Required citations
******************


General references
==================

When you publish results in the scientific literature that were
obtained through the AMS driver program, you are required to include a
reference to the program package with the appropriate release number:

AMS 2026.1, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam,
The Netherlands, https://www.scm.com. Optionally, you may add the
following list of authors and contributors: R. Rüger, M. Franchini, T.
Trnka, A. Yakovlev, E. van Lenthe, P. Philipsen, T. van Vuren, B.
Klumpers, T. Soini

The engine used for a particular calculation might require you to
include other references. Please refer to the specific engine manuals
for required citations.

In addition to these general references, certain AMS features require
additional citations if you have used them. An overview of these is
given in the *Feature references* section below.

Note:

  If you have used a modified (by yourself, for instance) version of
  the code, you should mention in the citation that a modified version
  has been used.


Feature references
==================


Frequencies, IR Intensities, Raman, VCD
---------------------------------------

**Mode tracking**
   M. Reiher, J. Neugebauer, *A mode-selective quantum chemical method
   for tracking molecular vibrations applied to functionalized carbon
   nanotubes*, Journal of Chemical Physics 118, 1634 (2003)

   M. Reiher, J. Neugebauer, *Convergence characteristics and
   efficiency of mode-tracking calculations on pre-selected molecular
   vibrations*, Physical Chemistry Chemical Physics 6, 4621 (2004)

   C. Herrmann, M. Reiher, J. Neugebauer, *Finding a needle in a
   haystack: direct determination of vibrational signatures in complex
   systems*, New Journal of Chemistry 31, 818 (2007)

**Mode tracking based on intensities**
   M. Reiher, J. Neugebauer, *A mode-selective quantum chemical method
   for tracking molecular vibrations applied to functionalized carbon
   nanotubes*, Journal of Chemical Physics 118, 1634 (2003)

   S. Luber, J. Neugebauer, M. Reiher, *Intensity tracking for
   theoretical infrared spectroscopy of large molecules*, Journal of
   Chemical Physics 130, 064105 (2009)

**Mode refinement**
   T.Q. Teodoro, M.A.J. Koenis, S.E. Galembeck, V.P. Nicu, W.J. Buma,
   L. Visscher, *A frequency range selection method for vibrational
   spectra*, J. Phys. Chem. Lett., 9 (23), 6878 (2018)

**Mobile Block Hessian (MBH)**
   A. Ghysels, D. Van Neck, V. Van Speybroeck, T. Verstraelen and M.
   Waroquier, *Vibrational Modes in partially optimized molecular
   systems*  Journal of Chemical Physics 126, 224102 (2007)

**Raman scattering**
   S.J.A. van Gisbergen, J.G. Snijders and E.J. Baerends,
   *Application of time-dependent density functional response theory
   to Raman scattering*,  Chemical Physics Letters 259, 599 (1996)

**Resonance Raman: excited-state finite lifetime**
   L. Jensen, L. Zhao, J. Autschbach and G.C. Schatz, *Theory and
   method for calculating resonance Raman scattering from resonance
   polarizability derivatives*,  Journal of Chemical Physics 123,
   174110 (2005)

**Resonance Raman: excited-state gradient**
   J. Neugebauer, E.J. Baerends, E. Efremov, F. Ariese and C. Gooijer,
   *Combined Theoretical and Experimental Deep-UV Resonance Raman
   Studies of Substituted Pyrenes*,  Journal of Physical Chemistry A
   109, 2100 (2005)

**VROA: (Resonance) vibrational Raman optical activity**
   L. Jensen, J. Autschbach, M. Krykunov, and G.C. Schatz, *Resonance
   vibrational Raman optical activity: A time-dependent density
   functional theory approach*,  Journal of Chemical Physics 127,
   134101 (2007)

**Vibrational Circular Dichroism (VCD)**
   V.P. Nicu J. Neugebauer S.K. Wolff and E.J. Baerends,  *A
   vibrational circular dichroism implementation within a Slater-type-
   orbital based density functional framework and its application to
   hexa- and hepta-helicenes*, Theoretical Chemical Accounts 119, 245
   (2008)

VCD analysis: VCDtools
   V.P. Nicu, J. Neugebauer and E.J. Baerends, *Effects of Complex
   Formation on Vibrational Circular Dichroism Spectra*, Journal of
   Physical Chemistry A 112, 6978 (2008)

   M.A.J. Koenis, O. Visser, L. Visscher, W.J. Buma, V.P. Nicu, *GUI
   Implementation of VCDtools, A Program to Analyze Computed
   Vibrational Circular Dichroism Spectra*, J. Chem. Inf. Model 60,
   259 (2020)

   V.P. Nicu, *Revisiting an old concept: the coupled oscillator model
   for VCD. Part 1: the generalised coupled oscillator mechanism and
   its intrinsic connection to the strength of VCD signals*, Physical
   Chemistry Chemical Physics 18, 21202 (2016).

**Franck-Condon factors**
   J.S. Seldenthuis, H.S.J. van der Zant, M.A. Ratner and J.M.
   Thijssen, *Vibrational Excitations in Weakly Coupled Single-
   Molecule Junctions: A Computational Analysis*,  ACS Nano 2, 1445
   (2008)


PES Exploration
---------------

Samuel T Chill, Matthew Welborn, Rye Terrell, Liang Zhang, Jean-Claude
Berthet, Andreas Pedersen, Hannes Jónsson and Graeme Henkelman *EON:
software for long time simulations of atomic scale systems*, Modelling
Simul. Mater. Sci. Eng. 22 055002 (2014)


Molecular Dynamics and Monte Carlo
----------------------------------

Collective Variable-Driven Hyperdynamics (CVHD)
   K.M. Bal and E.C. Neyts, *Merging Metadynamics into Hyperdynamics:
   Accelerated Molecular Simulations Reaching Time Scales from
   Microseconds to Seconds*, J. Chem. Theory Comput., 11, 4545-4554
   (2015)

Force-bias Monte Carlo (fbMC)
   M.J. Mees, G. Pourtois, E.C. Neyts, B.J. Thijsse, A. Stesmans,
   *Uniform-acceptance force-bias Monte Carlo method with time scale
   to study solid-state diffusion*,  Physical Review B 85, 134301
   (2012)

Grand Canonical Monte Carlo (GCMC)
   Th.P. Senftle, R.J. Meyer, M.J. Janik and A.C.T. van Duin,
   *Development of a ReaxFF potential for Pd/O and application to
   palladium oxide formation*,  J. Chem. Phys. 139, 044109 (2013)

   Th.P. Senftle, A.C.T. van Duin, M.J. Janik, *Determining in situ
   phases of a nanoparticle catalyst via grand canonical Monte Carlo
   simulations with the ReaxFF potential*,  Catalysis Communications
   **volume 52**, 5 July 2014, Pages 72–77


External programs and Libraries
-------------------------------

Third-party software used in the 2026.1 version of the Amsterdam
Modeling Suite can be found in the file titled "third-party-
software.txt" in the root of your AMS installation.
