Chiral effects on helicity studied via the energy landscape of short (<scp>d, l</scp>)-alanine peptides

Neelamraju, Sridhar; Oakley, Mark T.; Johnston, Roy L.

doi:10.1063/1.4933428

Cited by 8 publications

(19 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Additionally, theoretical and experimental analysis of photoelectron spectra demonstrated chemically distinct behaviour between diglycine and GLY adsorbed on Cu{110}, 24,94 which justifies our focus on a single adlayer. Moreover, the formation of a peptide bond between GLY molecules would involve a substantially higher barrier than for self-assembly, similar to what has been found in studies of adenine, 95 serine, 96 and ALA. 97,98 Because the moves from one minimum to another are independent, and the energy minima are uncorrelated, the sum of rates…”

Section: General Methodologymentioning

confidence: 99%

Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}

Rommel

Wales

2017

J. Phys. Chem. C

View full text Add to dashboard Cite

Nanofabrication and the growth of self-assembled monolayers (SAM) of organic molecules are increasingly important in various industries, including microelectronics and health care. Glycine adsorbed on Cu{110} provides a good model with a rich phenomenological space to explore and understand the self-assembly of more complex amino acids. We focus on (a) the dynamics exhibited by glycine molecules already adsorbed on Cu{110} when diffusing on the metal surface, and (b) the chemical kinetics of how these molecules form clusters, networks, and islands. The stochastic discrete event algorithm we employ can be viewed as a multiscale approach, based on density functional energies and transition barriers. The method covers from the femtosecond timescale of molecular rotations to the microsecond range of molecular self-assembly. Hydrogen-bonds and van der Waals forces play a crucial role in pattern formation. Investigations of chemical kinetics show that enantiopure, homochiral islands are an intermediate step during the formation process of larger stable racemic, heterochiral islands, especially when two islands merge. At lower temperature, defects stabilise mainly homochiral clusters, and prevent the molecules from synchronising their footprint orientation, in contrast to higher temperature. On the way we solve the long standing puzzle of how the pseudo-centered (3×2) enantiopure clusters can have glide plane symmetry. We end with a comparison to similar amino acids, such as alanine and proline. The results provide insight into mechanisms for fine-tuning the self-organisation of organic molecules on metal surfaces.

show abstract

Section: General Methodologymentioning

confidence: 99%

Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}

Rommel

Wales

2017

J. Phys. Chem. C

View full text Add to dashboard Cite

show abstract

“…Other methods suitable for biomolecules, in vacuum or on surfaces, are e.g. the recently proposed so-called threshold-minimization algorithm for the investigation of flexible molecules [153], and a variety of genetic or evolutionary algorithms [154][155][156], and numerous hybrid approaches combining elements of several methods.…”

Section: Exploration and Simulation Methodsmentioning

confidence: 99%

“…The [152,155,184], where the latter one was often modeled as an effective medium [188]. For small systems like e.g.…”

Section: Structure Predictionmentioning

confidence: 99%

Prediction and clarification of structures of (bio)molecules on surfaces

Schön

Oligschleger

Cortés³

2016

Zeitschrift Für Naturforschung B

View full text Add to dashboard Cite

The design of future materials for biotechnological applications via deposition of molecules on surfaces will require not only exquisite control of the deposition procedure, but of equal importance will be our ability to predict the shapes and stability of individual molecules on various surfaces. Furthermore, one will need to be able to predict the structure patterns generated during the self-organization of whole layers of (bio)molecules on the surface. In this review, we present an overview over the current state of the art regarding the prediction and clarification of structures of biomolecules on surfaces using theoretical and computational methods.

show abstract

“…46,47 Thus, one way to better understand structural changes that occur in cyclic peptides as a function of amino-acid substitutions is to predict stable isomers of various combinations of amino acids in various solvents and establish structure-property relationships. 46,48 Furthermore, cyclic peptides are interesting test systems for landscape exploration methods, because their isomerism is well understood through experiment [49][50][51] and theory. 2,46,52 The cyclic tetraglycine system, cyclo-[Gly] 4 , was chosen for two main reasons.…”

Section: Energy Landscape Of Cyclo-[gly]mentioning

confidence: 99%

A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide

Neelamraju

Johnston

Schön

2016

J. Chem. Theory Comput.

Self Cite

View full text Add to dashboard Cite

We present a scheme, called the threshold-minimization method, for globally exploring the energy landscapes of small systems of biomolecular interest where typical exploration moves always require a certain degree of subsequent structural relaxation in order to be efficient, e.g., systems containing small or large circular carbon chains such as cyclic peptides or carbohydrates. We show that using this threshold-minimization method we can not only reproduce the global minimum and relevant local minima but also overcome energetic barriers associated with different types of isomerism for the example of a cyclic peptide, cyclo-(Gly)4. We then apply the new method to the disaccharide α-d-glucopyranose-1-2-β-d-fructofuranose, report energetically preferred configurations and barriers to boat-chair isomerization in the glucopyranosyl ring, and discuss the energy landscape.

show abstract

Chiral effects on helicity studied via the energy landscape of short (d, l)-alanine peptides

Cited by 8 publications

References 54 publications

Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}

Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}

Prediction and clarification of structures of (bio)molecules on surfaces

A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide

Contact Info

Product

Resources

About