Molecular properties of p-(dimethylamino)benzaldehyde bound to liver alcohol dehydrogenase: a Raman spectroscopic study

Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde

The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34°C and decomposes at temperatures higher than 193°C.

Hydration of acetone in the gas phase and in water solvent

In water solvent, the hydration of acetone proceeds by a cyclic (cooperative) process in which concurrent C–O bond formation and proton transfer to oxygen take place through a solvent and (or) catalyst bridge. Reactivity is determined primarily by the concentration of a reactant complex and not the barrier from this complex. This situation is reversed in the gas phase; although the concentrations of reactive complexes are much higher than in solution, the barriers are also higher and dominant in determining reactivity. Calculations of isotope effects suggest that multiple hydron transfers are synchronous in the gas phase to avoid zwitterionic transition states. In solution, such transition states are stabilized by solvation and hydron transfers can be asynchronous.

Absorption, fluorescence studies and ab initio calculations on binary mixture of p-dimethylaminobenzaldehyde

Absorption as well as fluorescence emission studies of p-dimethylaminobenzaldehyde (DMABA) in solvents with different polarity have been reported by varying the concentration of the solute. Dual fluorescence corresponding to the non-polar (NP) and twisted intramolecular charge transfer (TICT) states has been observed. The optimized geometry of DMABA was evaluated using ab-initio theory at various levels. The optimized geometries of the hydrogen bonded complexes with the solvent molecules were also calculated with the theory Hartree Fock at the basis set 6-31+G (HF/6-31+G). The results have been used to understand the structure of the molecule and the spectral changes in terms of hydrogen bonding and solute-solvent interaction.

Vibrational spectra and normal coordinate analysis of 4-(dimethylamino)benzaldehyde and selected isotopic derivatives

Results of a normal coordinate analysis based on infrared and Raman spectra of six isotopic forms of 4-(dimethylamino)benzaldehyde are reported (DABA, DABA-CDO, DABA-13CDO, DABA-13CHO, DABA-CHO18O, and DABA-3,5-D). Cs point group symmetry has been applied and all motions except the internal rotations of the dimethylamino and the two methyl groups have been used to generate symmetry coordinates. The potential energy distributions have lead to revision and extension of previous assignments. The force field and the forms of the normal modes are in excellent agreement with those reported for similar molecules.

Details of the acyl-enzyme intermediate and the oxyanion hole in serine protease catalysis

Raman, absorbance, and kinetic measurements were used to determine how the serine protease active site feature known as the oxyanion hole interacts with an acyl-enzyme intermediate. The substrate, p-(dimethylamino)benzoylimidazolide (DAB-Im), was synthesized and used to prepare DAB-acyl-enzymes of wild-type (WT) and N155G subtilisin-BPN' (the N155G mutant lacks a fully functioning oxyanion hole), alpha-chymotrypsin (CHT), and bovine trypsin (TRY). DAB-acyl-enzyme deacylation rate constants, k3, were found to span a 720-fold range at pH 7.8 (DAB-WT > DAB-TRY > DAB-N155G > DAB-CHT). DAB-N155G was found to deacylate 80-fold slower than DAB-WT, indicating a 2.6 kcal/mol loss of transition-state binding energy due to this mutation. Absorbance spectra revealed strongly red-shifted absorbance lambda max values for all of the DAB-acyl-enzymes. The red shift was found to be 2.0 nm less in DAB-N155G, indicating that the oxyanion hole is partially responsible for this electronic perturbation of the DAB chromophore at the active site. Raman difference spectra of the DAB-acyl-enzymes measured at pH 5.0 and 8.6, with 18O-labeling of the carbonyl, show that the molecular motions most perturbed by the active site are three associated with the scissile acyl bond. Most interesting is the carbonyl stretching vibration, v(C = O), whose motion extends into the hydrolytic reaction coordinate. Comparison of the v(C = O) of DAB-WT and DAB-N155G reveals that the oxyanion hole does indeed form a hydrogen-bonding interaction with the carbonyl oxygen, the strength of which increases at pH 8.6. Interestingly, the DAB-TRY carbonyl forms very strong hydrogen bonds, even at pH 5.0, but DAB-CHT does not, even at pH 8.6. The low-frequency (1661 cm-1) v(C = O)'s of pH 5.0 DAB-TRY and pH 8.6 DAB-WT are proposed to correspond to a tetrahedrally distorted carbonyl center like that observed in the crystal structure of guanidinobenzoyl-TRY (Mangel et al., 1990). The strength of hydrogen bonding between the DAB-acyl-enzyme's carbonyl and the oxyanion hole, as gauged by the v(C = O) frequency, was found to correlate positively with an increased deacylation rate. This correlation, as well as calculated acyl-enzyme carbonyl bond lengths, which indicate a 0.015-A lengthening due to the oxyanion hole interaction, was found to be in good agreement with previously published resonance Raman data of alpha, beta-unsaturated arylacryloyl-acyl-enzymes (Tonge & Carey, 1990b, 1992).

Length of the acyl carbonyl bond in acyl-serine proteases correlates with reactivity

Resonance Raman (RR) spectroscopy has been used to obtain the vibrational spectrum of the acyl carbonyl group in a series of acylchymotrypsins and acylsubtilisins at the pH of optimum hydrolysis. The acyl-enzymes, which utilize arylacryloyl acyl groups, include three oxyanion hole mutants of subtilisin BPN', Asn155Leu, Asn155Gln, and Asn155Arg, and encompass a 500-fold range of deacylation rate constants. For each acyl-enzyme a RR carbonyl band has been identified which arises from a population of carbonyl groups undergoing nucleophilic attack in the active site. As the deacylation rate (k3) increases through the series of acyl-enzymes, the carbonyl stretching band (vC = O) is observed to shift to lower frequency, indicating an increase in single bond character of the reactive acyl carbonyl group. Experiments involving the oxyanion hole mutants of subtilisin BPN' indicate that a shift of vC = O to lower frequency results from stronger hydrogen bonding of the acyl carbonyl group in the oxyanion hole. A plot of log k3 against vC = O is linear over the range investigated, demonstrating that the changes in vC = O correlate with the free energy of activation for the deacylation reaction. By use of an empirical correlation between carbonyl frequency (vC = O) and carbonyl bond length (rC = O) it is estimated that rC = O increases by 0.015 A as the deacylation rate increases 500-fold through the series of acyl-enzymes. This change in rC = O is about 7% of that expected for going from a formal C = O double bond in the acyl-enzyme to a formal C-O single bond in the tetrahedral intermediate for deacylation. The data also allow us to estimate the energy needed to extend the acyl carbonyl group along its axis to be 950 kJ mol-1 A-1.

Molecular properties of pyruvate bound to lactate dehydrogenase: a Raman spectroscopic study

Lactate dehydrogenase (LDH; EC 1.1.1.27) catalyzes the addition of pyruvate to the four position of the nicotinamide ring of bound NAD+; this NAD-pyruvate adduct is bound tightly to the enzyme. We have used the adduct as a model for pyruvate in a competent ternary complex by comparing the Raman spectrum of the bound adduct with that for unliganded pyruvate. To understand the observed normal modes of pyruvate both as the bound adduct and in water, we have taken the Raman spectra of a series of 13C- and 18O-labeled pyruvates. We find that the carboxylate COO- moiety of pyruvate remains unprotonated at LDH's active site and forms an ion pair complex. The frequency of pyruvate's carbonyl C = O moiety shifts from 1710 cm-1 in water downward 34 cm-1 when pyruvate binds to LDH. This frequency shift corresponds to a ca. 34% polarization of the carbonyl bond, indicates a substantial interaction between the C = O group and enzyme, and is direct evidence for and is a measure of enzyme-induced electronic perturbation of the substrate needed for catalysis. This bond polarization is likely brought about by electrostatic interactions between the carbonyl moiety and the protonated imidazole group of His-195 and the guanidino group from Arg-109. We discuss how the data bear on the enzymatic chemistry of LDH.