We propose a method for computing the activation barrier for chemical reactions involving molecules subjected to mechanical stress. The method avoids reactant and transition-state saddle optimizations at every force by, instead, solving the differential equations governing the force dependence of the critical points (i.e., minima and saddles) on the system's potential energy surface (PES). As a result, only zero-force geometry optimization (or, more generally, optimization performed at a single force value) is required by the method. In many cases, minima and transition-state saddles only exist within a range of forces and disappear beyond a certain critical point. Our method identifies such force-induced instabilities as points at which one of the Hessian eigenvalues vanishes. We elucidate the nature of those instabilities as fold and cusp catastrophes, where two or three critical points on the force-modified PES coalesce, and provide a classification of various physically distinct instability scenarios, each illustrated with a concrete chemical example.

1.
P. E.
Marsalek
,
H.
Lu
,
H.
Li
,
M.
Carrion-Vazquez
,
A. F.
Oberhauser
,
K.
Schulten
, and
J.
Fernandez
,
Nature
402
,
100
(
1999
).
2.
E.
Paci
and
M.
Karplus
,
J. Mol. Biol.
288
,
441
459
(
1999
).
3.
D. K.
Klimov
and
D.
Thirumalai
,
Proc. Natl. Acad. Sci. U.S.A.
97
(
13
),
7254
(
2000
).
4.
A.
Minajeva
,
M.
Kulke
,
J. M.
Fernandez
, and
W. A.
Linke
,
Biophys. J.
80
,
1442
(
2001
).
5.
D. E.
Makarov
,
P. K.
Hansma
, and
H.
Metiu
,
J. Chem. Phys.
114
,
9663
(
2001
).
6.
A. F.
Oberhauser
,
P. K.
Hansma
,
M.
Carrion-Vazquez
, and
J. M.
Fernandez
,
Proc. Natl. Acad. Sci. U.S.A.
98
(
2
),
468
472
(
2001
).
7.
M.
Rief
,
J. M.
Fernandez
, and
H. E.
Gaub
,
Phys. Rev. Lett.
81
,
4764
(
1998
).
8.
M.
Rief
,
M.
Gautel
,
F.
Oesterhelt
,
J. M.
Fernandez
, and
H. E.
Gaub
,
Science
276
,
1109
1112
(
1997
).
9.
M.
Schlierf
,
H.
Li
, and
J. M.
Fernandez
,
Proc. Natl. Acad. Sci. U.S.A.
101
,
7299
(
2004
).
10.
S.
Kirmizialtin
,
L.
Huang
, and
D. E.
Makarov
,
J. Chem. Phys.
122
,
234915
(
2005
).
11.
D. J.
Lacks
,
Biophys. J.
88
,
3494
3501
(
2005
).
12.
B.
Isralewitz
,
M.
Gao
, and
K.
Schulten
,
Curr. Opin. Struct. Biol.
11
,
224
230
(
2001
).
13.
S.
Izrailev
,
S.
Stepaniants
,
M.
Balsera
,
Y.
Oono
, and
K.
Schulten
,
Biophys. J.
72
(
4
),
1568
1581
(
1997
).
14.
H.
Lu
,
B.
Isralewitz
,
A.
Krammer
,
V.
Vogel
, and
K.
Schulten
,
Biophys. J.
75
,
662
(
1998
).
15.
H.
Lu
and
K.
Schulten
,
Chem. Phys.
247
,
141
(
1999
).
16.
C.
Bustamante
,
Y. R.
Chemla
,
N. R.
Forde
, and
D.
Izhaky
,
Annu. Rev. Biochem.
73
,
705
748
(
2004
).
17.
E.
Evans
and
K.
Ritchie
,
Biophys. J.
72
,
1541
1555
(
1997
).
18.
E.
Evans
and
K.
Ritchie
,
Biophys. J.
76
,
2439
(
1999
).
19.
C.
Hyeon
and
D.
Thirumalai
,
Biophys. J.
90
(
10
),
3410
3427
(
2006
).
20.
C.
Hyeon
,
G.
Morrison
, and
D.
Thirumalai
,
Proc. Natl. Acad. Sci. U.S.A.
105
(
28
),
9604
9609
(
2008
).
21.
C.
Hyeon
and
D.
Thirumalai
,
Proc. Natl. Acad. Sci. U.S.A.
102
(
19
),
6789
6794
(
2005
).
22.
D. E.
Makarov
,
Biophys. J.
92
(
12
),
4135
4136
(
2007
).
23.
D. J.
Brockwell
,
E.
Paci
,
R. C.
Zinober
,
G. S.
Beddard
,
P. D.
Olmsted
,
D. A.
Smith
,
R. N.
Perham
, and
S. E.
Radford
,
Nat. Struct. Biol.
10
(
9
),
731
737
(
2003
).
24.
P.-C.
Li
and
D. E.
Makarov
,
J. Chem. Phys.
119
,
9260
(
2003
).
25.
V.
Barsegov
,
G.
Morrison
, and
D.
Thirumalai
,
Phys. Rev. Lett.
100
(
24
),
248102
(
2008
).
26.
V.
Barsegov
and
D.
Thirumalai
,
Proc. Natl. Acad. Sci. U.S.A.
102
(
6
),
1835
1839
(
2005
).
27.
O. K.
Dudko
,
G.
Hummer
, and
A.
Szabo
,
Phys. Rev. Lett.
96
(
10
),
108101
(
2006
).
28.
M.
Sotomayor
and
K.
Schulten
,
Science
316
(
5828
),
1144
1148
(
2007
).
29.
O. K.
Dudko
,
G.
Hummer
, and
A.
Szabo
,
Proc. Natl. Acad. Sci. U.S.A.
105
(
41
),
15755
15760
(
2008
).
30.
D. J.
Brockwell
,
G. S.
Beddard
,
E.
Paci
,
D. K.
West
,
P. D.
Olmsted
,
D. A.
Smith
, and
S. E.
Radford
,
Biophys. J.
89
(
1
),
506
519
(
2005
).
31.
R. B.
Best
,
E.
Paci
,
G.
Hummer
, and
O. K.
Dudko
,
J. Phys. Chem. B
112
,
5968
5976
(
2008
).
32.
O. V.
Prezhdo
and
Y. V.
Pereverzev
,
Acc. Chem. Res.
42
(
6
),
693
703
(
2009
).
33.
J.
Alegre-Cebollada
,
R.
Perez-Jimenez
,
P.
Kosuri
, and
J. M.
Fernandez
,
J. Biol. Chem.
285
,
18961
18966
(
2010
).
34.
D. E.
Makarov
, in
Single-Molecule Studies of Protein Structure and Function
, edited by
A.
Oberhauser
(
Springer
,
New York
,
2012
), p.
235
.
35.
I.
Franco
,
C. B.
George
,
G. C.
Solomon
,
G. C.
Schatz
, and
M. A.
Ratner
,
J. Am. Chem. Soc.
133
(
7
),
2242
2249
(
2011
).
36.
M.
McCullagh
,
I.
Franco
,
M. A.
Ratner
, and
G. C.
Schatz
,
J. Am. Chem. Soc.
133
(
10
),
3452
3459
(
2011
).
37.
O. K.
Dudko
,
J.
Mathe
,
A.
Szabo
,
A.
Meller
, and
G.
Hummer
,
Biophys. J.
92
(
12
),
4188
4195
(
2007
).
38.
S.
Matysiak
,
A.
Montesi
,
M.
Pasquali
,
A. B.
Kolomeisky
, and
C.
Clementi
,
Phys. Rev. Lett.
96
(
11
),
118103
(
2006
).
39.
L.
Huang
,
S.
Kirmizialtin
, and
D. E.
Makarov
,
J. Chem. Phys.
123
,
124903
(
2005
).
40.
D. K.
West
,
D. J.
Brockwell
, and
E.
Paci
,
Biophys. J.
91
,
L51
L53
(
2006
).
41.
L.
Huang
and
D. E.
Makarov
,
J. Chem. Phys
129
(
12
),
121107
(
2008
).
42.
D. E.
Makarov
,
Acc. Chem. Res.
42
(
2
),
281
289
(
2009
).
43.
D.
Panja
,
G. T.
Barkema
, and
A. B.
Kolomeisky
,
J. Phys.: Condens. Matter
25
(
41
),
413101
(
2013
).
44.
P.
Tian
and
I.
Andricioaei
,
J. Mol. Biol.
350
(
5
),
1017
1034
(
2005
).
45.
M. E.
Fisher
and
A. B.
Kolomeisky
,
Proc. Natl. Acad. Sci. U.S.A.
96
(
12
),
6597
6602
(
1999
).
46.
M. E.
Fisher
and
A. B.
Kolomeisky
,
Proc. Natl. Acad. Sci. U.S.A.
98
(
14
),
7748
7753
(
2001
).
47.
A. B.
Kolomeisky
,
J. Phys.: Condens. Matter
25
(
37
),
370301
(
2013
).
48.
M. M.
Caruso
,
D. A.
Davis
,
Q.
Shen
,
S. A.
Odom
,
N. R.
Sottos
,
S. R.
White
, and
J. S.
Moore
,
Chem. Rev.
109
(
11
),
5755
5798
(
2009
).
49.
J. M.
Lenhardt
,
M. T.
Ong
,
R.
Choe
,
C. R.
Evenhuis
,
T. J.
Martinez
, and
S. L.
Craig
,
Science
329
(
5995
),
1057
1060
(
2010
).
50.
M. K.
Beyer
and
H.
Clausen-Schaumann
,
Chem. Rev
105
(
8
),
2921
2948
(
2005
).
51.
C. R.
Hickenboth
,
J. S.
Moore
,
S. R.
White
,
N. R.
Sottos
,
J.
Baudry
, and
S. R.
Wilson
,
Nature
446
(
7134
),
423
427
(
2007
).
52.
J. N.
Brantley
,
K. M.
Wiggins
, and
C. W.
Bielawski
,
Science
333
,
1606
(
2011
).
53.
A. L.
Black
,
J. M.
Lenhardt
, and
S. L.
Craig
,
J. Mater. Chem.
21
,
1655
1663
(
2011
).
54.
J. N.
Brantley
,
K. M.
Wiggins
, and
C. W.
Bielawski
,
Polym. Int.
62
,
2
(
2013
).
55.
J. N.
Brantley
,
S. S. M.
Konda
,
D. E.
Makarov
, and
C. W.
Bielawski
,
J. Am. Chem. Soc.
134
(
24
),
9882
9885
(
2012
).
56.
P.
Dopieralski
,
P.
Anjukandi
,
M.
Ruckert
,
M.
Shiga
,
J.
Ribas-Arino
, and
D.
Marx
,
J. Mater. Chem.
21
(
23
),
8309
8316
(
2011
).
57.
J.
Ribas-Arino
and
D.
Marx
,
Chem. Rev.
112
(
10
),
5412
5487
(
2012
).
58.
S. S. M.
Konda
,
J. N.
Brantley
,
C. W.
Bielawski
, and
D. E.
Makarov
,
J. Chem. Phys.
135
,
164103
(
2011
).
59.
S. S. M.
Konda
,
J. N.
Brantley
,
B. T.
Varghese
,
K. M.
Wiggins
,
C. W.
Bielawski
, and
D. E.
Makarov
,
J. Am. Chem. Soc.
135
(
34
),
12722
12729
(
2013
).
60.
T. J.
Kucharski
and
R.
Boulatov
,
J. Mater. Chem.
21
(
23
),
8237
8255
(
2011
).
61.
A.
Bailey
and
N. J.
Mosey
,
J. Chem. Phys.
136
,
044102
(
2012
).
62.
J.
Ribas-Arino
,
M.
Shiga
, and
D.
Marx
,
Angew. Chem., Int. Ed.
48
(
23
),
4190
4193
(
2009
).
63.
Z.
Huang
and
R.
Boulatov
,
Chem. Soc. Rev.
40
(
5
),
2359
2384
(
2011
).
64.
G. S.
Kochhar
,
A.
Bailey
, and
N. J.
Mosey
,
Angew. Chem., Int. Ed.
49
(
41
),
7452
7455
(
2010
).
65.
R.
Boulatov
,
Pure Appl. Chem.
83
(
1
),
25
41
(
2011
).
66.
M. J.
Kryger
,
A. M.
Munaretto
, and
J. S.
Moore
,
J. Am. Chem. Soc.
133
,
18992
18998
(
2011
).
67.
C. R.
Hickenboth
,
J. D.
Rule
, and
J. S.
Moore
,
Tetrahedron
64
(
36
),
8435
8448
(
2008
).
68.
M. K.
Beyer
,
J. Chem. Phys.
112
(
17
),
7307
7312
(
2000
).
69.
Z.
Huang
and
R.
Boulatov
,
Pure Appl. Chem.
82
(
4
),
931
951
(
2010
).
70.
71.
H.
Eyring
,
J. Chem. Phys.
4
,
283
(
1936
).
72.
S. N.
Zhurkov
,
Int. J. Fract. Mech.
1
(
4
),
311
322
(
1965
).
73.
D. E.
Makarov
,
J. Chem. Phys.
135
(
19
),
194112
(
2011
).
74.
T. G.
Graham
and
R. B.
Best
,
J. Phys. Chem. B
115
(
6
),
1546
1561
(
2011
).
75.
Y.
Suzuki
and
O. K.
Dudko
,
Phys. Rev. Lett.
104
(
4
),
048101
(
2010
).
76.
Y.
Suzuki
and
O. K.
Dudko
,
J. Chem. Phys.
134
(
6
),
065102
(
2011
).
77.
R.
Gilmore
,
Catastrophe Theory for Scientists and Engineers
(
John Wiley and Sons
,
New York, Chichester/Brisbane/Toronto
,
1981
).
78.
D. J.
Wales
,
Science
293
(
5537
),
2067
2070
(
2001
).
79.
M.
Valiev
,
E. J.
Bylaska
,
N.
Govind
,
K.
Kowalski
,
T. P.
Straatsma
,
H. J. J.
Van Dam
,
D.
Wang
,
J.
Nieplocha
,
E.
Apra
,
T. L.
Windus
, and
W. A.
de Jong
,
Comput. Phys. Commun.
181
(
9
),
1477
1489
(
2010
).
80.
A. D.
Becke
,
J. Chem. Phys.
98
(
2
),
1372
(
1993
).
81.
See supplementary material at http://dx.doi.org/10.1063/1.4867500 for atomic coordinates and energies of structures at zero force and at critical values corresponding to the instability.
82.
S.
Chapra
and
R.
Canale
,
Numerical Methods for Engineers
(
McGraw-Hill
,
2009
).
83.
C. L.
Dias
,
M.
Dube
,
F. A.
Oliveira
, and
M.
Grant
,
Phys. Rev. E
72
(
1
),
011918
(
2005
).
84.
D. J.
Lacks
,
J.
Willis
, and
M.-P.
Robinson
,
J. Phys. Chem. B
114
(
33
),
10821
10825
(
2010
).
85.
C. E.
Maloney
and
D. J.
Lacks
,
Phys. Rev. E
73
(
6
),
061106
(
2006
).
86.
O. K.
Dudko
,
A. E.
Filippov
,
J.
Klafter
, and
M.
Urbakh
,
Proc. Natl. Acad. Sci. U.S.A.
100
(
20
),
11378
11381
(
2003
).
87.
It should be noted, however, that the “force-clamp” scenario where the molecule is subjected to a constant force is a theoretical idealization. A more careful analysis must include the effect of handles that pull on the molecule (e.g., an optical trap or AFM cantilever), which effectively modifies the molecular PES. The force-clamp scenario considered here corresponds to the experimentally common soft handle case (see Refs. 34 and 35). In contrast, stiff handles could, in principle, stabilize any molecular configuration.

Supplementary Material

You do not currently have access to this content.