Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field
Literature Information
Florian Thaunay, Jean-Pierre Dognon, Gilles Ohanessian, Carine Clavaguéra
The calculation of infrared spectra by molecular dynamics simulations based on the AMOEBA polarizable force field has recently been demonstrated [Semrouni et al., J. Chem. Theory Comput., 2014, 10, 3190]. While this approach allows access to temperature and anharmonicity effects, band assignment requires additional tools, which we describe in this paper. The Driven Molecular Dynamics approach, originally developed by Bowman, Kaledin et al. [Bowman et al. J. Chem. Phys., 2003, 119, 646, Kaledin et al. J. Chem. Phys., 2004, 121, 5646] has been adapted and associated with AMOEBA. Its advantages and limitations are described. The IR spectrum of the Ac-Phe-Ala-NH2 model peptide is analyzed in detail. In addition to differentiation of conformations by reproducing frequency shifts due to non-covalent interactions, DMD allows visualizing the temperature-dependent vibrational modes.
Recommended Journals

Nature

Journal of Catalysis

Kinetics and Catalysis

Pure and Applied Chemistry

European Journal of Wood and Wood Products

Journal of Organometallic Chemistry

Science Progress

Organic Preparations and Procedures International

Proceedings of the National Academy of Sciences of the United States of America

Israel Journal of Chemistry
Related Literature
Pd/P/dba-Promoted cascade annulations to produce fused medium-sized sulfoximine polyheterocycles
Xiaoyan Chen, Hao Zhou, Zhiyuan Chen
DOI: 10.1039/C9QO00880B
Regio- and stereo-selective decarbonylative alkylative arylation of terminal alkynes with aliphatic aldehydes and arenes via dual C–H bond functionalization
Yong Peng, Ting-Ting Qin, Cong-Ling Xu, Luo Yang
DOI: 10.1039/C9QO01009B
Access to polyfunctionalized carbazoles through π-extension of 2-methyl-3-oxoacetate indoles
Yingying Guo, Zhoulu Wang, Ying Zhu, Qiaochu Zhang, Donghui Wei, Xiang Liu, Zhenqian Fu
DOI: 10.1039/C9QO01093A
C(sp3)–H hydroxylation of fluorenes, oxindoles and benzofuranones with a Mg(NO3)2–HP(O)Ph2 oxidation system
Chen Hu, Gang Hong, Pradip D. Nahide, Yuchen He, Chen Zhou, Marisa C. Kozlowski, Limin Wang
DOI: 10.1039/C9QO00778D
Commiphorines A and B, unprecedented sesquiterpenoid dimers from Resina Commiphora with striking activities on anti-inflammation and lipogenesis inhibition
Da-Peng Qin, Qian-Qian Di, Ying Liu, Wei-Lin Chen, Shu-Mei Wang, Yong-Xian Cheng
DOI: 10.1039/C9QO01046G
Optimization of the synthesis of quinoline-based neutral cyclometalated iridium complexes via microwave irradiation: design of light harvesting and emitting complexes using bulky quinolines
Carlos A. Echeverry-Gonzalez, Carlos E. Puerto-Galvis, Carlos H. Borca, Martín A. Mosquera, Andrés F. Luis-Robles, Vladimir V. Kouznetsov
DOI: 10.1039/C9QO00870E
Synthesis of silacyclopent-2-en-4-ols via intramolecular [2 + 2] photocycloaddition of benzoyl(allyl)silanes
Arto Valkonen, Carlos A. M. Afonso, Nuno R. Candeias
DOI: 10.1039/C9QO01028A
1,3-Dipolar cycloaddition of nitrones to oxa(aza)bicyclic alkenes
Yongqi Yao, Wen Yang, Qifu Lin, Weitao Yang, Huanyong Li, Lin Wang, Fenglong Gu, Dingqiao Yang
DOI: 10.1039/C9QO00660E
You might also like
Is 6-(3-Fluorophenyl)picolinic acid (CAS: 887982-40-3) safe?
6-(3-Fluorophenyl)picolinic acid is generally considered safe for laboratory use...
What industries use (3R)-3-Pyrrolidinol (CAS: 2799-21-5)?
(3R)-3-Pyrrolidinol is used in the pharmaceutical industry as a precursor for dr...
What precautions should be taken when handling (4R,5R)-4,5-Diethoxycarbonyl-2,2-dimethyldioxolane (CAS: 59779-75-8)?
When handling (4R,5R)-4,5-Diethoxycarbonyl-2,2-dimethyldioxolane (CAS: 59779-75-...
How is 1-(6-Chloroimidazo[1,2-b]pyridazin-3-yl)ethanone (CAS: 90734-71-7) typically synthesized?
1-(6-Chloroimidazo[1,2-b]pyridazin-3-yl)ethanone is often synthesized via a mult...
What is the market or research trend for N-Ethyl-3,4-dimethylbenzylamine (CAS: 39180-83-1)?
The market for N-Ethyl-3,4-dimethylbenzylamine (CAS: 39180-83-1) remains steady,...
What is Tert-butyl 3-(pyrrolidin-1-yl)azetidine-1-carboxylate (CAS: 1019008-21-9)?
Tert-butyl 3-(pyrrolidin-1-yl)azetidine-1-carboxylate is a chemical compound wit...
What regulatory guidelines apply to 1-Bromo-3-chloro-2,4-dimethoxybenzene (CAS: 1228956-93-1)?
1-Bromo-3-chloro-2,4-dimethoxybenzene (CAS: 1228956-93-1) falls under the classi...
Is 8-Bromo-2-methyl-3,4-dihydroisoquinolin-1(2H)-one (CAS: 1368622-07-4) safe?
The safety of 8-Bromo-2-methyl-3,4-dihydroisoquinolin-1(2H)-one (CAS: 1368622-07...
Is Benzyl [(3S)-2,6-dioxo-3-piperidinyl]carbamate (CAS: 22785-43-9) safe?
Benzyl [(3S)-2,6-dioxo-3-piperidinyl]carbamate is generally safe when handled wi...
How should 1-{[4-(4,4,5,5-Tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]sulfonyl}pyrrolidine (CAS: 928657-21-0) be stored?
1-{[4-(4,4,5,5-Tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl]sulfonyl}pyrrolidine s...
Source Journal
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.

![3-[(3R,4R)-3-[(6-aminopyrimidin-4-yl)-methyl-amino]-4-methyl-1-piperidyl]-3-oxo-propanenitrile structure 3-[(3R,4R)-3-[(6-aminopyrimidin-4-yl)-methyl-amino]-4-methyl-1-piperidyl]-3-oxo-propanenitrile structure](https://static.chemtradehub.com/structs/164/1640971-60-3-83a4.webp)


