The latest release of M3C-store (version 1.0.3, released 2023-02-17) contains 3965 molecules including carbon clusters, hydrogenated and nitrogenated carbon clusters, fragments from the furan molecule fragmentation and protonated cysteine molecule. Its principal aim is to include the fragments necessary to describe the fragmentation of a given molecule. Some molecules are available at two levels of theory: B3LYP and CCSD(T), and two basis sets: 6-311++G(d,p) and 6-311++G(3df,2p). Adamantane fragments are available at B3LYP/6-31G(d). Cysteine fragments are available at M06-2X/6-311++G(d,p). The files format is an extension of the popular .xyz format. Each molecule's file contains the energy, geometry, vibrational frequencies, symmetry and the symmetry of the electronic state. This database has been specially adapted as the starting point of an M3C calculation (see M3C project).
Download the .zip file from this page and extract the files,
$ unzip M3C-store-master.zip
Archive: M3C-store-master.zip
012efb01d2b1ffb8b94e856e4cc720d7d5946639
creating: M3C-store-master/
extracting: M3C-store-master/README
creating: M3C-store-master/develop/
creating: M3C-store-master/develop/6-311++G.3df.2p/
creating: M3C-store-master/develop/6-311++G.3df.2p/C4N/
...
$ mv M3C-store-master/ M3C-store
or clone the repository using git
$ git clone https://github.com/nfaguirrec/M3C-store.git
The following should be the content of the M3C-store directory if previous steps were successful:
$ cd M3C-store
$ ls
develop master README.md utils
All files are stored in the .rxyz format, which is the standard format used by M3C. The name of the files follow the format <stoichiometry>.q<charge>.m<multiplicity>-<id>.rxyz e.g. H2C2.q0.m1-1.rxyz. This format basically the same than .xyz files (line 1: number of atoms n, line 2: comment, lines from 3 up to 3 + n: symbols and atomic positions in Å), except that in the second line the value of the energy is given in atomic units (it is not only a simple comment!). Additionally, calculated vibrational frequencies in cm-1, symmetry, and electronic state are also included. The following block shows the information of the lowest energy state of the acetylene molecule (H2C2) in the .rxyz format:
4
Energy = -77.1757558750
C 0.316435238 0.578031412 -0.011149452
C -0.455252451 -0.279767271 0.304468434
H 1.001639096 1.339720463 -0.291420995
H -1.140462527 -1.041456161 0.584725214
FREQUENCIES 7
659.4392
659.4392
765.5414
765.5414
2066.1167
3408.1288
3508.7083
SYMMETRY D*H
ELECTRONIC_STATE 1-SGG
To use the database with M3C follow the next steps:
- Choose the basis set and level of theory:
$ cd master/6-311++G.3df.2p/ccsdt
- Choose the parent molecule (e.g. acetylene H2C2) and its lowest energy state (in this example H2C2.q0.m1-1.rxyz):
$ grep Energy H2C2.q0.m* | sort -k3 -n
H2C2.q0.m1-1.rxyz:Energy = -77.1757558750
H2C2.q0.m1-3.rxyz:Energy = -77.1034510280
H2C2.q0.m3-4.rxyz:Energy = -77.0331091650
H2C2.q0.m3-3.rxyz:Energy = -77.0298114970
H2C2.q0.m3-2.rxyz:Energy = -77.0098651160
- Use the command M3C.store from the M3C project to create the FRAGMENTS_DATABASE block necessary for the M3C input file:
$ M3C.store makeDB H2C2.q0.m1-1.rxyz
BEGIN FRAGMENTS_DATABASE
store = /myurl/M3C-store/master/6-311++G.3df.2p/ccsdt
reference = H2C2(s1)
#------------------------------------------------------------------------------
# Label Z M WL SYM geomFile Eelec maxVib
#------------------------------------------------------------------------------
H(d1) 0 2 1 1 H.q0.m2-1.rxyz -13.667114 # R3(2-S)
C(s1) 0 1 5 1 C.q0.m1-1.rxyz -1026.574168 # R3(1-D)
C(t1) 0 3 3 1 C.q0.m3-1.rxyz -1028.024016 # R3(3-P)
H2(s1) 0 1 1 2 H2.q0.m1-1.rxyz -31.388074 H(d1)+H(d1) # 4.05 D*H(1-SGG)
HC(d1) 0 2 2 1 HC.q0.m2-1.rxyz -1044.975479 H(d1)+C(t1) # 3.28 C*V(2-PI)
HC(q1) 0 4 1 1 HC.q0.m4-1.rxyz -1044.307456 H(d1)+C(t1) # 2.62 C*V(4-SG)
C2(s1) 0 1 1 2 C2.q0.m1-1.rxyz -2062.151541 C(t1)+C(t1) # 6.10 D*H(1-SGG)
C2(t1) 0 3 2 2 C2.q0.m3-1.rxyz -2062.058719 C(t1)+C(t1) # 6.01 D*H(3-PIU)
H2C(s2) 0 1 1 2 H2C.q0.m1-2.rxyz -1062.850491 H2(s1)+C(t1) # 3.44 C2V(1-A1)
H2C(t2) 0 3 1 2 H2C.q0.m3-2.rxyz -1063.289273 H2(s1)+C(t1) # 3.88 C2V(3-B1)
H2C(t3) 0 3 1 2 H2C.q0.m3-3.rxyz -1060.078559 H2(s1)+C(t1) # 0.67 C2V(3-A2)
HC2(d1) 0 2 1 1 HC2.q0.m2-1.rxyz -2080.744453 H(d1)+C2(s1) # 4.93 C*V(2-SG)
HC2(d3) 0 2 1 2 HC2.q0.m2-3.rxyz -2079.791997 H(d1)+C2(s1) # 3.97 C2V(2-A1)
HC2(q2) 0 4 1 1 HC2.q0.m4-2.rxyz -2076.964678 H(d1)+C2(s1) # 1.15 CS(4-A")
H2C2(s1) 0 1 1 2 H2C2.q0.m1-1.rxyz -2100.060065 H(d1)+HC2(d1) # 5.65 D*H(1-SGG)
H2C2(s3) 0 1 1 2 H2C2.q0.m1-3.rxyz -2098.092549 H2(s1)+C2(s1) # 4.55 C2V(1-A1)
H2C2(t2) 0 3 1 2 H2C2.q0.m3-2.rxyz -2095.545946 H(d1)+HC2(d3) # 2.09 C2H(3-AU)
H2C2(t3) 0 3 1 2 H2C2.q0.m3-3.rxyz -2096.088715 C(t1)+H2C(s2) # 5.21 C2V(3-B2)
H2C2(t4) 0 3 1 2 H2C2.q0.m3-4.rxyz -2096.178449 H2(s1)+C2(s1) # 2.64 C2V(3-B2)
#------------------------------------------------------------------------------
END FRAGMENTS_DATABASE
This block consists in a table that contains as many rows as number of molecules or fragments are going to be considered in the process. Each row in the table contains the following information:
-
Label. Represents a unique identifier for the molecule. The format is (). The program will sort the molecules in several groups where each of those groups is identified by a group label. Additionally inside each group, each molecule is identified by a specifier label. This is specially advantageous to study observables which are to be discriminated by groups of molecules. For example: In a mass spectrum, a particular line represents the molecule A. However, this line is not a single signal but a superposition of signals produced by isomers or excited states of the same molecule A. In this sense, it is advantageous to label these isomers or excited states as A(s1), A(s2), A(tc), and so on, where the specifier label is arbitrary but useful for the user.
-
Charge (Z) Assigns the charge of the molecule.
-
Multiplicity (M) Assigns the multiplicity of the electronic state of the molecule.
-
Multiplicity (WL) Assigns the electronic state degeneracy due to the orbital angular momentum.
-
Rotational symmetry number (SYM) Assigns the rotational symmetry number of the molecule.
-
Geometry file name in .rxyz format
-
Electronic energy given in eV
-
Maximum vibrational energy allowed. This value is determined by the energy of the lowest transition state available, whereby the molecule can be breaking up, specifically by its energy barrier. This value may be written directly in the table (given in eV). One simple way to estimate this value is to suppose that the reverse activation barrier is very small, then the maximum vibrational energy is equivalent to the difference between the electronic energy of the molecule and the electronic energy of the fragmentation products. In this case, you can write directly in the table, the chosen fragmentation channel. For example: A(s1)+B(st).
M3C treats all the information after the # on a line as a comment. In this example, after # it is printed the actual value of the maximum vibrational energy in eV, and the symmetry of the molecule with the corresponding electronic state.
- Nestor F. Aguirre ( nfaguirrec@gmail.com )
- Manuel Alcamí ( manuel.alcami@uam.es )
- Karine Béroff ( karine.beroff@u-psud.fr )
- Marin Chabot ( chabot@ipno.in2p3.fr )
- Sergio Díaz-Tendero ( sergio.diaztendero@uam.es )
- Ewa Erdmann ( ewa.erdmann@pg.edu.pl )
- Paul-Antoine Hervieux ( paul-antoine.hervieux@ipcms.unistra.fr )
- Tijani IdBarkach ( idbarkach@ipno.in2p3.fr )
- Jaroslav Kočišek
- Marta Łabuda ( marta.labuda@pg.edu.pl )
- Thomas F. M. Luxford
- Fernando Martín ( fernando.martin@uam.es )
- Juan P. Sánchez ( juanp.sanchez@uam.es )
- Paul Scheier
- Lukas Tiefenthaler
The list below is a bibliography which specifies the citations appropriate for the M3C-store dataset depending of which molecules are used.
M3C-store dataset. N. F. Aguirre, M. Alcamí, K. Béroff, M. Chabot, S. Díaz-Tendero, E. Erdmann, P.-A. Hervieux, T. IdBarkach, J. Kočišek, M. Łabuda, T. F. M. Luxford, F. Martín, J. P. Sánchez, P. Scheier, and L. Tiefenthaler. 2023 URL: https://github.com/nfaguirrec/M3C-store
Other entries in the bibliography are some of the citations for specific molecular structures:
-
Cysteine-Water Cluster Cations Fragments Non-Ergodic Fragmentation upon Collision Induced Activation of Cysteine-Water Cluster Cations L. Tiefenthaler, P. Scheier, E. Erdmann, N. F. Aguirre, S. Díaz-Tendero, T. F. M. Luxford, and J. Kočišek Phys. Chem. Chem. Phys. 25 (2023) 5361
-
Doubly Charged Adamantane Fragments Dissociation dynamics of the diamondoid adamantane upon photoionization by XUV femtosecond pulses. S. Maclot, J. Lahl, J. Peschel, H. Wikmark, P. Rudawski, F. Brunner, H. Coudert-Alteirac, S. Indrajith, B. A. Huber, S. Díaz-Tendero, N. F. Aguirre, P. Rousseau, P. Johnsson Sci. Rep. 10 (2020) 2884
-
CnN+ (n=1-3)
Excitation, ionization, neutralization and anionic production in collisions of C+, N+ and CnN+ (n=1-3) with He atoms at 2.2 a.u velocity; cross sections and dissociation branching ratios.
T. Mahajan, K. Beroff, B. Pons, C. Illescas, M. Chabot, T. Idbarkach, T. Launoy, A. Le Padellec, A. Jallat, A. Jorge, N. F. Aguirre and S. Diaz-Tendero.
J. Phys. B: At. Mol. Opt. Phys. 52 (2019) 195204 -
Cn (n=0-5), CnHm (n=0-4, m=1-2), CnN (n=3-4)
Fully versus Constrained Statistical Fragmentation of Carbon Clusters and their Heteronuclear Derivatives.
N. F. Aguirre, S. Díaz-Tendero, T. IdBarkach, M. Chabot, K. Béroff, M. Alcamí, and F. Martín.
J. Chem. Phys. 150 (2019) 144301
- CnHmO (n=1-4, m=0-4)
Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations.
E. Erdmann, M. Łabuda, N. F. Aguirre, S. Díaz-Tendero, and M. Alcamí.
J. Phys. Chem. A 122 (2018) 4153-4166
-
CnNq+ (n=0-3, q=0-1)
Semiempirical breakdown curves of C2N(+) and C3N(+) molecules; application to products branching ratios predictions of physical and chemical processes involving these adducts.
T. IdBarkach, T. Mahajan, M. Chabot, K. Béroff, N.F. Aguirre, S. Diaz-Tendero, T. Launoy, A. Le Padelle, L. Perrot, M.A. Bonnin, K.C. Le, F. Geslin, N. de Séréville, F. Hammache, A. Jallat, A. Meyer, E. Charon, T. Pino, T. Hamelin, and V. Wakelam
Mol. Astrophysics 12 (2018) 25-32 -
Cn (n=1-9), Cn+ (n=1-5)
M3C: A Computational Approach To Describe Statistical Fragmentation of Excited Molecules and Clusters.
N. F. Aguirre, S. Díaz-Tendero, P.-A. Hervieux, M. Alcamí, and F. Martín.
J. Chem. Theory Comput. 13 (2017) 992-1009
- CnHmq+ (n=1-5, m=1-4, q=0-3)
Structure, Ionization, and Fragmentation of Neutral and Positively Charged Hydrogenated Carbon Clusters: CnHmq+ (n=1-5, m=1-4, q=0-3).
J. P. Sánchez, N. F. Aguirre, S. Díaz-Tendero, F. Martín, and M. Alcamí.
J. Phys. Chem. A 120 (2016) 588-605
