Literature DB >> 12720320

A flexible nudged elastic band program for optimization of minimum energy pathways using ab initio electronic structure methods.

Dominic R Alfonso1, Kenneth D Jordan.   

Abstract

A driver program for carrying out nudged elastic band optimizations of minimum energy reaction pathways is described. This approach allows for the determination of minimum energy pathways using only energies and gradient information. The driver code has been interfaced with the GAUSSIAN 98 program. Applications to two isomerization reactions and to a cluster model for H(2) desorption from the Si(100)-2 x 1 surface are presented. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 990-996, 2003

Entities:  

Year:  2003        PMID: 12720320     DOI: 10.1002/jcc.10233

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  9 in total

1.  Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change.

Authors:  Keith P Van Nostrand; Scott D Kennedy; Douglas H Turner; David H Mathews
Journal:  J Chem Theory Comput       Date:  2011-11-08       Impact factor: 6.006

2.  An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods.

Authors:  Kamila Réblová; Zora Střelcová; Petr Kulhánek; Ivana Beššeová; David H Mathews; Keith Van Nostrand; Ilyas Yildirim; Douglas H Turner; Jiří Sponer
Journal:  J Chem Theory Comput       Date:  2010-01-01       Impact factor: 6.006

3.  Synthesis and Hydrolysis of Atmospherically Relevant Monoterpene-Derived Organic Nitrates.

Authors:  Yuchen Wang; Ivan R Piletic; Masayuki Takeuchi; Tianchang Xu; Stefan France; Nga Lee Ng
Journal:  Environ Sci Technol       Date:  2021-10-20       Impact factor: 9.028

4.  Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints.

Authors:  Peng Tao; Milan Hodošček; Joseph D Larkin; Yihan Shao; Bernard R Brooks
Journal:  J Chem Theory Comput       Date:  2012-09-27       Impact factor: 6.006

5.  Epoxide as a precursor to secondary organic aerosol formation from isoprene photooxidation in the presence of nitrogen oxides.

Authors:  Ying-Hsuan Lin; Haofei Zhang; Havala O T Pye; Zhenfa Zhang; Wendy J Marth; Sarah Park; Maiko Arashiro; Tianqu Cui; Sri Hapsari Budisulistiorini; Kenneth G Sexton; William Vizuete; Ying Xie; Deborah J Luecken; Ivan R Piletic; Edward O Edney; Libero J Bartolotti; Avram Gold; Jason D Surratt
Journal:  Proc Natl Acad Sci U S A       Date:  2013-04-03       Impact factor: 11.205

6.  Barrierless Reactions with Loose Transition States Govern the Yields and Lifetimes of Organic Nitrates Derived from Isoprene.

Authors:  Ivan R Piletic; Edward O Edney; Libero J Bartolotti
Journal:  J Phys Chem A       Date:  2017-10-20       Impact factor: 2.781

7.  Decarboxylative and dehydrative coupling of dienoic acids and pentadienyl alcohols to form 1,3,6,8-tetraenes.

Authors:  Ghina'a I Abu Deiab; Mohammed H Al-Huniti; I F Dempsey Hyatt; Emma E Nagy; Kristen E Gettys; Sommayah S Sayed; Christine M Joliat; Paige E Daniel; Rupa M Vummalaneni; Andrew T Morehead; Andrew L Sargent; Mitchell P Croatt
Journal:  Beilstein J Org Chem       Date:  2017-02-28       Impact factor: 2.883

8.  The influence of hydrogen concentration in amorphous carbon films on mechanical properties and fluorine penetration: a density functional theory and ab initio molecular dynamics study.

Authors:  Hwanyeol Park; Daekwang Woo; Jong Myeong Lee; Se Jun Park; Sungwoo Lee; Ho Jun Kim; Euijoon Yoon; Gun-Do Lee
Journal:  RSC Adv       Date:  2020-02-13       Impact factor: 4.036

9.  First principles investigation on energetics, structure, and mechanical properties of amorphous carbon films doped with B, N, and Cl.

Authors:  Hwanyeol Park; Daekwang Woo; Jong Myeong Lee; Se Jun Park; Sungwoo Lee; Ho Jun Kim; Euijoon Yoon; Gun-Do Lee
Journal:  Sci Rep       Date:  2019-12-12       Impact factor: 4.379

  9 in total

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