Rotational–vibrational resonance states

2020 ◽  
Vol 22 (27) ◽  
pp. 15081-15104 ◽  
Author(s):  
Attila G. Császár ◽  
Irén Simkó ◽  
Tamás Szidarovszky ◽  
Gerrit C. Groenenboom ◽  
Tijs Karman ◽  
...  
Keyword(s):  
First Principles ◽  
Quantum Chemical ◽  
Vibrational Resonance ◽  
Resonance States ◽  
Molecular Systems ◽  
Chemical Techniques

All molecular systems possess a significant number of rovibrational resonance states accessible via spectroscopic and scattering experiments, which can also be computed and rationalized by a variety of first-principles quantum-chemical techniques.

Computationally Augmented Retrosynthesis: Total Synthesis of Paspaline A and Emindole PB

2018 ◽  
Author(s):  
Timothy Newhouse ◽  
Daria E. Kim ◽  
Joshua E. Zweig
Keyword(s):  
Chemical Synthesis ◽  
Total Synthesis ◽  
Small Molecules ◽  
First Principles ◽  
Quantum Chemical ◽  
Computational Analysis ◽  
Empirical Evaluation ◽  
Synthetic Strategy ◽  
Catalyzed Reactions ◽  
Enzyme Catalyzed Reactions

The diverse molecular architectures of terpene natural products are assembled by exquisite enzyme-catalyzed reactions. Successful recapitulation of these transformations using chemical synthesis is hard to predict from first principles and therefore challenging to execute. A means of evaluating the feasibility of such chemical reactions would greatly enable the development of concise syntheses of complex small molecules. Herein, we report the computational analysis of the energetic favorability of a key bio-inspired transformation, which we use to inform our synthetic strategy. This approach was applied to synthesize two constituents of the historically challenging indole diterpenoid class, resulting in a concise route to (–)-paspaline A in 9 steps from commercially available materials and the first pathway to and structural confirmation of emindole PB in 13 steps. This work highlights how traditional retrosynthetic design can be augmented with quantum chemical calculations to reveal energetically feasible synthetic disconnections, minimizing time-consuming and expensive empirical evaluation.

scholarly journals Computational Methods for Ab Initio Molecular Dynamics

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Eric Paquet ◽  
Herna L. Viktor
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
First Principles ◽  
Density Functional ◽  
Path Integrals ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Computational Perspective

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

scholarly journals Квантово-химическое моделирование эндофуллеренов металлов подгруппы скандия

2020 ◽  
Vol 22 (3) ◽  
pp. 360-372
Author(s):  
Дмитрий Александрович Мачнев ◽  
Игорь Владимирович Нечаев ◽  
Александр Викторович Введенский ◽  
Олег Александрович Козадеров
Keyword(s):  
Gas Phase ◽  
Quantum Chemical ◽  
Chem Phys ◽  
Program System ◽  
Separation Processes ◽  
Molecular Systems ◽  
De Vries ◽  
Free Molecules ◽  
New Form ◽  
Buckminsterfullerene C60

Эндофуллерены, содержащие один или несколько атомов металла внутри углеродного каркаса (металлофуллерены), представляют большой практический интерес в связи с возможностью создания на их основе эффективных контрастирующих агентов для магнитно-резонансной томографии (МРТ), антиоксидантных и противораковых средств. Данные соединения могут быть также использованы в спинтронике для создания наноразмерных электронных устройств. В настоящей работе в рамках теории функционала плотности произведен расчет структурных, электронных и термодинамических характеристик эндофуллеренов металлов подгруппы скандия с числом инкапсулированных атомов от одного до семи в газовой фазе. Описаны стабильные структуры с симметриямиCs, C2, C3 и Ci, соответствующие позициям, занимаемым атомами металла внутри каркаса фуллерена. Установлен теоретический предел числа атомов металла, при котором структура эндофуллерена сохраняет устойчивость – шесть атомов для скандия, четыре для иттрия и три для лантана. Расчет показывает, что наиболее устойчивыми являются структуры с двумя и тремя инкапсулированными атомами. Описана зависимость между числом инкапсулированных атомов металла и характером распределения электронной плотности. Общий заряд на инкапсулированном металлическом кластере положителен для соединений Me@C60 – Me3@C60, слабо положителен для Me4@C60(отдельные атомы имеют отрицательный заряд) и отрицателен для соединений Me5C60 – Me6@C60. Описан эффект спиновой утечки для структур с основным дублетным спиновым состоянием. Для соединений с тремя и более инкапсулированными атомами данный эффект незначителен, что указывает на нецелесообразность создания контрастирующих агентов для МРТ на их основе.         ЛИТЕРАТУРА 1. Kroto H. W., Heath J. R., O’Brien S. C., Curl R. F., Smalley R. E. C60: Buckminsterfullerene. Nature.1985;318(6042): 162–163. DOI: https://doi.org/10.1038/318162a02. Kratschmer W., Lamb L. D., Fostiropoulos K., Huffman D. R. Solid C60: a new form of carbon. Nature.1990;347(6291): 354–358. DOI: https://doi.org/10.1038/347354a03. Buchachenko A. L. Compressed atoms. J. Phys. Chem. B. 2001;105(25): 5839–5846. DOI: https://doi.org/10.1021/jp003852u4. Koltover V. K., Bubnov V. P., Estrin Y. I., Lodygina V. P., Davydov R. M., Subramoni M., Manoharan P. T.Spin-transfer complexesofendohedralmetallofullerenes: ENDOR and NMR evidences. Phys. Chem. Chem. Phys. 2003;5(13): 2774–2777. DOI:https://doi.org/10.1039/b302917d5. Raebiger J. W., Bolskar R. D. Improved production and separation processes for gadoliniummetallofullerenes. J. Phys. Chem. C. 2008;112(17): 6605–6612. DOI:  https://doi.org/10.1021/jp076437b6. Gaussian 09, Revision D.01. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb,J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. Marenich, J. Bloino,B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski,J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida,T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven,K. Throssell, J. A. Montgomery, Jr., J. E. Peralta,F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi,J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene,C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox,Gaussian, Inc., Wallingford CT, 2016. Available at: http://gaussian.com/g09citation7. Neese F. The ORCA program system. WIREs Computational Molecular Science. 2012;2(1): 73–78.DOI: https://doi.org/10.1002/wcms.818. Laikov D. N., Ustynyuk Y. A. PRIRODA-04: a quantum-chemical program suite. New possibilitiesin the study of molecular systems with the application of parallel computing. Russian Chemical Bulletin.2005;54(3): 820–826. DOI: https://doi.org/10.1007/s11172-005-0329-x9. Chandrasekharaiah M. S., Gingerich K. A. Chapter 86 Thermodynamic properties of gaseousspecies. In: Handbook on the Physics and Chemistry of Rare Earths. 1989;12: 409–431. DOI: https://doi.org/10.1016/s0168-1273(89)12010-810. Kohl F. J., Stearns C. A. Vaporization thermodynamics of yttrium dicarbide–carbon systemand dissociation energy of yttrium dicarbide and tetracarbide. J. Chem. Phys., 1970;52(12): 6310–6315.DOI: https://doi.org/10.1063/1.167294211. Gingerich K. A., Nappi B. N., Pelino M., Haque R. Stability of complex dilanthanum carbide molecules.Inorganica Chimica Acta. 1981;54: L141–L142. DOI: https://doi.org/10.1016/s0020-1693(00)95414-812. Hedberg K., Hedberg L., Bethune D. S., Brown C. A., Dorn H. C., Johnson R. D., de Vries M. S.Bond lengths in free molecules of buckminsterfullerene, C60, from gas-phase electron diffraction.Science. 1991;254(5030): 410–412. DOI: https://doi.org/10.1126/science.254.5030.41013. Bethune D. S., Meijer G., Tang W. C., Rosen H. J., Golden W. G., Seki H., Brown C. F., de Vries M. S.Vibrational Raman and infrared spectra of chromatographically separated C60 and C70 fullereneclusters Chem. Phys. Lett., 1991; 179(1–2): 181–186.DOI: https://doi.org/10.1016/0009-2614(91)90312-w14. Эмсли Дж. Элементы. М.: Мир; 1993. 256 c.15. Раков Э. Г. Нанотрубки и фуллерены. Учебн. пособие. М.: Логос; 2006. 376 с.16. Елецкий А. В., Смирнов В. М. Фуллерены. Успехи физических наук.1993;2: 33–60. Режим доступа: https://ufn.ru/ru/articles/1993/2/b/

3D Structural Bioinformatics of Proteins and Antibodies: State of the Art Perspectives and Challenges

2013 ◽  
Vol 2 (3) ◽  
pp. 67-74
Author(s):  
Arianna Filntisi ◽  
Dimitrios Vlachakis ◽  
George Matsopoulos ◽  
Sophia Kossida
Keyword(s):  
Quantum Mechanics ◽  
Quantum Chemical ◽  
State Of The Art ◽  
Three Dimensional ◽  
Research Field ◽  
Important Class ◽  
Structural Components ◽  
Molecular Systems ◽  
Mechanical Methods ◽  
Harmful Substances

Proteins are an important class of biochemical molecules, as the structural components of animal and human tissue are based on them. Antibodies are proteins that play a crucial role in the preservation of life since they are produced by the body's immune system as a response to harmful substances. The modelling of proteins and antibodies in particular is a vibrant research field which facilitates the design of drugs, a process otherwise demanding in terms of time and resources. A variety of computational methods and tools are being developed towards that goal, among which are hybrid quantum chemical/molecular mechanical methods and three-dimensional antibody modelling. In this review the authors discuss the knowledge concerning proteins and antibodies, as well as the use of quantum mechanics in the simulation of molecular systems and the three-dimensional antibody modelling.

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