Conformers of Gaseous Serine

Abstract

The myriad conformers of the neutral form of natural amino acid serine (Ser) have been investigated by systematic computations with reliable electronic wave function methods. A total of 85 unique conformers were located using the MP2/cc-pVTZ level of theory. The 12 lowest-energy conformers of serine fall within a 8 kJ mol(-1) window, and for these species, geometric structures, precise relative energies, equilibrium and vibrationally averaged rotational constants, anharmonic vibrational frequencies, infrared intensities, quartic and sextic centrifugal distortion constants, dipole moments, and (14)N nuclear quadrupole coupling constants were computed. The relative energies were refined through composite focal-point analyses employing basis sets as large as aug-cc-pV5Z and correlation treatments through CCSD(T). The rotational constants for seven conformers measured by Fourier-transform microwave spectroscopy are in good agreement with the vibrationally averaged rotational constants computed in this study. Our anharmonic vibrational frequencies are compared to the large number of experimental vibrational absorptions attributable to at least six conformers.

The effect of surfactants on hydrate particle agglomeration in liquid hydrocarbon continuous systems: a molecular dynamics simulation study

“…5d) in the water phase using the integral equation formalism variant (IEFPCM). 50 It was known that both cis-COOH and trans-COOH belong to the ensemble of possible conformations, 59 but analysis of the energies revealed that the ciscarboxyl was intrinsically more favourable than the transcarboxyl by approximately 3.1 kcal mol À1 , with a barrier of 10.9 kcal mol À1 (Fig. 5d).…”

Quantum chemical study of hydrogen-bonded complexes of serine with water and $$\hbox {H}_{2}\hbox {O}_{2}$$ H 2 O 2

“…In the present study, we have selected the four lowest energy serine conformers labeled as I, II, III and IV ( Figure 1) out of 85 conformers reported in literature. 1 Conformer I possess a trans-COOH, allowing a strong intra-molecular HB (N • • • H-O) to be formed between the hydroxyl (O-H) group of the carboxylic moiety and non-bonding electron pair at the nitrogen atom. Also, a weaker intra-molecular HB (N-H • • • O) is established between one of the amino H atoms and the 'O' atom of the side chain -CH 2 OH.…”

“…It is a component of brain proteins, nerve sheaths and is important in the formation of cell membranes. Over the past few years, the conformational behaviour of serine has been the subject of many theoretical [1][2][3][4][5][6][7][8][9][10][11] as well as experimental studies. [5][6][7][8][9][10][11] The hydrogen bond (HB) is an extremely important molecular interaction as it is inherently present in many biological systems and plays a crucial role in a number of biochemical reactions.…”

autodE: Automated Calculation of Reaction Energy Profiles – Application to Organic and Organometallic Reactions

“…For example, CREST generated 90 conformers for serine for which 85 were found in ref. 1 while CONFAB did not identify the correct rotatable bonds and afforded only 36 conformers. Figure S3.…”

“…Automating the search for new chemical reactions is seen as one of the 'grand challenges' in computational chemistry. 1,2 Discovering such thermodynamically and kinetically accessible reactions requires knowledge of the underlying potential energy surface (PES), which to a first approximation, involves the characterization of reactants, products, intermediates, and transition states (TSs). [3][4][5] While this has been routine for computational chemists for decades, locating TSs remains time consuming and a highly non-systematic endeavour.…”