shifts and limited internal vibrational redistribution. Chem Phys 137(1–3):109–120
127. Agbo JK, Leitner DM, Myshakin EM, Jordan
KD (2007) Quantum energy flow and the
kinetics of water shuttling between hydrogen
bonding sites on trans-formanilide (TFA). J
Chem Phys 127:064310–064311
128. Agbo JK, Leitner DM, Evans DA, Wales DJ
(2005) Influence of vibrational energy flow
on isomerization of flexible molecules: incorporating non-RRKM kinetics in the simulation of dipeptide isomerization. J Chem Phys
123:124304
129. Agbo JK, Jain A, Leitner DM (2010) Quantum localization, dephasing and vibrational
energy flow in a trans-formanilide (TFA)H2O complex. Chem Phys 374:111–117
130. Patra S, Keshavamurthy S (2015) Classicalquantum correspondence in a model for conformational dynamics: connecting phase
space reactive islands with rare events sampling. Chem Phys Lett 634:1–10
131. Toda M (2005) Global aspects of chemical
reactions in multidimensional phase space.
Adv Chem Phys 130A:337–399
132. Hamm P, Lim M, Hochstrasser RM (1998)
Structure of the amide I band of peptides
measured by fs nonlinear-infrared spectroscopy. J Phys Chem B 102:6123–6138
133. Zhang Y, Fujisaki H, Straub JE (2009) Direct
evidence for mode-specific vibrational energy
relaxation from quantum time-dependent
perturbation theory. 1. Five-coordinate ferrous iron porphydin model. J Chem Phys
130:025102
134. Zhang Y, Fujisaki H, Straub JE (2009) Mode
specific vibrational energy relaxation of amide
I and II modes in N-methylacetamide/water
clusters: the intra- and inter-molecular energy
transfer mechanisms. J Phys Chem A
113:3051–3060
135. Austin RH, Xie A, Lvd M, Redlich B, Linga ˚rd
P-A, Frauenfelder H, Fu D (2005) Picosecond thermometer in the amide I band of
myoglobin. Phys Rev Lett 94:128101
136. Peterson KA, Rella CW, Engholm JR,
Schwettman HA (1999) Ultrafast vibrational
dynamics of the myoglobin amide I band. J
Phys Chem B 103:557–561
137. Moritsugu K, Miyashita O, Kidera A (2003)
Temperature dependence of vibrational
energy transfer in a protein molecule. J Phys
Chem B 107:3309–3317
138. Moritsugu K, Miyashita O, Kidera A (2000)
Vibrational energy transfer in a protein molecule. Phys Rev Lett 85:3970–3973
139. Newman M (2005) A measure of betweenness centrality based on random walks. Soc
Networks 27:39–54
140. Dijkstra EW (1959) A note on two problems
in connection with graphs. Numerische Math
1:269–271
141. Ren Z, Srajer V, Knapp JE, Royer WE (2012)
Cooperative macromolecular device revealed
by meta-analysis of static and time-resolved
structures. Proc Natl Acad Sci U S A
109:107–112
142. Nakayama T, Kousuke Y, Orbach RL (1994)
Dynamical properties of fractal networks:
scaling, numerical simulations, and physical
realizations. Rev Mod Phys 66:381–443
143. Reid KM, Yamato T, Leitner DM (2018)
Scaling of rates of vibrational energy transfer
in proteins with equilibrium dynamics and
entropy. J Phys Chem B 122:9331–9339.
https://doi.org/10.1021/acs.jpcb.8b07552
144. Maier JA, Martinez C, Kasavajhala K,
Wickstrom L, Hauser KE, Simmerling C
(2016) ff14SB: improving the accuracy of
protein side chain and backbone parameters
from ff99SB. J Chem Theor Compute
11:3696–3713
145. Berendsen H, Postma J, vanGunsteren W,
DiNola A, Haak J (1984) Moleculardynamics with coupling to an external bath.
J Chem Phys 81:3684–3690
146. Meister K, Ebbinghaus S, Xu Y, Duman JG,
DeVries A, Gruebele M, Leitner DM, Havenith M (2013) Long-range protein–water
dynamics in hyperactive insect antifreeze proteins. Proc Natl Acad Sci U S A
110:1617–1622
147. Leitner DM, Havenith M, Gruebele M
(2006) Biomolecule large amplitude motion
and solvation dynamics: modeling and probes
from THz to X-rays. Int Rev Phys Chem
25:553–582
148. Ebbinghaus S, Kim S-J, Heyden M, Yu X,
Heugen U, Gruebele M, Leitner DM, Havenith M (2007) An extended dynamical solvation shell around proteins. Proc Natl Acad Sci
U S A 104:20749–20752
149. Ebbinghaus S, Kim SJ, Heyden M, Yu X,
Gruebele M, Leitner DM, Havenith M
(2008)
Protein
sequenceand
pH-dependent hydration probed by terahertz
spectroscopy.
J
Am
Chem
Soc
130:2374–2375
150. Heugen U, Schwaab G, Bru ¨ndermann E,
Heyden M, Yu X, Leitner DM, Havenith M
(2006) Solute induced retardation of water
dynamics: hydration water probed directly
58
Korey M. Reid and David M. Leitner
127. Agbo JK, Leitner DM, Myshakin EM, Jordan
KD (2007) Quantum energy flow and the
kinetics of water shuttling between hydrogen
bonding sites on trans-formanilide (TFA). J
Chem Phys 127:064310–064311
128. Agbo JK, Leitner DM, Evans DA, Wales DJ
(2005) Influence of vibrational energy flow
on isomerization of flexible molecules: incorporating non-RRKM kinetics in the simulation of dipeptide isomerization. J Chem Phys
123:124304
129. Agbo JK, Jain A, Leitner DM (2010) Quantum localization, dephasing and vibrational
energy flow in a trans-formanilide (TFA)H2O complex. Chem Phys 374:111–117
130. Patra S, Keshavamurthy S (2015) Classicalquantum correspondence in a model for conformational dynamics: connecting phase
space reactive islands with rare events sampling. Chem Phys Lett 634:1–10
131. Toda M (2005) Global aspects of chemical
reactions in multidimensional phase space.
Adv Chem Phys 130A:337–399
132. Hamm P, Lim M, Hochstrasser RM (1998)
Structure of the amide I band of peptides
measured by fs nonlinear-infrared spectroscopy. J Phys Chem B 102:6123–6138
133. Zhang Y, Fujisaki H, Straub JE (2009) Direct
evidence for mode-specific vibrational energy
relaxation from quantum time-dependent
perturbation theory. 1. Five-coordinate ferrous iron porphydin model. J Chem Phys
130:025102
134. Zhang Y, Fujisaki H, Straub JE (2009) Mode
specific vibrational energy relaxation of amide
I and II modes in N-methylacetamide/water
clusters: the intra- and inter-molecular energy
transfer mechanisms. J Phys Chem A
113:3051–3060
135. Austin RH, Xie A, Lvd M, Redlich B, Linga ˚rd
P-A, Frauenfelder H, Fu D (2005) Picosecond thermometer in the amide I band of
myoglobin. Phys Rev Lett 94:128101
136. Peterson KA, Rella CW, Engholm JR,
Schwettman HA (1999) Ultrafast vibrational
dynamics of the myoglobin amide I band. J
Phys Chem B 103:557–561
137. Moritsugu K, Miyashita O, Kidera A (2003)
Temperature dependence of vibrational
energy transfer in a protein molecule. J Phys
Chem B 107:3309–3317
138. Moritsugu K, Miyashita O, Kidera A (2000)
Vibrational energy transfer in a protein molecule. Phys Rev Lett 85:3970–3973
139. Newman M (2005) A measure of betweenness centrality based on random walks. Soc
Networks 27:39–54
140. Dijkstra EW (1959) A note on two problems
in connection with graphs. Numerische Math
1:269–271
141. Ren Z, Srajer V, Knapp JE, Royer WE (2012)
Cooperative macromolecular device revealed
by meta-analysis of static and time-resolved
structures. Proc Natl Acad Sci U S A
109:107–112
142. Nakayama T, Kousuke Y, Orbach RL (1994)
Dynamical properties of fractal networks:
scaling, numerical simulations, and physical
realizations. Rev Mod Phys 66:381–443
143. Reid KM, Yamato T, Leitner DM (2018)
Scaling of rates of vibrational energy transfer
in proteins with equilibrium dynamics and
entropy. J Phys Chem B 122:9331–9339.
https://doi.org/10.1021/acs.jpcb.8b07552
144. Maier JA, Martinez C, Kasavajhala K,
Wickstrom L, Hauser KE, Simmerling C
(2016) ff14SB: improving the accuracy of
protein side chain and backbone parameters
from ff99SB. J Chem Theor Compute
11:3696–3713
145. Berendsen H, Postma J, vanGunsteren W,
DiNola A, Haak J (1984) Moleculardynamics with coupling to an external bath.
J Chem Phys 81:3684–3690
146. Meister K, Ebbinghaus S, Xu Y, Duman JG,
DeVries A, Gruebele M, Leitner DM, Havenith M (2013) Long-range protein–water
dynamics in hyperactive insect antifreeze proteins. Proc Natl Acad Sci U S A
110:1617–1622
147. Leitner DM, Havenith M, Gruebele M
(2006) Biomolecule large amplitude motion
and solvation dynamics: modeling and probes
from THz to X-rays. Int Rev Phys Chem
25:553–582
148. Ebbinghaus S, Kim S-J, Heyden M, Yu X,
Heugen U, Gruebele M, Leitner DM, Havenith M (2007) An extended dynamical solvation shell around proteins. Proc Natl Acad Sci
U S A 104:20749–20752
149. Ebbinghaus S, Kim SJ, Heyden M, Yu X,
Gruebele M, Leitner DM, Havenith M
(2008)
Protein
sequenceand
pH-dependent hydration probed by terahertz
spectroscopy.
J
Am
Chem
Soc
130:2374–2375
150. Heugen U, Schwaab G, Bru ¨ndermann E,
Heyden M, Yu X, Leitner DM, Havenith M
(2006) Solute induced retardation of water
dynamics: hydration water probed directly
58
Korey M. Reid and David M. Leitner