The potential energy landscape of noradrenaline: An electronic structure study

Torsional Potentials of Glyoxal, Oxalyl Halides, and Their Thiocarbonyl Derivatives: Challenges for Popular Density Functional Approximations

The reliability of popular density functionals was studied for the description of torsional profiles of 36 molecules: glyoxal, oxalyl halides, and their thiocarbonyl derivatives. HF and 18 functionals of varying complexity, from local density to range-separated hybrid approximations and double-hybrid, have been considered and benchmarked against CCSD(T)-level rotational profiles. For molecules containing heavy halogens, most functionals fail to reproduce barrier heights accurately and a number of functionals introduce spurious minima. Dispersion corrections show no improvement. Calibrated torsion-corrected atom-centered potentials rectify the shortcomings of PBE and also improve on σ-hole based intermolecular binding in dimers and crystals.

Structural confirmation and spectroscopic study of a biomolecule: Norepinephrine

The present work deals with the conformational and vibrational spectroscopic study of an important bio-molecule named norepinephrine in gas phase. The FTIR and FTRaman spectrum of norepinephrine in amorphous form were recorded in wavenumber range 4000-400 cm^-1 and 4000-50 cm^-1 respectively. We have investigated twenty-seven stable conformational structures of norepinephrine molecule. All the calculations have been done using Density Functional Theory with exchange functional B3LYP incorporated with the 6-31++G(d, p) basis set. The effect of hydrochloride on different bond lengths, bond angles and dihedral angles in the most stable conformer has also been studied. The total potential energy distribution for both the most stable conformer and the most stable conformer in hydrochloride was performed with the help Normal coordinate analysis method. Most of the calculated vibrational frequencies are in good agreement with the experimental frequencies. The natural bond orbital analysis was also performed to ensure the stability of electronic structures of norepinephrine. To know chemical reactivity of norepinephrine molecule we have calculated the energy gap between HOMO and LUMO orbitals and it has found above 5 eV in all the conformers.

Theoretical investigation of the conformational intricacies and thermodynamic functions of noradrenaline

Noradrenaline is a neurotransmitter that is involved in various psychological processes. In the neurotransmission process, noradrenaline binds to an adrenergic receptor by forming a complex of hydrogen bonds between its two catechol ring hydroxyl groups and the amino acid residues of adrenergic receptors. Although the two catechol ring hydroxyl groups play a crucial role in making hydrogen bonds to the binding site of the adrenergic receptor, the contribution of the catechol ring hydroxyl groups to the intramolecular stability that may affect docking has not been fully studied. To reveal the specific role that the catechol ring hydroxyl groups might play in stabilizing noradrenaline, the quantum chemical computations of geometry optimization and thermodynamic functions of N-protonated noradrenaline conformers were performed at both the B3LYP/6–31G(d,p) and G3MP2B3 levels of theory, using the Gaussian 03 program. The results were compared with those of N-protonated β-hydroxy-β-phenylethylamine, which is identical to noradrenaline except it lacks two catechol ring hydroxyl groups. For the first time, post-Hartree–Fock computations were used to obtain thermodynamic functions to establish relative stabilities of all possible conformers of N-protonated noradrenaline. In this study, 18 distinct structures of N-protonated noradrenaline were revealed, and the catechol ring hydroxyl groups were found to affect noradrenaline stability positively or negatively depending on the conformational orientations. On the basis of available experimental results, the issue that the least stable conformation of two catechol ring hydroxyl groups may be involved in the docking process has been raised. These findings may be useful in synthesis of derivatives of noradrenaline in drug design.

The effect of solvation on biomolecular conformation: 2-amino-1-phenylethanol

Small molecule neurotransmitters form one the most important classes of pharmaceutical molecules. While the behavior of these molecules in their neutral forms in the gas phase is well understood, their behavior in more biologically relevant scenarios (protonated and in aqueous solution) has received comparatively little attention. Here we address this problem by using molecular mechanics simulations to build up a detailed picture of the conformational behavior of 2-amino-1-phenylethanol, a noradrenaline analogue, in aqueous solution in both its neutral and protonated forms. For the sake of comparison, equivalent simulations are also performed on the gas-phase molecules and gas-phase hydrated clusters. These calculations reveal the important role that water has to play in determining the conformational preferences and dynamic behavior of the molecules. Water molecules are found to bridge between the various functional groups within the molecule, significantly affecting their relative stabilities in comparison to the gas-phase values. The reorganization of these solvation structures also provides a mechanism for conformational interconversion. The role of the solvent in mediating interactions between the various functional groups within the molecule suggests that in noradrenaline the catechol groups will be able to interact, albeit indirectly, with the other functional groups, thereby influencing the behavior of the molecule.

Quantum Simulation of a Hydrated Noradrenaline Analog with the Torsional Path Integral Method

An extended version of the torsional path integral Monte Carlo (TPIMC) method is presented and shown to be useful for studying the conformation of flexible molecules in solvated clusters. The new technique is applied to the hydrated clusters of the 2-amino-1-phenyl-ethanol (APE) molecule. APE + nH2O clusters with n = 0-4 are studied at 100 and 300 K using both classical and quantum simulations. Only at the lower temperature is the hydration number n found to impact the conformational distribution of the APE molecule. This is shown to be a result of the temperature-dependent balance between the internal energy and entropy contributions to the relative conformer free energies. Furthermore, at 100 K, large quantum effects are observed in the calculated conformer populations. A particularly large quantum shift of 30% of the total population is calculated for the APE + 2H2O cluster, which is explained in terms of the relative zero point energy of the lowest-energy hydrated structures for this cluster. Finally, qualitative agreement is found between the reported calculations and recent spectroscopy experiments on the hydrated clusters of APE, including an entropically driven preference for the formation of AG-type hydrated structures and the formation of a water "droplet" in the APE + 4H2O cluster.

First-principles quantum chemistry in the life sciences

The area of computational quantum chemistry, which applies the principles of quantum mechanics to molecular and condensed systems, has developed drastically over the last decades, due to both increased computer power and the efficient implementation of quantum chemical methods in readily available computer programs. Because of this, accurate computational techniques can now be applied to much larger systems than before, bringing the area of biochemistry within the scope of electronic-structure quantum chemical methods. The rapid pace of progress of quantum chemistry makes it a very exciting research field; calculations that are too computationally expensive today may be feasible in a few months' time! This article reviews the current application of 'first-principles' quantum chemistry in biochemical and life sciences research, and discusses its future potential. The current capability of first-principles quantum chemistry is illustrated in a brief examination of computational studies on neurotransmitters, helical peptides, and DNA complexes.