Publications (1991 - )
Miro

PUBLICATIONS OF

STAVROS C. FARANTOS




THEORETICAL AND COMPUTATIONAL CHEMISTRY IN CRETE (TCCC)



Publications (1991 - )

47
S. C. Farantos and H. S Taylor.
The Photodissociation of O3: A Classical Dynamical Approach for the Interpretation of the Recurrences in the Autocorrelation Function.
J. Chem. Phys.
, 94, 4887, 1991.

48
S. C. Farantos, J. M. Gomez Llorente, O. Hahn and H. S. Taylor.
On the Consistency Between Recent Experimental Results and a Previous Theoretical Analysis of HCN/HNC.
J. Chem. Phys.
, 94, 2376, 1991.

49
L. Zachilas and S. C. Farantos.
Periodic Orbits and Quantum Localization in the van der Waals System CO-Ar.
Chem. Phys.
, 154, 55, 1991.

50
S. C. Farantos.
The Importance of Periodic Orbits in Analysing Photodissociation Resonances: the O3 Case.
Chem. Phys.
, 159, 329, 1992.

51
S. C. Farantos.
Spectroscopy and Dynamics of Vibrationally Excited Molecules: A Phase Space Structure Analysis. In T. Bountis, editor, Chaotic Dynamics: Theory and Practice.
Plenum Co. Ltd., 1992.

52
S. C. Farantos.
Chemical Dynamics: A Periodic Orbits Approach. In J. Broeckhove, editor, Time Dependent Quantum Mechanics: Experiments and Theory.
Plenum Co. Ltd, 1992.

53
A. Vegiri and S. C. Farantos.
Classical Dynamics of Hydrogen Bonded Systems: Water Clusters.
J. Chem. Phys.
, 98, 4059, 1993.

54
S. C. Farantos.
Periodic Orbits as a Probe to Reveal Exotic States: The Saddle-Node States.
Laser Chemistry
, 13, 87, 1993.

55
S. C. Farantos and L. Zachilas.
Testing Molecular Potential Functions with Bifurcation Diagrams of Periodic Obits.
Mol. Phys.
, 80, 1499, 1993.

56
S. C. Farantos, S. Kapetanakis and A. Vegiri.
Minimum Structures and Dynamics of Small Water Clusters.
J. Phys. Chem.
, 97, 12158, 1993.

57
B. R. Eggen, A. J. Marks, J. N. Murrell and S. C. Farantos.
Water Clusters - a speculation.
Chem. Phys. Letters
, 219, 247, 1994.

58
S. C. Farantos.
Water Clusters: The (H2O)64 case.
Z. Phys. D
, 31, 213, 1994.

59
R. Prosmiti, S. C. Farantos and H. S. Taylor.
A Periodic Orbit Approach to Spectroscopy and Dynamics of SO2(C1B2 -> X1A1).
Mol. Phys.
, 82, 1213, 1994.

60
G. Contopoulos, S. C. Farantos, H. Papadaki and C. Polymilis.
Complex Unstable Periodic Orbits and their Manifestation in Classical and Quantum Dynamics.
Phys. Rev. E
, 50, 4399, 1994.

61
S. C. Farantos.
Methods for locating periodic orbits in highly unstable systems.
THEOCHEM J. Mol. Struct.
, 341, 91, 1995.

62
R. Prosmiti and S. C. Farantos.
Periodic Orbits, Bifurcation Diagrams and the Spectroscopy of C2H2 System.
J. Chem. Phys.
, 103, 3299, 1995.

63
R. Prosmiti, S. C. Farantos, R. Guantes, F. Borondo and R. M. Benito.
A Periodic Orbit Analysis of the Vibrationally Highly Excited LiNC/LiCN: a comparison with quantum mechanics.
J. Chem. Phys.
, 104, 2921, 1996.

64
G. Fanourgakis and S. C. Farantos.
Potential Functions and Static and Dynamic Properties of Mgm+Arn, m=1,2; n=1-18 Clusters.
J. Phys. Chem.
, 100, 3900, 1996.

65
S. C. Farantos.
Exploring Molecular Vibrations with Periodic Orbits.
Int. Rev. Phys. Chem
, 15, 345, 1996.

66
S. C. Farantos, Hans-Martin Keller, R. Schinke, K. Yamashita and K. Morokuma.
Normal Mode and Isomerization Bending States in HCP: Periodic Orbit Assignment and Spectroscopic Signature.
J. Chem. Phys. (Communication)
, 104, 10055, 1996.

67
J. S. Papadakis, G. Fanourgakis, S. C. Farantos and M. Founargiotakis.
Comparison of Line Search Minimization Algorithms for Exploring Topography of Multidimensional Potential Energy Surfaces: the Mg+Arn case.
J. Comput. Chem.
, 18, 1011, 1997.

68
G. S. Fanourgakis, S. C. Farantos, P. Parneix and Ph. Brechignac.
An Effective Transition State for a Complex Cluster Isomerisation Processe: Comparison between anharmonic and harmonic models for Mg+Ar12.
J. Chem. Phys.
, 106, 4954, 1997.

69
M. Founargiotakis, S. C. Farantos, H. Skokos and G. Contopoulos.
Bifurcation Diagrams of Periodic Orbits for Unbound Molecular Systems: FH2.
Chem. Phys. Letters,
277, 456, 1997.

70
Ch. Beck, Hans-Martin Keller, S. Yu. Grebenshchikov, R. Schinke, S. C. Farantos, K. Yamashita and K. Morokuma.
Highly Excited Vibrational States of HCP and their Analysis in Terms of Periodic Orbits: The genesis of saddle-node states and their spectroscopic signature.
J. Chem. Phys.
107, 9818, 1997.

71
S. S. Xantheas, G. C. Fanourgakis, S. C. Farantos and M. Velegrakis.
Spectroscopic Constants of the X2+ and A2 States of Sr+Ar from First Principles: Comparison with experiment.
J. Chem. Phys.,
108, 46, 1998.

72
S. C. Farantos.
POMULT: A Program for Computing Periodic Orbits in Hamiltonian Systems Based on Multiple Shooting Algorithms.
Computer Physics Communications,
108, 240, 1998.

73
S. Yu. Grebenshchikov, C. Beck, R. Schinke and S. C. Farantos.
Three-Dimensional Molecular Wave Packets: Calculation of Revival Times from Periodic Orbits.
Phys. Letters A,
in 243, 208, 1998.

74
G. C. Fanourgakis, S. C. Farantos and M. Velegrakis and S. S. Xantheas.
Photofragmentation Spectra and Structures of Sr+Arn, n=2-8 Clusters: Experiment and Theory.
J. Chem. Phys.,
109, 108, 1998.

75
M. Velegrakis, G. E. Froudakis and S. C. Farantos.
Stability and Structure of Ni+Arn and Pt+Arn Clusters.
J. Chem. Phys.,
109, 4687, 1998.

76
G. E. Froudakis, G. S. Fanourgakis, S. C. Farantos and S. S. Xantheas.
Binding Energies and Structures of C+Arn, (n=1-5), Clusters from First Principles.
Chem. Phys. Letters,
294, 109, 1998.

77
S. C. Farantos, C. Beck and R. Schinke.
Periodic Orbits and Vibrational Wave Functions for DCP: nonlinear resonances in isotopically substituted molecules.
Theoretical Chemistry Accounts,
100, 147, 1998.

78
Pankaj Bhatia, Biswajit Maiti, N. Sathyamurthy, S. Stamatiadis and S. C. Farantos
Exploring Molecular Motions in Collinear HeH2+ and its isotopic Variants Using Periodic Orbits
Phys. Chem. Chem. Phys. (PCCP),
1, 1105, 1999.

79
G. S. Fanourgakis, S. C. Farantos, Ch. Luder, M. Velegrakis and S. S. Xantheas.
Photofragmentation Spectra and Potential Energy Surfaces of Sr+Ar2.
Phys. Chem. Chem. Phys. (PCCP),
1, 977, 1999.

80
M. Velegrakis, G. E. Froudakis and S. C. Farantos.
Coordination of Ti Cation Embedded in Argon Clusters.
Chem. Phys. Letters,
302, 595, 1999.

81
R. Prosmiti, S. C. Farantos and H. Guo.
Assigning the Transition from Normal to Local Vibrational Mode in SO 2 by Periodic Orbits.
Chem. Phys. Letters,
311, 241, 1999.

82
H. Ishikawa, R. W. Field, S. C. Farantos, M. Joyeux, J. Koput, C. Beck and R. Schinke
HCP - CPH Isomerization: Caught in the Act
Annual Review of Physical Chemistry (postscript),
50, 443-484, 1999,

83
R. Guantes and S. C. Farantos
High Order Finite Difference Algorithms for Solving the Schroedinger Equation in Molecular Dynamics. I.
J. Chem. Phys.,
111, 10827, 1999,

84
R. Guantes, A. Nezis and S. C. Farantos.
Periodic Orbit - Quantum Mechanical Investigation of the Inversion Mechanism of Ar3.
J. Chem. Phys.,
111, 10836, 1999.

85
S. Kapetanakis and S. C. Farantos.
A Classical Mechanical Study of cis-trans Isomerization Reaction in (H2O)4 Cluster: An example of non-ergodic behaviour in
Recent Theoretical and Experimental Advances in Hydrogen Bonded Clusters, 1998, Editor S. S. Xantheas.

86
J. Weish, J. Hauschildt, R. Duren, R. Schinke, J. Koput, S. Stamatiadis and S. C. Farantos.
Saddle-node Bifurcations and their Quantum Mechanical Fingerprints in the Spectrum of HOCl.
J. Chem. Phys.,
112, 77, 2000.

87
S. Stamatiadis, R. Prosmiti and S. C. Farantos
AUTO_DERIV: Tool for automatic differentiation of a FORTRAN code.
Comp. Phys. Comm.,
127, 343, 2000.

88
Biswajit Maiti, N. Sathyamurthy, S. Stamatiadis and S. C. Farantos.
Periodic Orbit Analysis for HeH2+ in Three Dimensions.
Indian Journal of Chemistry A,
39A, 338, 2000.

89
G. E. Froudakis, S. C. Farantos and M. Velegrakis.
Mass Spectra and Theoretical Modeling of Li+Nen, Li+Arn and Li+Krn Clusters.
Chem. Phys.,
258, 13, 2000.

90
J. Bredenbeck, C. Beck, R. Schinke, J. Koput, S. Stamatiadis, S. C. Farantos and M. Joyeux
The Vibrational Spectrum of deuterated phosphaethyne: A quantum nechanical, classical and semiclassical analysis.
J. Chem. Phys.,
112, 8855, 2000.

91
S. C. Farantos.
THE-ELEMENTS: A Beowulf-Class Computer.
NewsLetters in SIMU (postscript),
1, 99, 2000.

92
A. Vegiri and S. C. Farantos.
Cluster Collisions of Water Tetramers: A classical dynamical study.
Chem. Phys.,
262, 337, 2000.

93
R. Guantes and S. C. Farantos.
High Order Finite Difference Algorithms for Solving the Schroedinger Equation in Molecular Dynamics. II. Periodic variables.
J. Chem. Phys.,
113, 10429, 2000.

94
M.N. Vrahatis, A.E. Perdiou, V.S. Kalantonis, E.A. Perdios, K. Papadakis, R. Prosmiti and S. C. Farantos
Application of the Characteristic Bisection Method for Locating and Computing Periodic Orbits in Molecular Systems.
Comp. Phys. Comm.,
138, 53, 2001.

95
S. Stamatiadis, S. C. Farantos, H.-M. Keller and R. Schinke.
Saddle-node states in the spectra of HCO and DCO: a periodic orbit classification of vibrational levels.
Chem. Phys. Lett.,
344, 565, 2001.

96
R. Guantes and S. C. Farantos.
Reply to the comment ``High Order Finite Difference Algorithms for Solving the Schroedinger Equation in Molecular Dynamics''.
J. Chem. Phys.,
115, 6796, 2001.

97
G. E. Froudakis, M. Muhlhauser, S. C. Farantos, A. Sfounis and M. Velegrakis.
Mass Spectra and Structures of Cu+Rgn Clusters (Rg = Ne, Ar).
Chem. Phys.,
280, 43, 2002.

98
M. Joyeux, S. C. Farantos and R. Schinke.
Highly Excited Motion in Molecules: Saddle-Node Bifurcations and their Fingerprints in Vibrational Spectra.
J. Phys. Chem. A (Feature Article),
106, 5407, 2002.

99
Rudiger Siebert, Paul Fleurat-Lessard, R. Schinke, Martina Bittererovand and S. C. Farantos.
The Vibrational Spectrum of Ozone up to Dissociation Threshold: Dynamics calculations on an accurate potential energy surface.
J. Chem. Phys.,
116, 9749, 2002.

100
S. C. Farantos, E. Filippou, S. Stamatiadis, G. E. Froudakis, M. Muhlhauser, M. Massauti, A. Sfounis and M. Velegrakis.
Photofragmentation Spectra of Sr+CO Complex: experiment and ab initio calculations.
Chem. Phys. Letters,
366, 231, 2002.

101
Stavros C. Farantos, Stamatis Stamatiadis, Nello Nellari and Djordje Maric.
ENACTS/Grid Enabling Technologies
Report (http://www.epcc.ed.ac.uk/enacts),
December 2002.

102
R. Prosmiti and S. C. Farantos.
Periodic Orbits and Bifurcation Diagrams of Acetylene/Vinylidene Revisited.
J. Chem. Phys.,
118, 8275, 2003.

103
T. Azzam, R. Schinke, S. C. Farantos, M. Joyeux and K. A. Peterson.
The Bound State Spectrum of HOBr up to Dissociation Limit: Evolution of saddle-node bifurcations.
J. Chem. Phys.,
118, 9643, 2003.

104
S. C. Farantos, E. Filippou, S. Stamatiadis, G. E. Froudakis, M. Muhlhauser, M. Peric, M. Massauti, A. Sfounis and M. Velegrakis.
The Excited States of Sr+CO: photofragmentation spectra and ab initio calculations.
Chem. Phys. Letters,
379, 242, 2003.

105
Z.W. Qu, H. Zhu, M. Tashiro, R. Schinke and S. C. Farantos.
The Huggins band of ozone: Unambiguous electronic and vibrational assignment.
J. Chem. Phys. (Communication),
120, 6811, 2004.

106
S. C. Farantos, Shi Ying Lin and Hua Guo.
A regular isomerization path among chaotic vibrational states of CH2(a1A1).
Chem. Phys. Letters,
399, 260, 2004.

107
Z.W. Qu, H. Zhu, R. Schinke and S. C. Farantos.
The Huggins band of ozone: A theoretical analysis.
J. Chem. Phys.,
121, 11731, 2004.

108
Stavros C. Farantos.
ENACTS/Dissemination Report.
ENACTS/Dissemination Report,
February 2005.

109
M. Joyeux, S. Yu. Grebenshchikov, J. Bredenbeck, R. Schinke, and S. C. Farantos.
Intramolecular Dynamics Along Isomerization and Dissociation Pathways, in
"Geometrical Structures of Phase Space in Multi-Dimensional Chaos".
Adv. Chem. Phys.,
130, 267-303, 2005.

110
Shi Ying Lin, Hua Guo and Stavros C. Farantos.
Resonances of CH2(a1A1) and their roles in unimolecular and bimolecular reactions.
J. Chem. Phys.,
122, 124308, 2005.

111
S. C. Farantos, S. Stamatiadis, L. Lathouwers, and R. Guantes.
Grid Enabled Molecular Dynamics: classical and quantum algorithms.
ICCMSE2005,
3, 35-50, 2005.

112
S. C. Farantos, Z.W. Qu, H. Zhu, and R. Schinke.
Reactions Paths and elementary bifurcations tracks: the diabatic 1B2-state of ozone.
Int. J. Bif. Chaos Appl. Sci. Eng.,
16(7), 1913-1928, 2006.

113
Andreas Mavrandonakis, Stavros C. Farantos and George E. Froudakis.
Glycine Interaction with Carbon Nanotubes: An ab Initio Study.
J. Phys. Chem. B,
110, 6048-6050, 2006.

114
Andreas Mavrandonakis, Stavros C. Farantos and George E. Froudakis.
Theoretical Modelling of the Glycine Radical Addition to Carbon Nanotubes.
Rev.Adv.Mater.Sci.,
11, 88-91, 2006.

115
Stavros C. Farantos.
Periodic Orbits in Biological Molecules: Phase Space Structures and Selectivity.
ICCMSE2006,
6, 350-356, 2006.

116
S. C. Farantos.
Periodic Orbits in Biological Molecules: Phase Space Structures and Selectivity in Alanine Dipeptide.
J. Chem. Phys.,
126, 175101, 2007.

117
Stavros C. Farantos.
Non-Linear Vibrational Normal Modes of Biomolecules.
CPS-IEEE Computer Society,
ICCSA2007,444-450, 2007.

118
Vangelis Daskalakis, Stavros C. Farantos and Constantinos Varotsis.
Protein dynamics and spectroscopy for ferryl intermediate of Cytochrome c Oxydase: A molecular dynamics approach.
JCP-Proceedings,
963-V2A, 31-34, 2007.

119
Chuanxiu Xu, Bin Jiang, Daiqian Xie, Stavros C. Farantos, Shi Ying Lin and Hua Guo.
Analysis of the HO2 Vibrational Spectrum on an Accurate Ab Initio Potential Energy Surface.
J. Phys. Chem. A,
111, 10353-10361, 2007.

120
Vangelis Daskalakis, Stavros C. Farantos, and Constantinos Varotsis.
Assigning vibrational spectra of ferryl-oxo intermediates of Cytochrome c Oxidase by periodic orbits and Molecular Dynamics.
J. Am. Chem. Soc.,
130, 12385-12393, 2008.

121
A. Mavrandonakis, S. C. Farantos, and G. Froudakis.
Analytical Potential Functions Based on Force-Fields for Studying the Dynamics of Vibrationally Excited and Reactive Carbon Nanotubes Interacting with Aminoacids.
J. Comput. and Theor. Nanosci.,
6, 880-885, 2009.

122
Stavros C. Farantos, Reinhard Schinke, Hua Guo, and Marc Joyeux.
Energy Localization in Molecules, Bifurcation Phenomena, and their Spectroscopic Signatures: The Global View.
Chem. Rev.,
109, 4248-4271, 2009.

124
Jaime Suarez, Stavros C. Farantos, Stamatis Stamatiadis, and Lucas Lathouwers.
A method for solving the molecular Schroedinger Equation in Cartesian coordinates via angular momentum projection operators.
Comp. Phys. Comm.,
180, 2025-2033, 2009.

125
Massimiliano Porrini, Vangelis Daskalakis, S. C. Farantos, and Constantinos Varotsis.
Heme Cavity Dynamics of Photodissociated CO from ba3-Cytochrome c Oxidase: the Role of Ring-D Propionate.
J. Phys. Chem. B,
113(35), 12129-12135, 2009.

126
Vangelis Daskalakis, Stavros C. Farantos, Victor Guallar, and Constantinos Varotsis.
Vibrational Resonances and CuB displacement controlled by proton motion in Cytochrome c Oxidase.
J. Phys. Chem. B,
114(2), 1136-1143, 2010.

127
Frederic Mauguiere, Vladimir Tyuterev, and Stavros C. Farantos.
Bifurcation effects and patterns in the vibrational excited states of isotopically substituted water.
Chem. Phys. Lett.,
494, 163-169, 2010.

128
Frederic Mauguiere, Michael Rey, Vladimir Tyuterev, Jaime Suarez, and Stavros C. Farantos.
A periodic orbit bifurcation analysis of vibrationally excited isotopologues of sulfur dioxide and water molecules: symmetry breaking substitutions.
J. Phys. Chem. A,
114, 9836-9847, 2010.

129
R. Schinke, J. Suarez, and S. C. Farantos.
Photodissociation of N2O: Frustrated NN bond breaking causes diffuse vibrational structures.
J. Chem. Phys.,
133, 091103(Communication), 2010.

130
S. Stamatiadis, and S. C. Farantos.
AUTO_DERIV: Tool for automatic differentiation of a Fortran code (New Version).
Comp. Phys. Comm.,
181(10), 1818-1819, 2010.

131
V. Daskalakis, S. C. Farantos, V. Guallar, and C. Varotsis.
Regulation of Electron and Proton Transfer by the Protein Matrix of Cytochrome c Oxidase.
J. Phys. Chem. B,
115(13), 3648 - 3655, 2011.

132
Frederic Mauguiere, Stavros C. Farantos, Jaime Suarez, and Reinhard Schinke.
Non-linear dynamics of the photodissociation of nitrous oxide: Equilibrium points, periodic orbits, and transition states.
J. Chem. Phys.,
134(24), 244302-12, 2011.

133
V. Daskalakis, M. Giatromanolakis, M. Porrini, S. C. Farantos, and O. Gervasi.
Grid Computing Multiple Shooting Algorithms for Extended Phase Space Sampling and Long Time Propagation in Molecular Dynamics.
Nova Science Publishing Co.,

Computer Physics, Volume ISBN: 978-1-61324-790-7, Chapter 4: pages 297-314, 2012.

134
A. Kampanarakis, S. C. Farantos, V. Daskalakis, and C. Varotsis.
Non-Linear Vibrational Modes in Biomolecules: a periodic orbits description.
Chem. Phys.,
399:258-263, 2012 (doi:10.1016/j.chemphys.2011.07.031).

135
M. Porrini, V. Daskalakis, and S. C. Farantos.
Thermodynamic Perturbation Calculations on Cytochrome c Oxidases interacting with small ligands.
RSC Adv.,
2:5828-5836, 2012 (doi:10.1039/C2RA20625K).

136
V. Daskalakis, S. C. Farantos, and C. Varotsis.
Tuning heme functionality: the cases of Cytochrome c Oxidase and Myoglobin Oxidation.
LNCS-Springer-Verlag Berlin, Heidelberg,
ISBN: 978- 3-642-31124-6:304-315, 2012.

137
Frederic A. L. Mauguiere, Peter Collins, Gregory S. Ezra, Stavros C. Farantos, and Stephen Wiggins.
Multiple Transition States and Roaming in Ion-Molecule Reactions: a Phase Space Perspective.
Chem. Phys. Letters,
592:282-287, 2014.
arxiv.org,

138
Frederic A. L. Mauguiere, Peter Collins, Gregory S. Ezra, Stavros C. Farantos, and Stephen Wiggins.
Roaming dynamics in ion-molecule reactions: phase space reaction pathways and geometrical interpretation.
J. Chem. Phys.
, 140:134112-17, 2014.
arxiv.org,

139
Frederic A. L. Mauguiere, Peter Collins, Gregory S. Ezra, Stavros C. Farantos, and Stephen Wiggins.
Roaming dynamics in Ketene isomerization.
Theor. Chem. Acc., 133, 1507(13), 2014
.
arxiv.org,


SCF
Thu Mar 27 16:06:36 EET 2014.