Calculating vibrational frequencies of amides: From formamide to concanavalin A
Literature Information
Tim M. Watson, Jonathan D. Hirst
The infrared (IR) is an information rich region of molecular spectra. From characteristic absorptions it is possible to determine much structural information about molecules. This has been used to a large degree in the study of protein structure as a complementary technique to circular dichroism, X-ray crystallography and NMR. However, the current understanding of protein IR spectra is predicated largely on empirical structure–spectra relationships that are not infallible. Providing a theoretical basis for protein spectra will help to reduce these problems. In this paper, we review our recent work on accurate and computationally efficient small molecule gas phase calculations and examine how point charge environments can mimic features of proteins. We then develop a general automated strategy for applying the transition dipole coupling method for computing the IR spectra of proteins. Finally, we study the effect of conformational dynamics on the amide I band of concanavalin A.
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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.











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