significantly influence the mtratriplex conformations,loop conformations,however,depend partly on its length.Loop also makes strand Ⅱ of every intra-triplex DNA longer than that of the inter-triplex DNA.Most of residue sugar conformations of triple-helical DNAs are S-type,there aiso exist,however,N-type conformation and the conformations between S-type and N-type Possible models of the five triplex DNAs are presented.     

Determination of aqueous acid‐dissociation constants of aspartic acid using PCM/DFT method

Determination of acid‐dissociation constants, pK_a, of aspartic acid in aqueous solution, using density functional theory calculations combined with the conductor‐like polarizable continuum model (CPCM) and with integral‐equation‐formalism polarizable continuum model (IEFPCM) based on the UAKS and UAHF radii, was carried out. The computed pK_a values derived from the CPCM and IEFPCM with UAKS cavity model of bare structures of the B3LYP/6‐31+G(d,p)‐optimized tetrahydrated structures of aspartic acid species are mostly close to the experimental pK_a values. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Thermodynamic Estimate of pKa Values of the Carboxylic Acids in Aqueous Solution with the Density Functional Theory

The 96 pK_a values of 85 carboxylic acids in aqueous solution were calculated with the density functional theory method at the level of B3LYP/6‐31+G(d,p) and the polarizable continuum model (PCM) was used to describe the solvent. In the calculations of pK_a values, the dissociation Gibbs free energies were directly calculated using carboxylic acid dissociation reactions in aqueous solution, i. e., no thermodynamic cycle was employed, which is different from the previous literatures. A highly significant correlation of R²=0.95 with a standard deviation (SD) of 0.36 between the experimental pK_a values and the calculated dissociation Gibbs free energies [ΔG(calc.)] was found. The slope of pK_a vs. (G(calc.)/(20303RT) is only 47.6% of the theoretically expected value, which implies that the ΔG(calc.) value from the theoretical calculation is larger than the actual one for all 85 carboxylic acids studied. Thus, by adding the 0.476 scaling‐factor into the slope, we can derive a reliably procedure that can reproduce the experimental pK_a values of carboxylic acids. The pK_a values furnished by this procedure are in good agreement with the experimental results for carboxylic acids in aqueous solution.     

Electronic structure of DNA dimer units,d(AG) · d, (CT), d(TG) · d(CA), · d(GT), and d(GA), in A and B conformations by DV–Xα cluster calculations

The electronic structure of d(AG) · d(CT), d(TG) · d(CA), d(AC) · d(GT), and d(TC) · d(GA), which are stacked base pairs in the DNA double helix, are elucidated for A and B conformations in detail by DV -X α cluster calculations. By using the S?_r values of the O2 (and O3) of each phosphate in the clusters together with those calculated in previous articles, it becomes possible to treat chemical reactivities of phosphates as recognition sites for all DNA fragments. Contour maps of the wave function of the HOMO and LUMO for bases differ subtly among the clusters and show the various fields around the P ion induced by the respective stacking constructed from four kinds of bases. © 1994 John Wiley & Sons, Inc.     

Determination of acidity constants of pyridines,imidazoles, and oximes by capillary electrophoresis

The acidity constant in the form of pK_a is one of the most important physicochemical quantities. There are prediction tools available for calculating the pK_a, but they only deliver precise calculated values for a relatively small set of chemicals. For complex structures with multiple functional groups in particular, the error in the predicted pK_a is high due to the application domain of the corresponding models. Thus, we aim to enlarge the dataset of experimentally determined pK_a values using capillary electrophoresis. We, therefore, selected various pyridines, imidazoles, and oximes to determine the pK_a values using the internal standard approach and the classical method. Especially oximes were not investigated in the past, and predictions for them include larger errors. Thus, our experimentally determined values could contribute to an improved understanding of various functional groups impacting the pK_a values and serve as additional datasets to develop improved pK_a prediction tools.     

Quantum-chemical DFT study of acid properties of thiols RSH and ligand power of their anions RS<Superscript>−</Superscript>

The DFT calculations of electronic and geometry structure, dissociation energies of S-H and S-C bonds, and acid dissociation constants (pK _a) for ten RSH thiols were fulfilled. Calibration corrections to the calculated pK _a^DFT values, which allowed obtaining a good correspondence with experimental data were introduced. Donor power of thiolate anions RS- was estimated for the prediction of stability of their compounds with ions of d-elements.     

SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules

The physicochemical properties of a drug molecule determine the therapeutic effectiveness of the drug. Thus, the development of fast and accurate theoretical approaches for the prediction of such properties is inevitable. The participation to the SAMPL7 challenge is based on the estimation of logP coefficients and pK_a values of small drug-like sulfonamide derivatives. Thereby, quantum mechanical calculations were carried out in order to calculate the free energy of solvation and the transfer energy of 22 drug-like compounds in different environments (water and n-octanol) by employing the SMD solvation model. For logP calculations, we studied eleven different methodologies to calculate the transfer free energies, the lowest RMSE value was obtained for the M06L/def2-TZVP//M06L/def2-SVP level of theory. On the other hand, we employed an isodesmic reaction scheme within the macro pK_a framework; this was based on selecting reference molecules similar to the SAMPL7 challenge molecules. Consequently, highly well correlated pK_a values were obtained with the M062X/6–311+G(2df,2p)//M052X/6–31+G(d,p) level of theory.

     

Theory of titration curves. VIII. A new interpretation of acid-base titration curves for polymeric acids. The significance of the Kern-equation parameters pKa and n

The Kern equation, pH = pK_a + n logf/(1 ? f), has been widely used in interpreting the potentiometric titration curves obtained on titrating polymeric acids with bases, and various interpretations of its empirical parameters pK_a and n have been advanced. Values of n similar to those generally obtained for polymeric acids are also obtained for dibasic and other monomeric polybasic acids for which the ratios of successive dissociation constants, K_i/K_(i+1), exceed the corresponding statistical values by a constant factor. The dependences of n on this factor and on the basicity of the acid are described. It is argued that the traditional picture of a dissociation constant varying continuously with the fraction titrated cannot be correct, and that the data can be more properly interpreted in terms of a constant non-statistical free-energy contribution to the successive values of K_i/K_(i+1).     

Ruthenium(II) carbonyl complexes of P,P and P,O donor diphosphine ligands,Ph2P(CH2)nPPh2 and Ph2P(CH2)nP(O)Ph2, n = 2, 3 and their activities in catalytic transfer hydrogenation reactions

The polymeric precursor [RuCl₂(CO)₂]_n reacts with the ligands, P∩P (a, b) and P∩O (c, d), in 1:1 M ratio to generate six-coordinate complexes [RuCl₂(CO)₂(?²-P∩P)] (1a, 1b) and [RuCl₂(CO)₂(?²-P∩O)] (1c, 1d), where P∩P: Ph₂P(CH₂)_nPPh₂, n = 2(a), 3(b); P∩O: Ph₂P(CH₂)_nP(O)Ph₂, n = 2(c), 3(d). The complexes are characterized by elemental analyses, mass spectrometry, thermal studies, IR, and NMR spectroscopy. 1a–1d are active in catalyzed transfer hydrogenation of acetophenone and its derivatives to corresponding alcohols with turnover frequency (TOF) of 75–290 h^?1. The complexes exhibit higher yield of hydrogenation products than catalyzed by RuCl₃ itself. Among 1a–1d, the Ru(II) complexes of bidentate phosphine (1a, 1b) show higher efficiency than their monoxide analogs (1c, 1d). However, the recycling experiments with the catalysts for hydrogenation of 4-nitroacetophenone exhibit a different trend in which the catalytic activities of 1a, 1b, and 1d decrease considerably, while 1c shows similar activity during the second run.     

Estimation of acidity constants,ionic mobilities and charges of antimicrobial peptides by capillary electrophoresis

Capillary electrophoresis (CE) was employed for the determination of thermodynamic acidity constants (pK_a) and actual ionic mobilities of polycationic antimicrobial peptides (AMPs). The effective electrophoretic mobilities of AMPs were measured by CE in a series of the background electrolytes within a wide pH range (2.00–12.25), at constant ionic strength (25 mM) and ambient temperature, using polybrene coated fused silica capillaries to suppress sorption of cationic AMPs to the capillary wall. Eventually, Haarhoff–Van der Linde peak fitting function was used for the determination of correct migration times of some AMPs peaks that were distorted by electromigration dispersion. The measured effective mobilities were corrected to 25°C. Mixed acidity constants, , and actual ionic mobilities, m_i, of AMPs were determined by the nonlinear regression analysis of pH dependence of their effective mobilities. The values were recalculated to thermodynamic pK_as using the Debye–Hückel theory. Thermodynamic pK_a of imidazolium group of histidine residues was found to be in the range 3.72–4.98, pK_a of α‐NH₃⁺ group was in the range 6.14–6.93, and pK_a of ε‐NH₃⁺ group of lysine spanned the interval 7.26–9.84, depending on the particular amino acid sequence of the AMPs. Actual ionic mobilities of AMPs with positive charges from one to six elementary units achieved values (9.8 – 36.5) × 10^?9 m²V^?1s^?1.     

Determination of acidity constants,ionic mobilities,and hydrodynamic radii of carborane-based inhibitors of carbonic anhydrases by capillary electrophoresis

Capillary electrophoresis (CE) has been applied for determination of the thermodynamic acidity constants (pK_a) of the sulfamidoalkyl and sulfonamidoalkyl groups, the actual and limiting ionic mobilities and hydrodynamic radii of important compounds, eight carborane-based inhibitors of carbonic anhydrases, which are potential new anticancer drugs. Two types of carboranes were investigated, (i) icosahedral cobalt bis(dicarbollide)(1-) ion with sulfamidoalkyl moieties, and (ii) 7,8-nido-dicarbaundecaborate with sulfonamidoalkyl side chains. First, the mixed acidity constants, pK_a^mix, of the sulfamidoalkyl and sulfonamidoalkyl groups of the above carboranes and their actual ionic mobilities were determined by nonlinear regression analysis of the pH dependences of their effective electrophoretic mobility measured by capillary electrophoresis in the pH range 8.00−12.25, at constant ionic strength (25 mM), and constant temperature (25°C). Second, the pK_a^mix were recalculated to the thermodynamic pK_as using the Debye–Hückel theory. The sulfamidoalkyl and sulfonamidoalkyl groups were found to be very weakly acidic with the pK_as in the range 10.78−11.45 depending on the type of carborane cluster and on the position and length of the alkyl chain on the carborane scaffold. These pK_as were in a good agreement with the pK_as (10.67−11.27) obtained by new program AnglerFish (freeware at https://echmet.natur.cuni.cz ), which provides thermodynamic pK_as and limiting ionic mobilities directly from the raw CE data. The absolute values of the limiting ionic mobilities of univalent and divalent carborane anions were in the range 18.3−27.8 TU (Tiselius unit, 1 × 10⁻⁹ m²/Vs), and 36.4−45.9 TU, respectively. The Stokes hydrodynamic radii of univalent and divalent carborane anions varied in the range 0.34−0.52 and 0.42−0.52 nm, respectively.     

Calculating the acidity constants of homologues and isomers of organic acids by means of recurrence relations

It is noted that the pK _a values of organic acids can be calculated using the unique recurrence relation pK _a(n + 1) = apK _a(n) + b from the pK _a values of other (usually the simplest and, consequently, better characterized) homologues of the same series. It is shown that this relation is valid within two taxonomic groups: insertion homologues of the ω-substituted acids X(CH₂) _n CO₂H (n ≥ 1) and isomers that differ in the position of substituents X in their alkyl fragments, k-X(C _n H_2n )CO₂H (n ≥ 1, 1 ≤ k ≤ n + 1). It is concluded that this algorithm is a consequence of the unique mathematical properties of recurrence relations.     

Localization of Hydrogen and Content of Oxonium Cations in Alunite via Neutron Diffraction

Polycrystalline alunite‐d₆ KAl₃(OD)₆(SO₄)₂, prepared by hydrothermal reaction of Al₂(SO₄)₃, K₂SO₄ and D₂SO₄, was studied by neutron powder diffraction performed on the diffractometer E2 (HMI‐BENSC, Berlin). Rietveld refinement of the data set for T = 2 K yielded the crystallographic data: space group R3m, Z = 3, trigonal setting, a = 694.3(1) pm, c = 1722.7(2) pm, N(I/σ(I) > 1) = 172, N(Var.) = 19, R_p = 0.036, wR_p = 0.046, R_B(I/σ(I) > 1) = 0.020. The deuterium nuclei could be located precisely. Three equivalent O–D bonds with nuclear distances r(O(4)–D) = 96.6(3) pm directed to each of the terminal oxygen atoms of the SO₄ groups are found. Partial substitution of K⁺ by D₃O⁺ was also considered in the refinement procedure. In good agreement with results of other methods a site occupation fraction n(D₃O⁺) = 0.0104 was obtained.     

Determination of acid dissociation constants of flavin analogues by capillary zone electrophoresis

Acid dissociation constants (pK_a) of nine kinds of flavin analogues as molecular catalyst candidates were determined by CZE. Although some of the analogues are instable and degradable under the light exposure or in alkaline aqueous solutions, the effective electrophoretic mobility of the flavin analogue of interest has been measured with the residual substance. The pK_a values of the flavin analogues were analyzed through the changes in the effective electrophoretic mobility with varying pH of the separation buffer. One or two steps pK_a values were determined by the analysis. One of the degraded species from the flavin analogues, lumichrome, was also detected in the CZE analysis, and its pK_a values were also determined. While coexisting impurities generated over the storage conditions were found in some analogues, the pK_a values of the target analogues were successfully determined with the help of the CZE separations. A pressure-assisted CZE was utilized for the determination or the estimation of the pK_a values of such analogues as possessing carboxylic acid moiety.     

Potentiometric and Voltammetric Study of 6‐Benzylaminopurine and Its Derivatives

The protonation‐deprotonation equilibrium of 6‐benzylaminopurine (6‐BAP) and its derivatives was studied by potentiometry and voltammetry. The effect of Cl‐ or OCH₃‐group in position 2′, 3′ and 4′ of the benzene ring of 6‐BAP on both pK_a values was investigated. To determine the enthalpy and entropy, the temperature dependence of pK_a was employed. It was found that with increasing temperature the pK_a decreased. In comparison with 6‐BAP the chloro‐ or methoxy‐ group resulted in pK_a increase. The first pK_a values were also determined by linear sweep (LSV) and elimination voltammetry with linear scan (EVLS). New approaches were shown not only for the determination of pK_a from voltammetric titration curves but also for the evaluation of the reduction processes of benzylaminopurines.     

Parallel vector analysis based soft resolution of spectral data from pH‐metric titration using symmetry constraint

In this study, a soft method is proposed to calculate concentration and spectral profiles for the two‐way spectral data from dissociation equilibria of polyprotic acids (H_nA). This method has four main distinct steps: (i) a fixed size moving window evolving factor analysis (FSMWEFA) was used to identify the local rank map, (ii) WFA was applied to calculate the concentration profiles of H_nA and Aⁿ⁻ (selection of the window for application of WFA was performed using EFA), (iii) PVA was used to calculate H_{n − 1}A to HA spectral profiles, and (iv) a symmetry constraint, in addition to the non‐negativity constraint, was utilized to obtain the unique concentration and spectral profiles from different acceptable sets of profiles. In the absence of any selective region in the spectral data, the proposed soft method resulted in unique solution without rotational ambiguity. This study is the first application of symmetry constraint on concentration profiles. The rotational ambiguity drastically decreased on considering the constraint of symmetry of the H_{n − 1}A and HA concentration profiles, in addition to non‐negativity of profiles. Simulated examples were used to confirm these approaches. Effect of closeness of dissociation constants on the estimated values of constants was investigated. The results showed that when the difference between pK_a values is more than 1.2, the obtained errors in the estimation of pK_a values are less than about 6.5%. The considered real data were from pH‐metric titration of fluorescein. The obtained spectral and concentration profiles and the estimated pK_a values for fluorescein were in good agreement with the previously reported data. Copyright © 2009 John Wiley & Sons, Ltd.     

Theoretical pKa calculations of proteins; the tyrosine and lysine residues of b-elicitin

Elicitins are small proteins that are secreted by plant pathogenic fungi. In this work we have used a computer program that utilizes the boundary element method for heterogeneous dielectrics with ionic strength to calculate the pK _a of all titrating groups in the 98-residue protein β-cryptogein. Our results are in reasonable agreement with the experimentally determined pK _a values for the Tyr residues in the protein. We find that the functionally important Lys13 residue has a normal pK _a of 10.3. Our work also shows that there is no direct correlation between the exposure of an amino acid sidechain and its pK _a. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 11 November 1998     

Kristallstruktur,Schwingungsspektren und Normalkoordinatenanalyse von K2[IrCl5(NH3)]

Crystal Structure, Vibrational Spectra, and Normal Coordinate Analysis of K₂[IrCl₅(NH₃)] The X-ray structure determination of K₂[IrCl₅(NH₃)] (orthorhombic, space group Pnma, a = 13.426(4), b = 10.015(2), c = 6.8717(7) Å, Z = 4) revealed the C_s point symmetry of the complex anion [IrCl₅(NH₃)]^2? (Ir? Cl = 2.337–2.365, Ir? N = 2.067(10); N? H = 0.73–0.79 Å). Using the molecular parameters the IR and Raman spectra are assigned by normal coordinate analysis. The valence force constants are f_d(NH) = 5.88, f_d(IrN) = 2.66, f_d(IrCl) = 1.68 mdyn/Å.     

Experimentation with different thermodynamic cycles used for pKa calculations on carboxylic acids using complete basis set and Gaussian‐n models combined with CPCM continuum solvation methods

Complete basis set and Gaussian‐n methods were combined with Barone and Cossi's implementation of the polarizable conductor model (CPCM) continuum solvation methods to calculate pK_a values for six carboxylic acids. Four different thermodynamic cycles were considered in this work. An experimental value of ?264.61 kcal/mol for the free energy of solvation of H⁺, ΔG_s(H⁺), was combined with a value for G_gas(H⁺) of ?6.28 kcal/mol, to calculate pK_a values with cycle 1. The complete basis set gas‐phase methods used to calculate gas‐phase free energies are very accurate, with mean unsigned errors of 0.3 kcal/mol and standard deviations of 0.4 kcal/mol. The CPCM solvation calculations used to calculate condensed‐phase free energies are slightly less accurate than the gas‐phase models, and the best method has a mean unsigned error and standard deviation of 0.4 and 0.5 kcal/mol, respectively. Thermodynamic cycles that include an explicit water in the cycle are not accurate when the free energy of solvation of a water molecule is used, but appear to become accurate when the experimental free energy of vaporization of water is used. This apparent improvement is an artifact of the standard state used in the calculation. Geometry relaxation in solution does not improve the results when using these later cycles. The use of cycle 1 and the complete basis set models combined with the CPCM solvation methods yielded pK_a values accurate to less than half a pK_a unit. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001