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A Cuban Campesino in Chemistry’s Academic Court

  • Rigoberto Hernandez*
    Rigoberto Hernandez
    Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
    Departments of Chemical & Biomolecular Engineering and Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
    *Email: [email protected]
    More by Rigoberto Hernandez
    Orcidhttps://orcid.org/0000-0001-8526-7414
Cite this: J. Phys. Chem. A 2021, 125, 30, 6505–6511
Publication Date (Web):July 23, 2021
https://doi.org/10.1021/acs.jpca.1c06072
Copyright © Published 2021 by American Chemical Society
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1. Introduction

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I doubt that Mark Twain ever envisioned the homage contained in the title. A Cuban campesino is quite a departure from the 19th century engineer who unexpectedly found himself transplanted to medieval England after a blow to the head. I have never worked in the fields in Cuba. My father, grandfather, and those before them did and can rightfully be called “campesinos.” That would have been my destiny had I not been teleported out of Cuba at a young age. My transition was no less dramatic than that experienced by Twain’s Connecticut Yankee but it did not violate the known laws of physics. Growing up in a low- to middle-class neighborhood filled with recent immigrants, it was equally unimaginable to be transported from Hialeah, FL, to Princeton, NJ, for college. The photos of me captured in Figure 1 show the contrast between my best high school self (from my high school yearbook) and later, ca. 2015. Both of these magical transitions shaped me from the beginning to think outside of the box and perhaps gave me a taste for the search for “insight” that is a cornerstone trait of most of the physical chemists that I have known.

Figure 1

Figure 1. Then and now. At left, Hernandez is pictured in his high school yearbook in a stylish cotton suit, gray leather shoes, and open collar which was on trend if different from the fashion of polos and tweed that would be the norm just a few months later upon teleporting to Princeton (photo by Mark Maynard). At right, Hernandez is pictured in his current work uniform featuring a tie, white dress shirt, and a jacket (photo by Robert R. Felt).

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Such out-of-the-box thinking may very well be reflected in the parallel research programs that I lead. Some of the work that I have done spanning across theoretical and computational chemistry, and in advancing diversity equity, is illustrated by the cover art shown in Figure 2. Like the Connecticut Yankee, I came to this duality by chance. Before I earned tenure, I was focused on doing what was required so that I could ensure the security of a permanent position. It is only through such security that I could then feel comfortable to take truly unconventional risks in pursuing new research directions and in advancing others.

Figure 2

Figure 2. A selected snapshot of Hernandez’s research efforts shown (clockwise from top left) through journal covers spanning across transition state theory (reprinted with permission from ref (1), copyright 2010 Elsevier), Janus and striped particles (reprinted with permission from ref (2), copyright 2014 AIP Publishing), diffusion through complex environments (reprinted with permission from ref (3), copyright 2010 American Chemical Society), stochastic hard collisions (reprinted with permission from ref (4), copyright 2018 Elsevier), sustainable nanoparticles (reprinted with permission from ref (5), copyright 2016 American Chemical Society), and diversity equity (reprinted with permission from ref (6), copyright 2018 American Chemical Society).

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2. Preliminaries

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Initially, my choice of path seemed simple, though the logistics of moving through it were less clear. I was curious about how the world worked. Science, math, and engineering offered both solutions to some of my questions, and a road to figuring out answers to the others. I stumbled through standardized testing without taking any of the now-standard prep courses, figured out how to fill out the financial-aid forms, applied to only 5 colleges because that was all that I could afford, and was lucky to receive full financial aid packages together with my college offers. I flew from Hialeah to Princeton alone and carried the entirety of my belongings in my travel bags. This was a far cry from the packed U-Hauls that some of my peers brought with them. My mother had started her tears three years prior when she first learned that I would be leaving home for college, but she was unable to see me to campus. In my freshman year, I used the menu posted in the cafeteria to learn about the foreign foods that were being served. What exactly is a casserole or asparagus? As the winter progressed, I quickly discovered that my Florida wardrobe was ill-suited for the cold and snow. Without the funds to purchase what I needed, I learned to layer my jackets. These representative challenges are no different than those faced by many other first-generation Pell-eligible students. I made it through because of the many classmates who accepted me for who I was, the mentors who came to my rescue, and the resources that Princeton provided to help me through the rough patches. The question for us lies in ensuring that such a support system is available for all of our students, not just the lucky ones.
At the moment of transition between two worlds, what would you change and what would you keep the same? Is each such change an adaptation or concession? In Florida, I had always gone by my full name because my father had instilled a sense of identity that should not be diminished by a nickname. However, I feared that few in college would be able to pronounce my full name and that using it might present a barrier to fitting in. So not long before I decided to apply to Princeton, I resolved to go by a nickname, Rig, in preparation for that transition. The nickname resolved most of the requirements and inadvertently removed the “Cuban” from my name. (7) In so doing, I also sent a message to everyone that I was willing to make accommodations even to the point of changing my identity. Later, in my late 30s, I decided to reclaim my identity and switched to asking everyone to call me by my full name once again. In so doing, I am asking to be seen for who I am, and it provides a way to bring my whole self into the interaction. It is important for all of us to choose our identity and how we want to be seen. It is equally important for us as mentors to allow our students and our colleagues to bring their true selves. It is about respect, and the fact that a truly diverse working group is more effective than one that is confined by the lens of a single culture.
At Princeton, thanks to the earlier advice from my junior high school chess coach, I resolved to study chemical engineering. The subject was interesting, and it solved the problem of satisfying my father’s desire for me to have a remunerative career. I worked in the laboratory of Kevin Lehman, then an assistant professor, starting in the summer after my freshman year through to my graduation. I eventually managed to contribute to a paper using random matrix theory to understand spectroscopic energy levels. (8) But I got the job mostly because I had taught myself how to build electronic circuits as a kid. Unfortunately, none of my experimental work in his laboratory was ever published. I went to Berkeley for graduate school because I discovered during my campus visits that a significant percentage of the faculty who were recruiting me had gone to Berkeley. Later I learned that this was not just anecdotally true but actually nearly representative across the academy because roughly 50% of the faculty received their degrees or postdoctoral training from one of the “top” 5–10 departments. (9) At the time, I was generally color-blind and ignored the fact that I was not like the others. I have no idea whether such color-blindness was equally applied to me, but there is no doubt that I was trying to figure out the rules the entire time. It is no different a challenge faced by our foreign students. It is also typical for those of us who are first-generation college students, whether they were born here or, like me, entered this country at an early age. I was lucky, though, because I was metaphorically adopted by many mentors along the way.
In graduate school, I fell into a project that was already using random matrix theory to describe the statistics of the quasi-bound states of formaldehyde in assessing its decay. We identified how the statistics of the decay distributions change as you vary the symmetries which are preserved through dissociation. (10,11) Doing so also required us to obtain an approach for obtaining the transition probabilities through the barrier. An older theory by my doctoral advisor, Bill Miller, (12) had established the approach for one-dimensional systems, (13) which we generalized to multidimensional systems using perturbation theory (PT). (14,15) The key was the use of canonical transformations—whether it is van Vleck PT in quantum mechanics or Lie Transform PT in classical mechanics—so that the perturbed (and generally nonseperable) Hamiltonian is labeled by good actions (or quantum numbers through Bohr–Sommerfeled correspondence). This led us to construct a fully consistent semiclassical transition state theory (16,17) which has since been used to obtain rates for even larger systems. (18−20) While we did not calculate the family of classical dividing surfaces parametrized by the reaction coordinate, (21−25) we did observe that such surfaces would be candidates for a more accurate rate flux as prescribed by variational transition state theory. (16,17)
I spent the first half of my PostDoc with Eli Pollak in part because of his early success in developing periodic orbit dividing surfaces for the exact determination of rates in two-dimensional systems. (26−28) However, the larger reason for me to work with Pollak (1,29) and later with Greg Voth (30,31) was to move away from gas phase reactions. Chemistry in the condensed phase is necessarily more complex because the number of degrees of freedom shoots up, dramatically increasing the effects from nonlinear coupling and heterogeneity. I later learned that choosing to pursue such occupational segregation (32) is typical among scientists from under-represented groups—e.g., women and under-represented people of color (URPOC)—as they tend to move in research directions that offer seemingly more hospitable career prospects. I do not know the degree to which this subconsciously affected my choice of research projects at the time, but I do know that I felt that I needed to come up with something novel and unusual if I was to succeed in finding an academic position.
The ethos at Georgia Tech when I first started as an assistant professor in 1996 was captured later by sophomore student Nick Selby during his 2013 New Student Convocation when he quoted Issac Newton, “If I have seen further, it is by standing on the shoulders of giants” but advised instead to “crush the shoulders of the giants upon whom we stand.” As a recent immigrant from a low-income background, I could not have afforded to take that advice. Instead, during my formative years, I took every opportunity to rise with the giants that had been before me and who were willing to champion me. Mostafa El-Sayed was my first champion at Georgia Tech. He took a big risk on me as he led my hire as a tenure-track assistant professor to venture into areas in which I had not previously worked. I took the risk of trying to go against the grain in polymer and protein science by introducing concepts that went against the dogma of both fields. In polymer reaction dynamics, I included the possible molecular scale interactions that could make polymerization not quite independent of molecular identity, (33−35) whereas in protein folding/unfolding we implemented a generic lattice model to demonstrate misfolding that ignored the degree of amino-acid specificity that is critical to much of biophysics. (36) Certainly there were skeptics, but there were also those who saw that I was breaking into new grounds. Besides El-Sayed, who had earlier reestablished the rethinking of physical chemistry to include all that physical chemists do, (37−39) I had new champions in Turgay Uzer (1,40) and Charles Eckert. (41,42) They saw that I was open to new ideas, and indeed actively working in areas that others had not ventured. It was enough for me to be awarded tenure and promotion.
While the value of tenure has been under assault because of a concern that it can lead to stagnation, for me, it has been a platform to take scientific and professional risks. To be honest, I was driven to take the uncharted path because I had few other choices. Perhaps this is not that unusual for those of us in physical chemistry. Anecdotally, I see most of you as thinking outside the box as you look for the insight that helps explain the intrinsic structure and function of atomic and molecular systems.
Perhaps the most important mindset switch in evolving as a professor was that I was no longer the center of my research universe. That is, my focus switched to my students and mentees, and I had to learn how to be effective in this new role. They, together with my collaborators, did all of the work in my group’s papers cited throughout this narrative. I do not call them out by name as I fear that there is not enough room to do so, and I would not want to leave any out. I am very thankful for the work that they did in my group, and for what they taught me over the past 25 years. More generally, a key takeaway from this article is the importance of mentoring to advance all doctoral students, and the need for providing mentoring equitably to ensure the commensurate success of students with backgrounds from under-represented groups. (43)

3. Research Track in Theoretical and Computational Chemistry

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As I considered how to steer my research program beyond tenure, I realized that while much of rate theory had been successful by assuming that reactions took place in nearly homogeneous solvents, the harder truth was that solvents are heterogeneous both in space and time. So I reimagined my evolving research program into a search for the full characterization of dynamics in complex environments. The concept was so foreign that my application to host a symposium on the topic in ca. 2000 was rejected by the Division of Physical Chemistry. However, at the suggestion of Joel Bowman, (44) I teamed up with Suzi Tucker (45) to pitch the topic as a workshop to the Telluride Science Research Center. I had known Suzi since when I was a graduate student attending the West Coast Theoretical Chemistry conference at PNNL, where she delivered an invited lecture. She was equally adept at deriving equations in transition state theory as in mountain biking down a double-diamond slope in the summer. Her success had already helped me believe that I too could be different and think differently as a professor, and I had no doubt that she would embrace Chemical Dynamics in Complex Environments (Chem-DiCE) as a topic. The workshop has now been held biennially since 2001, and we just staged the eleventh one in the series this summer. We invite theoretical and experimental researchers from distant disciplines to share in the techniques and tools that they are using to tease out phenomena at various scales. Examples in my work include the connections that I found between nonequilibrium rate theories and thermosetting polymers. (34) We also examined the nontrivial dynamics of energy landscapes with multiple deep funnels (36) and found evidence that some frustration could be an important driver in protein funding. (46) In recent years, Chem-DiCE has become more mainstream, though it has been narrowed a bit to include mostly ultrafast and related phenomenon. (47−49) I invite all of us to think differently and once again reimagine the need to resolve Chem-DiCE as part of this century’s grand challenge to resolve space and time across multiple chemical scales simultaneously. (50)
The Nobel Prize, well earned by Levitt, Karplus, and Warshell in 2013, cited them “for the development of multiscale models for complex chemical systems.” (51) Together with the tools that followed, (52−56) this has led to many advances in molecular simulations, including the recent signature achievement by Rommie Amaro and her co-workers demonstrating the structure of the spike protein using all-atom MD. (57) However, the bridge between electrons and nuclei only resolves one of the multiscale challenges, and Herculean computer efforts to use all-atom simulations are likely not enough to bridge the scales to moles and seconds. So the challenge for this century, and indeed one that is being tackled by many of us in physical chemistry, lies in developing transferable and correct equations of motion at multiple scales. I have termed the requirement on such equivalences as dynamical consistency. (5,58) Searching for these multiscale equations remains a fertile area for my research group and indeed our entire community. To resolve it, we have no choice but to think differently.
In our academic court, we have a range of professional titles qualifying our roles as professors. Notably, my program—that is, the Open Chemistry Collaborative in Diversity Equity (OXIDE)—found in our recent survey of the top 50 chemistry departments that of its 1,053 full professors, only 40 are under-represented people of color (URPOC). (59) Of these 40, even fewer are chaired or distinguished professors. When Johns Hopkins invited me to join their chemistry department as the Gompf Family Professor while also investing in ways for us to think differently about chemistry, I felt compelled to accept because of the opportunity it afforded both my group and me. I was also fully aware that I would now be among the few URPOC chaired professors in chemistry, and that this would be one more step toward shifting representation toward equity. I rallied my research group to join me in the move and to explore truly multidisciplinary and collaborative chemistry. (60,61) The move helped me to concentrate our research into several disparate lines of research: transition state theory in driven systems, (62−64) adaptive steered molecular dynamics, (65−67) nonequilibrium Chem-DiCE, (4,68) and the multiscale dynamics of nanoparticles in heterogeneous systems. (5,69−72) That is, thinking differently does not have to come at the expense of order and clarity within each research silo. Students considering their entry into our profession do not always have to make the same choices, but they should feel comfortable in the fact that their academic careers can reach across their varied interests.
Meanwhile, those of us already in the academy need to rethink how we evaluate the future potential of our junior colleagues because their present portfolios may not match those of our own experience. We need to think differently in lock-step with each other. This does not mean that we need to look like our mentors or mentees. We simply have to be open to the fact that being different, like thinking differently, can enrich us as we learn from each other.

4. Research Track in Diversity Equity

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Shortly after I was awarded tenure at Georgia Tech, I was invited to attend an NRC workshop on Diversity Models That Work. (73) Despite the many successes they reported, it seemed to me that many of them were ignoring the elephant in the room: Why had the academic track been statistically less desirable—and perhaps less hospitable—to URPOC scientists? They are familiar with the professorial profession from their time at undergraduate and graduate schools and yet were preferentially choosing to go to other careers. One challenge to those who are tempted to pursue academic careers lies in justifying the academic track to themselves and their families given the many obstacles to success in comparison to seemingly less risky and highly remunerative alternatives. These were the questions that I had faced throughout my own career path. I navigated through it only because of the many mentors who helped me find solutions, but even then, it was not without substantial risk and perhaps a naively optimistic inner drive. Unfortunately, my choice has been all too rare among URPOC scientists. (74) If we are to start increasing representation, then we certainly need to be more intentional in training and recruiting women and URPOC scientists, and that means developing and supporting pipeline programs. (75) We also need to make the academy more hospitable and equitable, and therefore a desirable destination. This latter perspective was somewhat unique at the time, and I felt compelled to join the cause. My remarks also drew the attention of Robert Lichter, who invited me to join the ACS Minorities in Academe Implementation team in 2003. Once again, I was an unusual guest. The rest of the members were ACS governance insiders, present or future ACS presidents, long-time heroes in the fight to lower inequities, or all of the above. I learned much from their mentoring, and they encouraged me toward my second research and advocacy program in advancing diversity equity.
I later learned from Isiah Warner that diversity is a planned event. That is, one must ensure that every part of its program and location does not contain stereotype threats (76) that dissuade equitable participation. So when I had the opportunity to chair and host the 75th Herty Medalist Celebration, (77) I steered all the events to be as inclusive as possible following the example of the Herty Medal Undergraduate Research Symposium (HMURS), which I had founded three years earlier to provide more interactions between undergraduate students in the greater Atlanta area. We staged it at Morehouse to encourage broader participation, and we invited speakers that represented inclusive excellence. This annual event continues to be hosted by the Georgia Section of the ACS, and it has helped provide mentoring opportunities for nearly 1,000 students. The other events of the 75th Herty Medalist Celebration, including a graduate student symposium and several high school outreach events, were equally successful in engaging broad and diverse participants and speakers.
I then turned my attention to change the academic court itself. In 2006, a number of mavens at the NSF, NIH, and DOE instigated a workshop on gender equity at which they highly encouraged the participation of chairs and heads from the top 50 federally funded chemistry departments. (78) It led to many gains, but there was no clear path for continued follow-up with the chairs regarding gender equity. The success of the program did lead to the staging of subsequent workshops on equity for under-represented minorities and disability equity. I was a member of the organizing committee for the NSF Workshop on Excellence Empowered by a Diverse Workforce held in 2007 with the chairs of the top 50 chemistry departments. (79) It was successful in engaging the community toward finding new practices and policies to reduce inequities, but again, there was no clear path for continued follow-up. A few of us recognized that each department has only one chair or head, and they would not likely have the time to attend four distinct workshops every one to two years. To the question of how the diversity equity workshops would be sustained, I was advised that the agencies could do so only if the community submitted an appropriate proposal to hold such workshops. I led a planning committee to identify the principal investigators to write the proposal to support the advancement and equity for all of the under-represented groups—women, URPOC, gender identity and orientations, and people with disabilities. The planning committee convinced me that I should lead the staging of what would become biennial National Diversity Equity Workshops (NDEWs) through the ensuing OXIDE effort. (80) This opened up a parallel effort in my research group. (81) Most of the prior workshop reports had been published in ad hoc locations which were not easily citable. We made it an objective not only to make our reports citable but also to include them in DOI linked locations. (82−85) This was the beginning of establishing our scholarship in the context of the lens of discipline-based diversity research. There are, of course, many other precedents; see, e.g, refs (86), (73), and (9). Our discipline-based diversity research is distinguished by the fact that we learned from the social science community how to identify barriers to diversity equity in chemistry and how to adapt possible solutions within our academic culture in chemistry. This led us to publish recommendations on our Web site and in print. (87) We have been driven by the top-down hypothesis that solutions must be led intentionally from the top—that is, department heads and chairs or other powerful administrators—because they are the stewards of the infrastructure. (80,81) Any systemic bias or inequity in the academic culture must be eradicated collectively by its leaders. As Warner says, this can only happen by intention, and much of OXIDE’s work has been driven to mobilize that intention.

5. Concluding Remarks

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So what is the insight gained from these anecdotal stories? Years ago, I read the book Think Like a Grandmaster, (88) which entreated readers to understand positional chess, not just the immediate tactics. To train the next generation of physical chemists, we must teach them to think like a physical chemist, not just to learn the body of physical chemistry enshrined in our Journal and textbooks. As we mentor them, we also need to appreciate that their context—that is, the environment in which they live—is diverse. We cannot expect that each such future colleague will transform themselves to look like those already in the academic court. Instead, we must transform ourselves to be diverse and inclusive. Or, to put it simply, we do not need to fix the student, we need to fix the system. This way of thinking is precisely what has driven our OXIDE research effort, and my research group’s work in theoretical and computational chemistry. In the former case, we learned that diversity in the academic court is not achieved accidentally but rather by the intentional work of the people in leadership guiding it at all levels. In the latter case, we continue to drive toward resolving complexity, not just through the tactics required for a particular solution, but also through a positional approach. Within my chemical research, my group aims to resolve dynamical consistency in the equations of motion across multiple time and length scales (89) because it is a grand challenge for this century.

Author Information

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  • Corresponding Author
    • Rigoberto Hernandez,  Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States;  Departments of Chemical & Biomolecular Engineering and Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States,  Orcidhttps://orcid.org/0000-0001-8526-7414,  Email: [email protected]
    • Notes
      The author declares no competing financial interest.

      This Viewpoint is jointly published in The Journal of Physical Chemistry A/B/C.


      Views expressed in this Viewpoint are those of the author and not necessarily those of the ACS.

    Acknowledgments

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    My recent theoretical and computational chemistry work has been supported by the National Science Foundation (NSF) through Grant No. CHE-1700749, No. CHE 2001611, and No. OAC-1940152. My recent diversity equity work has been supported by the Sloan Foundation. I am grateful for the recognition and support from the Research Corporation for Science Advancement throughout my academic career. My deep thanks to my research collaborator, Alex Popov, who has been a leader in my theoretical and computational chemistry group since 2004. The OXIDE program would not have succeeded were it not for the work of Dontarie Stallings, Srikant Iyer, and Shannon Watt. Finally, in addition to those already called out by name in the main text, I thank the many mentors that helped me throughout my career, including Dorothy Takos (my sixth grade teacher), Robert Reichert (my junior high school chess coach and math teacher), Charlie Fefferman, Pablo Debenedetti, Rob Tycko, John Tully, Peter Rossky, Silvia Ronco, Linda Raber, Michael Doyle, Peter Saalfrank, Elizabeth Boylan, Celeste Rohlfing, Janice Hicks, Michelle Francl, George Shields, Peter Dorhout Jörg Main, Tom Connelly, and Luis Echegoyen. Many thanks also to my Hialeah High School colleagues and Isaura Delgado, in particular, for helping to identify the photographer who had the rights to the “then” photo in Figure 1.

    References

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    This article references 89 other publications.

    1. 1
      Hernandez, R.; Bartsch, T.; Uzer, T. Transition State Theory in Liquids Beyond Planar Dividing Surfaces. Chem. Phys. 2010, 370, 270– 276,  DOI: 10.1016/j.chemphys.2010.01.016
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      Transition state theory in liquids beyond planar dividing surfaces
      Hernandez, Rigoberto; Uzer, T.; Bartsch, Thomas
      Chemical Physics (2010), 370 (1-3), 270-276CODEN: CMPHC2; ISSN:0301-0104. (Elsevier B.V.)
      The success of transition state theory (TST) in describing the rates of chem. reactions has been less-than-perfect in soln. (and sometimes even in the gas phase) because conventional dividing surfaces are only approx. free of recrossings between reactants and products. Recent advances in dynamical systems theory have helped to identify the interconnected manifolds-"superhighways"-leading from reactants to products. The existence of these manifolds has been proven rigorously, and explicit algorithms are available for their calcn. We now show that these extended structures can be used to obtain reaction rates directly in dissipative systems. We also suggest a treatment for the substantially more general case in which the mol. solvent is fully specified by the positions of all its atoms. Specifically, we can construct effective solvent configurations for which the exact TST manifolds can be constructed and used to sample the rates of an open system.
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    2. 2
      Hagy, M. C.; Hernandez, R. Dynamical simulation of electrostatic striped colloidal particles. J. Chem. Phys. 2014, 140, 034701,  DOI: 10.1063/1.4859855
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      2
      Dynamical simulation of electrostatic striped colloidal particles
      Hagy, Matthew C.; Hernandez, Rigoberto
      Journal of Chemical Physics (2014), 140 (3), 034701/1-034701/13CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The static and dynamic properties of striped colloidal particles are obtained using mol. dynamics computer simulations. Striped particles with n = 2 to n = 7 stripes of alternating elec. charge are modeled at a high level of detail through a pointwise (PW) representation of the particle surface. We also consider the extent to which striped particles are similar to comparable isotropically attractive particles-such as depletion attracting colloids-by modeling striped particles with an isotropic pair interaction computed by coarse-graining (CG) over orientations at a pair level. Surprisingly, the CG models reproduce the static structure of the PW models for a range of vol. fractions and interaction strengths consistent with the fluid region of the phase diagram for all n. As a corollary, different n-striped particle systems with comparable pair affinities (e.g., dimer equil. const.) have similar static structure. Stronger pair interactions lead to a collapsed structure in simulation as consistent with a glass-like phase. Different n-striped particle systems are found to have different phase boundaries and for certain n's no glass-like state is obsd. in any of our simulations. The CG model is found to have accelerated dynamics relative to the PW model for the same range of fluid conditions for which the models have identical static structure. This suggests striped electrostatic particles have slower dynamics than comparable isotropically attractive colloids. The slower dynamics result from a larger no. of long-duration reversible bonds between pairs of striped particles than seen in isotropically attractive systems. Higher n-striped particles systems generally have slower dynamics than lower n-striped systems with comparable pair affinities. (c) 2014 American Institute of Physics.
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    3. 3
      Tucker, A. K.; Hernandez, R. Observation of a trapping transition in the diffusion of a thick needle through fixed point scatterers. J. Phys. Chem. A 2010, 114, 9628– 9634,  DOI: 10.1021/jp100111y
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      3
      Observation of a Trapping Transition in the Diffusion of a Thick Needle through Fixed Point Scatterers
      Tucker, Ashley K.; Hernandez, Rigoberto
      Journal of Physical Chemistry A (2010), 114 (36), 9628-9634CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      The long-time correlation functions of an infinitesimally thin needle moving through stationary point scatterers--a so-called Lorentz model--exhibits surprisingly long-time tails. These long-time tails are now seen to persist in a two-dimensional model even when the needle has a finite thickness. If the needles are too thick, then the needles are effectively trapped at all nontrivial densities of the scatterers. At needle widths approx. equal to or smaller than σ = ε/20 where ε is the av. spacing between scatterers, the needle diffuses and exhibits the crossover transition from the expected Enskog behavior to the enhanced translation diffusion seen earlier by Hofling, Frey and Franosch. At this needle width, an increase in its center-of-mass diffusion with respect to increasing d. is seen after a crossover d. of n* ≈ 5 is reached. (The reduced d. n* is defined as n* = nL2 where n is the no. d. of particles and L is the needle length.). The crossover transition for needles with finite thickness is spread over a range of densities exhibiting intermediate behavior. The asymptotic divergence of the center of mass diffusion is suppressed compared to that of infinitely thin needles. Finally, a new diminished diffusion regime, apparently due to the increased importance of head-on collisions, now appears at high scattering densities.
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    4. 4
      Singh, R. S.; Hernandez, R. Modeling soft core-shell colloids using stochastic hard collision dynamics. Chem. Phys. Lett. 2018, 708, 233– 240,  DOI: 10.1016/j.cplett.2018.08.032
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      Modeling soft core-shell colloids using stochastic hard collision dynamics
      Singh, Rakesh S.; Hernandez, Rigoberto
      Chemical Physics Letters (2018), 708 (), 233-240CODEN: CHPLBC; ISSN:0009-2614. (Elsevier B.V.)
      The equil. structure and thermodn. behavior of a soft matter suspension of hard-core soft-shell (HCSS) colloids have been modeled using stochastic hard collision (SHC) dynamics [Craven et al., J. Chem. Phys. 2013, 138, 244901]. SHC dynamics includes the effects of inter-penetrability of soft particles while retaining the computational efficiency of hard collision dynamics. The HCSS colloids are characterized using two parameters: softness parameter (a measure of the propensity toward interpenetration), and core-to-shell ratio. In both, mol. dynamics and Monte-Carlo simulations, the softness parameter is seen to profoundly affect the effective packing fraction and the thermodn. behavior of the system. Once we accounted for the trivial effects from changes in the reduced vol. fraction on changing softness, we found that the inter-particle penetration continues to affect this thermodn. behavior. The structural origin of this nontrivial effect likely lies in the loss of translational order upon increasing softness.
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    5. 5
      Cui, Q.; Hernandez, R.; Mason, S. E.; Frauenheim, T.; Pedersen, J. A.; Geiger, F. Mini-review. Sustainable nanotechnology: Opportunities and challenges for theoretical/computational studies. J. Phys. Chem. B 2016, 120, 7297– 7306,  DOI: 10.1021/acs.jpcb.6b03976
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      5
      Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies
      Cui, Qiang; Hernandez, Rigoberto; Mason, Sara E.; Frauenheim, Thomas; Pedersen, Joel A.; Geiger, Franz
      Journal of Physical Chemistry B (2016), 120 (30), 7297-7306CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      For assistance in the design of the next generation of nanomaterials that are functional and have minimal health and safety concerns, it is imperative to establish causality, rather than correlations, in how properties of nanomaterials det. biol. and environmental outcomes. Due to the vast design space available and the complexity of nano/bio interfaces, theor. and computational studies are expected to play a major role in this context. In this minireview, we highlight opportunities and pressing challenges for theor. and computational chem. approaches to explore the relevant physicochem. processes that span broad length and time scales. We focus discussions on a bottom-up framework that relies on the detn. of correct intermol. forces, accurate mol. dynamics, and coarse-graining procedures to systematically bridge the scales, although top-down approaches are also effective at providing insights for many problems such as the effects of nanoparticles on biol. membranes.
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    6. 6
      Hernandez, R.; Stallings, D.; Iyer, S. K. In National Diversity Equity Workshops in Chemical Sciences (2011–2017); Hernandez, R., Stallings, D., Iyer, S. K., Eds.; ACS Symposium Series; American Chemical Society; Oxford University Press: Washington DC, 2018; Vol. 1277.
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    7. 7
      Hernandez, R. What’s in a name? (Part 1). 2013; http://everywherechemistry.blogspot.com/2013/04/whats-in-name-part-1.html, accessed January 15, 2021.
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    8. 8
      Coy, S. L.; Hernandez, R.; Lehmann, K. K. Limits on the transition to Gaussian orthogonal ensemble behavior: Saturated radiationless transitions between strongly coupled potential surfaces. Phys. Rev. A: At., Mol., Opt. Phys. 1989, 40, 5935– 5949,  DOI: 10.1103/PhysRevA.40.5935
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    9. 9
      Nolan, S. A.; Buckner, J. P.; Kuck, V. J.; Marzabadi, C. H. Analysis by Gender of the Doctoral and Postdoctoral Institutions of Faculty Members at the Top-Fifty Ranked Chemistry Departments. J. Chem. Educ. 2004, 81, 356,  DOI: 10.1021/ed081p356
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      9
      Analysis by gender of the doctoral and postdoctoral institutions of faculty members at the top-fifty ranked chemistry departments
      Kuck, Valerie J.; Marzabadi, Cecilia H.; Nolan, Susan A.; Buckner, Janine P.
      Journal of Chemical Education (2004), 81 (3), 356-363CODEN: JCEDA8; ISSN:0021-9584. (Journal of Chemical Education, Dept. of Chemistry)
      There is no expanded citation for this reference.
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    10. 10
      Miller, W. H.; Hernandez, R.; Moore, C. B.; Polik, W. F. A transition state theory-based statistical distribution of unimolecular decay rates, with application to unimolecular decomposition of formaldehyde. J. Chem. Phys. 1990, 93, 5657– 5666,  DOI: 10.1063/1.459636
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      10
      A transition state theory-based statistical distribution of unimolecular decay rates with application to unimolecular decomposition of formaldehyde
      Miller, William H.; Hernandez, Rigoberto; Moore, C. Bradley; Polik, William F.
      Journal of Chemical Physics (1990), 93 (8), 5657-66CODEN: JCPSA6; ISSN:0021-9606.
      A statistical distribution of state-specific unimol. decay rates is derived (within the framework of random matrix theory) that is detd. completely by the transition state properties of the potential energy surface. It includes the std. χ-square distributions as a special case. Model calcns. are presented to show the extent to which it can differ from the χ-square distribution, and specific application is made to the state-specific unimol. decay rate data for D2CO → D2 + CO.
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    11. 11
      Hernandez, R.; Miller, W. H.; Moore, C. B.; Polik, W. F. A Random Matrix/Transition State Theory for the Probability Distribution of State-Specific Unimolecular Decay Rates: Generalization to Include Total Angular Momentum Conservation and Other Dynamical Symmetries. J. Chem. Phys. 1993, 99, 950– 962,  DOI: 10.1063/1.465360
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      11
      A random matrix/transition state theory for the probability distribution of state-specific unimolecular decay rates: generalization to include total angular momentum conservation and other dynamical symmetries
      Hernandez, Rigoberto; Miller, William H.; Moore, C. Bradley; Polik, William F.
      Journal of Chemical Physics (1993), 99 (2), 950-62CODEN: JCPSA6; ISSN:0021-9606.
      A previously developed random matrix/transition state theory (RM/TST) model for the probability distribution of state-sp. unimol. decay rates was generalized to incorporate total angular momentum conservation and other dynamic symmetries. The model is made into a predictive theory by using a semiclassical method to det. the transmission probabilities of a nonseparable rovibrational Hamiltonian at the transition state. The overall theory gives a good description of the state-sp. rates for the D2CO → D2 + CO unimol. decay; in particular, it describes the dependence of the distribution of rates on total angular momentum J. Comparison of the exptl. values with results of the RM/TST theory suggests that there is mixing among the rovibrational states.
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    12. 12
      Miller, W. H. Autobiographical Sketch of William Hughes Miller. J. Phys. Chem. A 2001, 105, 2487– 2489,  DOI: 10.1021/jp0101920
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    13. 13
      Miller, W. H. Semi-classical theory for non-separable systems:. Construction of “good” action-angle variables for reaction rate constants. Faraday Discuss. Chem. Soc. 1977, 62, 40,  DOI: 10.1039/DC9776200040
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      13
      Semiclassical theory for non-separable systems: construction of good action-angle variables for reaction rate constants
      Miller, William H.
      Faraday Discussions of the Chemical Society (1977), 62 (Potential Energy Surf.), 40-6CODEN: FDCSB7; ISSN:0301-7249.
      A semiclassical expression for bimol. rate consts. for reactions which have a single activation barrier is obtained in terms of the good action variables of the classical Hamiltonian which are assocd. with the saddle point region of the potential energy surface. The formulas apply to nonseparable and separable saddle points.
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    14. 14
      Miller, W. H.; Hernandez, R.; Handy, N. C.; Jayatilaka, D.; Willetts, A. Ab initio calculation of anharmonic constants for a transition state, with application to semiclassical transition state tunneling probabilities. Chem. Phys. Lett. 1990, 172, 62– 68,  DOI: 10.1016/0009-2614(90)87217-F
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      14
      Ab initio calculation of anharmonic constants for a transition state, with application to semiclassical transition state tunneling probabilities
      Miller, William H.; Hernandez, Rigoberto; Handy, Nicholas C.; Jayatilaka, Dylan; Willetts, Andrew
      Chemical Physics Letters (1990), 172 (1), 62-8CODEN: CHPLBC; ISSN:0009-2614.
      "Good" (i.e. conserved) action variables exist in the vicinity of a saddle point (i.e. transition state) of a potential energy surface in complete analogy to those related to a min. on the surface. Transition state theory tunneling (or transmission) probabilities can be expressed semiclassically in terms of these "good" action variables, including the effects of non-separable coupling of all degrees of freedom with each other. This paper shows how ab initio quantum chem. methods recently developed for calcg. anharmonic consts. about a potential min. (i.e. for ordinary vibrational energy levels) can be readily adapted to obtain those related to a transition state, thus providing a rigorous and practical way to apply this non-separable transition state theory. Application is made to the transition state for the reaction D2CO → D2 + CO.
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    15. 15
      Cohen, M. J.; Handy, N. C.; Hernandez, R.; Miller, W. H. Cumulative reaction probabilities for H + H2 → H2 + H from a knowledge of the anharmonic force field. Chem. Phys. Lett. 1992, 192, 407– 416,  DOI: 10.1016/0009-2614(92)85491-R
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      15
      Cumulative reaction probabilities for atomic hydrogen + molecular hydrogen → molecular hydrogen + atomic hydrogen from a knowledge of the anharmonic force field
      Cohen, Michael J.; Handy, Nicholas C.; Hernandez, Rigoberto; Miller, William H.
      Chemical Physics Letters (1992), 192 (4), 407-16CODEN: CHPLBC; ISSN:0009-2614.
      In an earlier publication, the authors showed how knowledge of a quartic force field expanded about a transition state can be used to obtain transition-state-theory tunneling probabilities. Thus coupling between the reaction mode and other modes is included in this second-order perturbation theory approach. The authors study the very anharmonic reaction H+H2→H2+H and show that even in this extreme case, there is reasonable agreement between the cumulative reaction probabilities calcd. by this semiclassical approach, and full quantum calcns.
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    16. 16
      Hernandez, R.; Miller, W. H. Semiclassical Transition State Theory. A New Perspective. Chem. Phys. Lett. 1993, 214, 129– 136,  DOI: 10.1016/0009-2614(93)90071-8
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      16
      Semiclassical transition state theory. A new perspective
      Hernandez, Rigoberto; Miller, William H.
      Chemical Physics Letters (1993), 214 (2), 129-36CODEN: CHPLBC; ISSN:0009-2614.
      The semiclassical transition state theory (SCTST) introduced by W. H. Miller et al. (1990) requires the inversion of an (effectively integrable) Hamiltonian with respect to the action of the reactive coordinate. The inversion may be avoided in computing the thermal rate const.; the resulting expression provides an appealing link to conventional transition state theory. This reformulation of the SCTST rate is illustrated by application to the bimol. reaction, H + H2 → H2 + H, and to the unimol. dissocn., D2CO → D2 + CO.
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    17. 17
      Hernandez, R. A Combined Use of Perturbation Theory and Diagonalization: Application to Bound Energy Levels and Semiclassical Rate Theory. J. Chem. Phys. 1994, 101, 9534– 9547,  DOI: 10.1063/1.467985
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      17
      A combined use of perturbation theory and diagonalization: application to bound energy levels and semiclassical rate theory
      Hernandez, Rigoberto
      Journal of Chemical Physics (1994), 101 (11), 9534-47CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      A new method, mixed diagonalization, is introduced in which an effective Hamiltonian operator acting on a reduced dimensional space is constructed using the similarity transformations of canonical Van Vleck perturbation theory (CVPT). This construction requires the characterization of modes into two categories, global and local, which in the bound vibrational problem are tantamount to the large and small amplitude vibrations, resp. The local modes in the Hamiltonian are projected out by CVPT, and the resulting Hamiltonian operator acts only on the space of global modes. The method affords the treatment of energy levels of bound systems in which some vibrational assignments are possible. It systematically provides a reduced dimensional Hamiltonian which is more amenable to exact numerical soln. that the original full-dimensional Hamiltonian. In recent work, a semiclassical transition state theory (SCTST) rate expression was written in terms of a Hamiltonian operator parameterized by the imaginary action along the local reaction path in the transition state region [Chem. Phys. Lett. 214, 129(1993)]. The Hamiltonian constructed by mixed diagonalization has this form, and can be used to obtain more accurate semiclassical rate expressions.
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    18. 18
      Nguyen, T. L.; Stanton, J. F.; Barker, J. R. Ab Initio Reaction Rate Constants Computed Using Semiclassical Transition-State Theory: HO + H2 → H2O + H and Isotopologues. J. Phys. Chem. A 2011, 115, 5118– 5126,  DOI: 10.1021/jp2022743
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      18
      Ab Initio Reaction Rate Constants Computed Using Semiclassical Transition-State Theory: HO + H2 → H2O + H and Isotopologues
      Nguyen, Thanh Lam; Stanton, John F.; Barker, John R.
      Journal of Physical Chemistry A (2011), 115 (20), 5118-5126CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      A new algorithm for the semiclassical transition-state theory (SCTST) formulated by W.H. Miller and co-workers is used to compute rate consts. for the isotopologues of the title reaction, with no empirical adjustments. The SCTST and relevant results from second-order vibrational perturbation theory (VPT2) are summarized. VPT2 is used at the CCSD(T) level of electronic structure theory to compute the anharmonicities of the fully coupled vibrational modes (including the reaction coordinate) of the transition structure. The anharmonicities are used in SCTST to compute the rate consts. over the temp. range from 200 to 2500 K. The computed rate consts. are compared to exptl. data and theor. calcns. from the literature. The SCTST results for abs. rate consts. and for both primary and secondary isotope effects are in excellent agreement with the exptl. data for this reaction over the entire temp. range. The sensitivity of SCTST to various parameters is investigated by using a set of simplified models. The results show that multidimensional tunneling along the curved reaction path is important at low temps. and the anharmonic coupling among the vibrational modes is important at high temps. The theor. kinetics data are also presented as fitted empirical algebraic expressions.
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    19. 19
      Barker, J. R.; Nguyen, T. L.; Stanton, J. F. Kinetic Isotope Effects for Cl + CH4 → HCl + CH3 Calculated Using ab Initio Semiclassical Transition State Theory. J. Phys. Chem. A 2012, 116, 6408– 6419,  DOI: 10.1021/jp212383u
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      Kinetic Isotope Effects for Cl + CH4 .dblharw. HCl + CH3 Calculated Using ab Initio Semiclassical Transition State Theory
      Barker, John R.; Nguyen, Thanh Lam; Stanton, John F.
      Journal of Physical Chemistry A (2012), 116 (24), 6408-6419CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      Calcns. were carried out for 25 isotopologues of the title reaction for various combinations of 35Cl, 37Cl, 12C, 13C, 14C, H, and D. The computed rate consts. are based on harmonic vibrational frequencies calcd. at the CCSD(T)/aug-cc-pVTZ level of theory and Xij vibrational anharmonicity coeffs. calcd. at the CCSD(T) /aug-cc-pVDZ level of theory. For some reactions, anharmonicity coeffs. were also computed at the CCSD(T)/aug-cc-pVTZ level of theory. The classical reaction barrier was taken from Eskola et al. [J. Phys. Chem. A 2008, 112, 7391-7401], who extrapolated CCSD(T) calcns. to the complete basis set limit. Rate consts. were calcd. for temps. from ∼100 to ∼2000 K. The computed ab initio rate const. for the normal isotopologue is in good agreement with expts. over the entire temp. range (∼10% lower than the recommended exptl. value at 298 K). The ab initio H/D kinetic isotope effects (KIEs) for CH3D, CH2D2, CHD3, and CD4 are in very good agreement with literature exptl. data. The ab initio 12C/13C KIE is in error by ∼2% at 298 K for calcns. using Xij coeffs. computed with the aug-cc-pVDZ basis set, but the error is reduced to ∼1% when Xij coeffs. computed with the larger aug-cc-pVTZ basis set are used. Systematic improvements appear to be possible. The present SCTST results are found to be more accurate than those from other theor. calcns. Overall, this is a very promising method for computing ab initio kinetic isotope effects.
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    20. 20
      Nguyen, T. L.; Stanton, J. F. Ab Initio Thermal Rate Calculations of HO + HO → O(3P) + H2O Reaction and Isotopologues. J. Phys. Chem. A 2013, 117, 2678– 2686,  DOI: 10.1021/jp312246q
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      20
      Ab Initio Thermal Rate Calculations of HO + HO = O(3P) + H2O Reaction and Isotopologues
      Nguyen, Thanh Lam; Stanton, John F.
      Journal of Physical Chemistry A (2013), 117 (13), 2678-2686CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      The forward and reverse reactions, HO + HO .dblharw. O(3P) + H2O, which play roles in both combustion and lab. studies, were theor. characterized with a master equation approach to compute thermal reaction rate consts. at both the low and high pressure limits. Our ab initio k(T) results for the title reaction and two isotopic variants agree very well with expts. (within 15%) over a wide temp. range. The calcd. reaction rate shows a distinctly non-Arrhenius behavior and a strong curvature consistent with the expt. This characteristic behavior is due to effects of pos. barrier height and quantum mech. tunneling. Tunneling is very important and contributes more than 70% of total reaction rate at room temp. A prereactive complex is also important in the overall reaction scheme.
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    21. 21
      Komatsuzaki, T.; Berry, R. S. Regularity in chaotic reaction paths. I. Ar6. J. Chem. Phys. 1999, 110, 9160– 9173,  DOI: 10.1063/1.478838
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      21
      Regularity in chaotic reaction paths. I. Ar6
      Komatsuzaki, Tamiki; Berry, R. Stephen
      Journal of Chemical Physics (1999), 110 (18), 9160-9173CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      We scrutinize the saddle crossings of a simple cluster of six atoms to show (a) that it is possible to choose a coordinate system in which the transmission coeff. for the classical reaction path is unity at all energies up to a moderately high energy, above which the transition state is chaotic; (b) that at energies just more than sufficient to allow passage across the saddle, all or almost all the degrees of freedom of the system are essentially regular in the region of the transition state; and (c) that the degree of freedom assocd. with the reaction coordinate remains essentially regular through the region of the transition state, even to moderately high energies. Microcanonical mol. dynamics simulation of Ar6 bound by pairwise Lennard-Jones potentials reveals the mechanics of passage. We use Lie canonical perturbation theory to construct the nonlinear transformation to a hyperbolic coordinate system which reveals these regularities. This transform "rotates away" the recrossings and nonregular behavior, esp. of the motion along the reaction coordinate, leaving a coordinate and a corresponding dividing surface in phase space which minimize recrossings and mode-mode mixing in the transition state region. The action assocd. with the reactive mode tends to be an approx. invariant of motion through the saddle crossings throughout a relatively wide range of energy. Only at very low energies just above the saddle could any other approx. invariants of motion be found for the other, nonreactive modes. No such local invariants appeared at energies at which the modes are all chaotic and coupled to one another.
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    22. 22
      Komatsuzaki, T.; Berry, R. S. Regularity in chaotic reactions paths II: Ar6. Energy dependence and visualization of the reaction bottleneck. Phys. Chem. Chem. Phys. 1999, 1, 1387– 1397,  DOI: 10.1039/a809424a
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      22
      Regularity in chaotic reaction paths II: Ar6. Energy dependence and visualization of the reaction bottleneck
      Komatsuzaki, Tamiki; Stephen Berry, R.
      Physical Chemistry Chemical Physics (1999), 1 (6), 1387-1397CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      Reaction trajectories reveal regular behavior in the reactive degree of freedom and unit transmission coeffs. as the system crosses the saddle region sepg. reactants and products. The regularity persists up to moderately high energies, even when all other degrees of freedom are chaotic. This behavior is apparent in a representation obtained by transformation with Lie canonical perturbation theory. The dividing surface in this representation is analogous to the conventional dividing surface in the sense that it is the point set for which the reaction coordinate has the const. value it has at the saddle-point singularity. However the nonlinear, full phase-space character of the transformation makes the new crossing surface a complicated, abstr. object whose interpretation and visualization, the objective of this paper, can be realized by cataloging the recrossings as they disappear in successively higher orders of perturbation, and by projection into spaces of only a few dimensions. The result is a conceptual interpretation of how regular behavior persists in a reactive degree of freedom.
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    23. 23
      Komatsuzaki, T.; Berry, R. S. Local regularity and non-recrossing path in transition state—a new strategy in chemical reaction theories. J. Mol. Struct.: THEOCHEM 2000, 506, 55– 70,  DOI: 10.1016/S0166-1280(00)00402-4
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      23
      Local regularity and non-recrossing path in transition state - a new strategy in chemical reaction theories
      Komatsuzaki, T.; Berry, R. S.
      Journal of Molecular Structure: THEOCHEM (2000), 506 (), 55-70CODEN: THEODJ; ISSN:0166-1280. (Elsevier Science B.V.)
      We analyze local regularities in the regions of transition states of a 6-atom Lennard-Jones cluster to demonstrate how one can choose a non-recrossing reaction path in phase space along which the transmission coeff. for the classical reaction path is unity from threshold up to a moderately high energy, above which the transition state is chaotic, and how one can picture the nonlinear, full-phase-space character of the dividing hypersurface by projecting it into spaces of only a few dimensions. These overcome one of the long-standing ambiguities in chem. reaction theories, the recrossing problem, up to moderately high energies, and make transition state theory more generalized, applicable even in cases in which apparent recrossings spoil the conventional theory.
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    24. 24
      Komatsuzaki, T.; Berry, R. S. Regularity in chaotic reaction paths III: Ar6 local invariances at the reaction bottleneck. J. Chem. Phys. 2001, 115, 4105– 4117,  DOI: 10.1063/1.1385152
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      24
      Regularity in chaotic reaction paths III: Ar6 local invariances at the reaction bottleneck
      Komatsuzaki, Tamiki; Berry, R. Stephen
      Journal of Chemical Physics (2001), 115 (9), 4105-4117CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      We recently developed a new method to ext. a many-body phase-space dividing surface, across which the transmission coeff. for the classical reaction path is unity. The example of isomerization of a 6-atom Lennard-Jones cluster showed that the action assocd. with the reaction coordinate is an approx. invariant of motion through the saddle regions, even at moderately high energies, at which most or all the other modes are chaotic [J. Chem. Phys. 105, 10838 (1999); Phys. Chem. Chem. Phys. 1, 1387 (1999)]. In the present article, we propose a new algorithm to analyze local invariances about the transition state of N-particle Hamiltonian systems. The approx. invariants of motion assocd. with a reaction coordinate in phase space densely distribute in the sea of chaotic modes in the region of the transition state. Using projections of distributions in only two principal coordinates, one can grasp and visualize the stable and unstable invariant manifolds to and from a hyperbolic point of a many-body nonlinear system, like those of the one-dimensional, integrable pendulum. This, in turn, reveals a new type of phase space bottleneck in the region of a transition state that emerges as the total energy increases, which may trap a reacting system in that region.
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    25. 25
      Komatsuzaki, T.; Berry, R. S. Dynamical hierarchy in transition states: Why and how does a system climb over the mountain?. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 7666– 7671,  DOI: 10.1073/pnas.131627698
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      Dynamical hierarchy in transition states: why and how does a system climb over the mountain?
      Komatsuzaki, Tamiki; Berry, R. Stephen
      Proceedings of the National Academy of Sciences of the United States of America (2001), 98 (14), 7666-7671CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      How a reacting system climbs through a transition state during a reaction was an intriguing subject for decades. Here the authors present and quantify a technique to identify and characterize local invariance about the transition state of an N-particle Hamiltonian system, using Lie canonical perturbation theory combined with microcanonical mol. dynamics simulation. At least three distinct energy regimes of dynamical behavior occur in the region of the transition state, distinguished by the extent of their local dynamical invariance and regularity. Isomerization of a six-atom Lennard-Jones cluster illustrates this: up to energies high enough to make the system manifestly chaotic, approx. invariants of motion assocd. with a reaction coordinate in phase space imply a many-body dividing hypersurface in phase space that is free of recrossings even in a sea of chaos. The method makes it possible to visualize the stable and unstable invariant manifolds leading to and from the transition state, i.e., the reaction path in phase space, and how this regularity turns to chaos with increasing total energy of the system. This, in turn, illuminates a new type of phase space bottleneck in the region of a transition state that emerges as the total energy and mode coupling increase, which keeps a reacting system increasingly trapped in that region.
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    26. 26
      Pollak, E.; Pechukas, P. Unified statistical model for “complex” and “direct” reaction mechanisms: A test on the collinear H + H2 exchange reaction. J. Chem. Phys. 1979, 70, 325– 333,  DOI: 10.1063/1.437194
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      26
      Unified statistical model for "complex" and "direct" reaction mechanisms: a test on the collinear atomic hydrogen + molecular hydrogen exchange reaction
      Pollak, Eli; Pechukad, Philip
      Journal of Chemical Physics (1979), 70 (1), 325-33CODEN: JCPSA6; ISSN:0021-9606.
      Miller's unified statistical theory for bimol. chem. reactions is tested on the collinear H + H2 exchange reaction, treated classically. The reaction probability calcd. from unified statistical theory is more accurate than that calcd. from ordinary transition state theory or from variational transition state theory; in particular, unified statistical theory predicts the high-energy falloff of the reaction probability, which transition state theory does not. A derivation of unified statistical theory emphasizes the dynamical and statistical assumptions that are the foundation of the theory. These assumptions unambiguously define the "collision complex" in unified statistical theory and are tested in detail on the H + H2 reaction. Finally, a lower bound on the reaction probability is derived; this bound complements the upper bound provided by transition state theory and is significantly more accurate, for the H + H2 reaction, than either transition state theory or unified statistical theory.
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    27. 27
      Pollak, E. In Theory of Chemical Reaction Dynamics; Baer, M., Ed.; CRC Press: Boca Raton, FL, 1985; Vol. 3; p 123.
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    28. 28
      Grobgeld, D.; Pollak, E.; Zakrzewski, J. A Numerical Method for Locating Stable Periodic Orbits in Chaotic Systems. Phys. D 1992, 56, 368– 380,  DOI: 10.1016/0167-2789(92)90176-N
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    29. 29
      Moix, J. M.; Hernandez, R.; Pollak, E. Momentum and velocity autocorrelation functions of a diatomic molecule are not necessarily proportional to each other. J. Phys. Chem. B 2008, 112, 213– 218,  DOI: 10.1021/jp0730951
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      29
      Momentum and Velocity Autocorrelation Functions of a Diatomic Molecule Are Not Necessarily Proportional to Each Other
      Moix, Jeremy M.; Hernandez, Rigoberto; Pollak, Eli
      Journal of Physical Chemistry B (2008), 112 (2), 213-218CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
      We present a computation of the classical momentum and velocity correlation functions of Br2 considered as an idealized mol. wire connecting dissipated lead atoms at each end of the dimer. It is demonstrated that coupling of the diat. relative momentum to the leads may result in momenta that are not equal to the mass-weighted velocity. These differences show up in numerical simulations of both the av. value and time correlations of the bond momentum and velocity. These observations are supported by anal. predictions for the av. temp. of the diat. They imply that the "std. recipes" for modeling the system with a generalized Langevin equation are insufficient.
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    30. 30
      Hernandez, R.; Cao, J.; Voth, G. A. On the Feynman path centroid density as a phase space distribution in quantum statistical mechanics. J. Chem. Phys. 1995, 103, 5018– 5026,  DOI: 10.1063/1.470588
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      30
      On the Feynman path centroid density as a phase space distribution in quantum statistical mechanics
      Hernandez, Rigoberto; Cao, Jianshu; Voth, Gregory A.
      Journal of Chemical Physics (1995), 103 (12), 5018-26CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The phase space formulation of quantum statistical mechanics using the Feynman path centroid d. offers an alternative perspective to the std. Wigner prescription for the classical-like evaluation of equil. and/or dynamical quantities of statistical systems. The use of this formulation has been implicit in recent work on quantum rate theories, for example, in which the centroid d. distribution replaces the classical Boltzmann distribution. In order to further understand the approxns. involved in this and similar transcriptions, the present work elaborates and clarifies the issue of operator ordering in a rigorous centroid-based formulation. In particular, through the use of the Weyl correspondence, a precise definition of the centroid symbol of operators and their products is presented. Though we fall short of finding the algebraic structure tantamount to that found in the Weyl symbols-of which the Wigner distribution is an example- the resulting expressions have internal consistency and are amenable to approx. evaluation through cumulant expansions.
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    31. 31
      Hernandez, R.; Voth, G. A. Quantum time correlation functions and classical coherence. Chem. Phys. 1998, 233, 243– 255,  DOI: 10.1016/S0301-0104(98)00027-5
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      31
      Quantum time correlation functions and classical coherence
      Hernandez, Rigoberto; Voth, Gregory A.
      Chemical Physics (1998), 233 (2,3), 243-255CODEN: CMPHC2; ISSN:0301-0104. (Elsevier Science B.V.)
      Quantum time correlation functions for electronically adiabatic and nonadiabatic processes have recently been evaluated directly using the semiclassical initial value representation [J. Cao and G.A. Voth, J. Chem. Phys. 104 (1996) 271]. In this paper, the approach to the classical limit of this theory is analyzed and the nature of coherence in such limits is explored.
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    32. 32
      Verashchagina, A.; Bettio, F. Gender segregation in the labour market; Directorate-General for Employment, Social Affairs and Inclusion (European Commission), 2009.
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    33. 33
      Hernandez, R.; Somer, F. L. Stochastic dynamics in irreversible nonequilibrium environments. 1. The fluctuation-dissipation relation. J. Phys. Chem. B 1999, 103, 1064– 1069,  DOI: 10.1021/jp983625g
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      33
      Stochastic Dynamics in Irreversible Nonequilibrium Environments. 1. The Fluctuation-Dissipation Relation
      Hernandez, Rigoberto; Somer, Frank L.,Jr.
      Journal of Physical Chemistry B (1999), 103 (7), 1064-1069CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
      A generalization of the generalized Langevin equation (stochastic dynamics) is introduced in order to model chem. reactions which take place in changing environments. The friction kernel representing the solvent response is given a nonstationary form with respect to which the instantaneous random solvent force satisfies a natural generalization of the fluctuation-dissipation relation. Theor. considerations, as well as numerical simulations, show that the dynamics of this construction satisfy the equipartition theorem beyond its equil. limits.
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    34. 34
      Hernandez, R.; Somer, F. L. Stochastic dynamics in irreversible nonequilibrium environments. 2. A model for thermosetting polymerization. J. Phys. Chem. B 1999, 103, 1070– 1077,  DOI: 10.1021/jp9836269
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      34
      Stochastic Dynamics in Irreversible Nonequilibrium Environments. 2. A Model for Thermosetting Polymerization
      Hernandez, Rigoberto; Somer, Frank L. Jr.
      Journal of Physical Chemistry B (1999), 103 (7), 1070-1077CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
      A generalization of the generalized Langevin equation (GLE), the so-called irreversible GLE (iGLE) [Hernandez, R.; Somer, F. L. J. Phys. Chem. 1999, 103, XXXX], is further extended to describe non-stationary environments in which the non-stationarity is induced by the macroscopic behavior of the ensemble itself, rather than an external force. Such a formalism lends itself to the dynamical study of the length distributions of growing polymers.
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    35. 35
      Hernandez, R. The projection of a mechanical system onto the irreversible generalized Langevin equation (iGLE). J. Chem. Phys. 1999, 111, 7701– 7704,  DOI: 10.1063/1.480160
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      35
      The projection of a mechanical system onto the irreversible generalized Langevin equation
      Hernandez, Rigoberto
      Journal of Chemical Physics (1999), 111 (17), 7701-7704CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The so-called irreversible generalized Langevin equation [R. Hernandez and F. L. Somer, J. Phys. Chem. B 103, 1064 (1999)], which extends the generalized Langevin equation (stochastic dynamics) to include irreversible changes (nonstationarity) in the solvent response, is shown to be the projection of an explicit time-dependent Hamiltonian system.
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    36. 36
      Locker, C. R.; Hernandez, R. A minimalist model protein with multiple folding funnels. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 9074– 9079,  DOI: 10.1073/pnas.161438898
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      36
      A minimalist model protein with multiple folding funnels
      Locker, C. Rebecca; Hernandez, Rigoberto
      Proceedings of the National Academy of Sciences of the United States of America (2001), 98 (16), 9074-9079CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      Kinetic and structural studies of wild-type proteins such as prions and amyloidogenic proteins provide suggestive evidence that proteins may adopt multiple long-lived states in addn. to the native state. All of these states differ structurally because they lie far apart in configuration space, but their stability is not necessarily caused by cooperative (nucleation) effects. In this study, a minimalist model protein is designed to exhibit multiple long-lived states to explore the dynamics of the corresponding wild-type proteins. The minimalist protein is modeled as a 27-monomer sequence confined to a cubic lattice with three different monomer types. An order parameter-the winding index-is introduced to characterize the extent of folding. The winding index has several advantages over other commonly used order parameters like the no. of native contacts. It can distinguish between enantiomers, its calcn. requires less computational time than the no. of native contacts, and reduced-dimensional landscapes can be developed when the native state structure is not known a priori. The results for the designed model protein prove by existence that the rugged energy landscape picture of protein folding can be generalized to include protein "misfolding" into long-lived states.
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    37. 37
      Servos, J. W. Physical Chemistry from Ostwald to Pauling: The Making of a Science in America; Princeton University Press, 1990.
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    38. 38
      Hernandez, R. 6. Blurring of Physical Chemistry and Chemical Physics. 2013; http://everywherechemistry.blogspot.com/2013/08/6-blurring-of-physical-chemistry-and.html, accessed January 15, 2021.
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    39. 39
      Schatz, G. C. Celebrating Our 120th Anniversary. J. Phys. Chem. A 2016, 120, 9679– 9681,  DOI: 10.1021/acs.jpca.6b10935
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      39
      Celebrating Our 120th Anniversary
      Schatz, George C.
      Journal of Physical Chemistry A (2016), 120 (49), 9679-9681CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      There is no expanded citation for this reference.
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    40. 40
      Bartsch, T.; Hernandez, R.; Uzer, T. Transition state in a noisy environment. Phys. Rev. Lett. 2005, 95, 058301,  DOI: 10.1103/PhysRevLett.95.058301
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      40
      Transition State in a Noisy Environment
      Bartsch, Thomas; Hernandez, Rigoberto; Uzer, T.
      Physical Review Letters (2005), 95 (5), 058301/1-058301/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
      Transition state theory overestimates reaction rates in soln. because conventional dividing surfaces between reagents and products are crossed many times by the same reactive trajectory. We describe a recipe for constructing a time-dependent dividing surface free of such recrossings in the presence of noise. The no-recrossing limit of transition state theory thus becomes generally available for the description of reactions in a fluctuating environment.
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    41. 41
      Shukla, C.; Hallett, J. P.; Popov, A. V.; Hernandez, R.; Liotta, C.; Eckert, C. Molecular Dynamics Simulation of the Cybotactic Region in Gas-Expanded Methanol-Carbon Dioxide and Acetone-Carbon Dioxide Mixtures. J. Phys. Chem. B 2006, 110, 24101– 24111,  DOI: 10.1021/jp0648947
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      41
      Molecular Dynamics Simulation of the Cybotactic Region in Gas-Expanded Methanol-Carbon Dioxide and Acetone-Carbon Dioxide Mixtures
      Shukla, Charu L.; Hallett, Jason P.; Popov, Alexander V.; Hernandez, Rigoberto; Liotta, Charles L.; Eckert, Charles A.
      Journal of Physical Chemistry B (2006), 110 (47), 24101-24111CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
      Local solvation and transport effects in gas-expanded liqs. (GXLs) are reported based on mol. simulation. GXLs were found to exhibit local d. enhancements similar to those seen in supercrit. fluids, although less dramatic. This approach was used as an alternative to a multiphase atomistic model for these mixts. by utlilizing exptl. results to describe the necessary fixed conditions for a locally (quasi-) stable mol. dynamics model of the (single) GXL phase. The local anisotropic pair correlation function, orientational correlation functions, and diffusion rates are reported for two systems: CO2-expanded methanol and CO2-expanded acetone at 298 K and pressures up to 6 MPa.
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    42. 42
      Hallett, J. P.; Kitchens, C. L.; Hernandez, R.; Liotta, C.; Eckert, C. Probing the Cybotactic Region in Gas-Expanded Liquids (GXLs). Acc. Chem. Res. 2006, 39, 531– 538,  DOI: 10.1021/ar0501424
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      42
      Probing the Cybotactic Region in Gas-Expanded Liquids (GXLs)
      Hallett, Jason P.; Kitchens, Christopher L.; Hernandez, Rigoberto; Liotta, Charles L.; Eckert, Charles A.
      Accounts of Chemical Research (2006), 39 (8), 531-538CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
      Gas-expanded liqs. (GXLs) are a new and benign class of liq. solvents, which may offer many advantages for sepns., reactions, and advanced materials. GXLs are intermediate in properties between normal liqs. and supercrit. fluids, both in solvating power and in transport properties. Other advantages include benign nature, low operating pressures, and highly tunable properties by simple pressure variations. The chem. community has only just begun to exploit the advantages of these GXLs for industrial applications. This account focuses on the synergism of exptl. techniques with theor. modeling resulting in a powerful combination for exploring chem. structure and transport in the cybotactic region of GXLs (at the nanometer lengthscale).
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    43. 43
      Stockard, J.; Rohlfing, C. M.; Richmond, G. L. Equity for women and underrepresented minorities in STEM: Graduate experiences and career plans in chemistry. Proc. Natl. Acad. Sci. U. S. A. 2021, 118, e2020508118,  DOI: 10.1073/pnas.2020508118
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      43
      Equity for women and underrepresented minorities in STEM: Graduate experiences and career plans in chemistry
      Stockard, Jean; Rohlfing, Celeste M.; Richmond, Geraldine L.
      Proceedings of the National Academy of Sciences of the United States of America (2021), 118 (4), e2020508118CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      Recent events prompted scientists in the United States and throughout the world to consider how systematic racism affects the scientific enterprise. This paper provides evidence of inequities related to race-ethnicity and gender in graduate school experiences and career plans of PhD students in the top 100 ranked departments in one science, technol., engineering, and math (STEM) discipline, chem. Mixed-model regression analyses were used to examine factors that might moderate these differences. The results show that graduate students who identified as a member of a racial/ethnic group traditionally underrepresented in chem. (underrepresented minorities, URM) were significantly less likely than other students to report that their financial support was sufficient to meet their needs. They were also less likely to report having supportive relationships with peers and postdocs. Women, and esp. URM women, were significantly less likely to report supportive relationships with advisors. Despite their more neg. experiences in graduate school, students who identified as URM expressed greater commitment to finishing their degree and staying in the field. When there was at least one faculty member within their departments who also identified as URM they were also more likely than other students to aspire to a university professorship with an emphasis on research. Men were significantly more likely than women to express strong commitment to finishing the PhD and remaining in chem., but this difference was stronger in top-ranked departments. Men were also more likely than women to aspire to a professorship with an emphasis on research, and this difference remained when individual and departmental-level variables were controlled.
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    44. 44
      Bowman, J. M. Autobiography of Joel M. Bowman. J. Phys. Chem. A 2013, 117, 6907– 6909,  DOI: 10.1021/jp405529p
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      Tucker, S. C. Solvent Density Inhomogeneities in Supercritical Fluids. Chem. Rev. 1999, 99, 391– 418,  DOI: 10.1021/cr9700437
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      45
      Solvent Density Inhomogeneities in Supercritical Fluids
      Tucker, Susan C.
      Chemical Reviews (Washington, D. C.) (1999), 99 (2), 391-418CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      A review, with ∼184 refs., where fundamentals, evidence of local d. inhomogeneities, and addnl. characteristics of local d. inhomogeneities were discussed.
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    46. 46
      Locker, C. R.; Hernandez, R. Folding behavior of model proteins with weak energetic frustration. J. Chem. Phys. 2004, 120, 11292– 11303,  DOI: 10.1063/1.1751394
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      46
      Folding behavior of model proteins with weak energetic frustration
      Locker, C. Rebecca; Hernandez, Rigoberto
      Journal of Chemical Physics (2004), 120 (23), 11292-11303CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The native structure of fast-folding proteins, albeit a deep local free-energy min., may involve a relatively small energetic penalty due to nonoptimal, though favorable, contacts between amino acid residues. The weak energetic frustration that such contacts represent varies among different proteins and may account for folding behavior not seen in unfrustrated models. Minimalist model proteins with heterogeneous contacts-as represented by lattice heteropolymers consisting of three types of monomers-also give rise to weak energetic frustration in their corresponding native structures, and the present study of their equil. and nonequil. properties reveals some of the breadth in their behavior. In order to capture this range within a detailed study of only a few proteins, four candidate protein structures (with their cognate sequences) have been selected according to a figure of merit called the winding index-a characteristic of the no. of turns the protein winds about an axis. The temp.-dependent heat capacities reveal a high-temp. collapse transition, and an infrequently obsd. low-temp. rearrangement transition that arises because of the presence of weak energetic frustration. Simulation results motivate the definition of a new measure of folding affinity as a sequence-dependent free energy-a function of both a reduced stability gap and high accessibility to non-native structures-that correlates strongly with folding rates.
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    47. 47
      Leite, V. B. P.; Alonso, L. C. P.; Newton, M.; Wang, J. Single Molecule Electron Transfer Dynamics in Complex Environments. Phys. Rev. Lett. 2005, 95, 118301,  DOI: 10.1103/PhysRevLett.95.118301
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      47
      Single Molecule Electron Transfer Dynamics in Complex Environments
      Leite, Vitor B. P.; Alonso, Luciana C. P.; Newton, Marshall; Wang, Jin
      Physical Review Letters (2005), 95 (11), 118301/1-118301/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
      We propose a new theor. approach to study the kinetics of the electron transfer (ET) under the dynamical influence of the complex environments with the first passage times (FPT) of the reaction events. By measuring the mean and high order moments of FPT and their ratios, the full kinetics of ET, esp. the dynamical transitions across different temp. zones, is revealed. The potential applications of the current results to single mol. electron transfer are discussed.
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    48. 48
      Sension, R.; Tokmakoff, A. Proceedings of “Optical Probes of Dynamics in Complex Environments”; OSTI, 2008; https://www.osti.gov/servlets/purl/1062182, accessed January 15, 2021.
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    49. 49
      Virshup, A. M.; Punwong, C.; Pogorelov, T. V.; Lindquist, B. A.; Ko, C.; Martínez, T. J. Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics. J. Phys. Chem. B 2009, 113, 3280– 3291,  DOI: 10.1021/jp8073464
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      49
      Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics
      Virshup, Aaron M.; Punwong, Chutintorn; Pogorelov, Taras V.; Lindquist, Beth A.; Ko, Chaehyuk; Martinez, Todd J.
      Journal of Physical Chemistry B (2009), 113 (11), 3280-3291CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
      Our picture of reactions on electronically excited states has evolved considerably in recent years, due to advances in our understanding of points of degeneracy between different electronic states, termed "conical intersections" (CIs). CIs serve as funnels for population transfer between different electronic states, and play a central role in ultrafast photochem. Because most practical photochem. occurs in soln. and protein environments, it is important to understand the role complex environments play in directing excited-state dynamics generally, as well as specific environmental effects on CI geometries and energies. In order to model such effects, we employ the full multiple spawning (FMS) method for multistate quantum dynamics, together with hybrid quantum mech./mol. mech. (QM/MM) potential energy surfaces using both semiempirical and ab initio QM methods. In this article, we present an overview of these methods, and a comparison of the excited-state dynamics of several biol. chromophores in solvent and protein environments. Aq. solvation increases the rate of quenching to the ground state for both the photoactive yellow protein (PYP) and green fluorescent protein (GFP) chromophores, apparently by energetic stabilization of their resp. CIs. In contrast, solvation in methanol retards the quenching process of the retinal protonated Schiff base (RPSB), the rhodopsin chromophore. Protein environments serve to direct the excited-state dynamics, leading to higher quantum yields and enhanced reaction selectivity.
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    50. 50
      Hernandez, R.; Popov, A. Molecular dynamics out of equilibrium: Mechanics and measurables. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2014, 4, 541– 561,  DOI: 10.1002/wcms.1190
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      50
      Molecular dynamics out of equilibrium: mechanics and measurables
      Hernandez, Rigoberto; Popov, Alexander V.
      Wiley Interdisciplinary Reviews: Computational Molecular Science (2014), 4 (6), 541-561CODEN: WIRCAH; ISSN:1759-0884. (Wiley-Blackwell)
      Mol. dynamics is fundamentally the integration of the equations of motion over a representation of an at. and mol. system. The most rigorous choice for performing mol. dynamics entails the use of quantum-mech. equations of motion and a representation of the mol. system through all of its electrons and atoms. For most mol. problems involving at least hundreds of atoms, but generally many more, this is simply computationally prohibitive. Thus the art of mol. dynamics lies in choosing the representation and the appropriate equations of motion capable of addressing the requisite measurables. When used adroitly, it can provide both equil. (averaged) and time-dependent properties of a mol. system. Many computational packages now exist that perform mol. dynamics simulations. They generally include force fields to represent the interactions between atoms and mols. (smoothing out electrons through the Born-Oppenheimer approxn.) and integrate the remaining particles classically. Despite these simplifications, all-atom mol. dynamics remains computationally inaccessible if one includes the no. of atoms required to simulate mesoscopic solvents. Here we use anal. models to demonstrate how mol. dynamics can be used to limit the solvent size in systems experiencing either equil. or nonequil. conditions. It is equally important to address the measurables (such as reaction rates) that are to be obtained prior to the generation of the data-intensive trajectories. WIREs Comput Mol Sci 2014, 4:541-561. doi: 10.1002/wcms.1190 For further resources related to this article, please visit the . Conflict of interest: The authors have declared no conflicts of interest for this article.
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    51. 51
      Press release: Nobel Prize in Chemistry 2013. https://www.nobelprize.org/prizes/chemistry/2013/press-release/, accessed January 15, 2021.
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      MacKerell, A. D., Jr. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586– 3616,  DOI: 10.1021/jp973084f
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      All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
      MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.
      Journal of Physical Chemistry B (1998), 102 (18), 3586-3616CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
      New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used exptl. gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the at. charges, were detd. by fitting ab initio interaction energies and geometries of complexes between water and model compds. that represented the backbone and the various side chains. In addn., dipole moments, exptl. heats and free energies of vaporization, solvation and sublimation, mol. vols., and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in a crystal. A detailed anal. of the relationship between the alanine dipeptide potential energy surface and calcd. protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in soln. and in crystals. Extensive comparisons between mol. dynamics simulation and exptl. data for polypeptides and proteins were performed for both structural and dynamic properties. Calcd. data from energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with exptl. crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of mols. of biol. interest.
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    53. 53
      Mackerell, A. D., Jr.; Feig, M.; Brooks, C. L., III Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 2004, 25, 1400– 1415,  DOI: 10.1002/jcc.20065
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      53
      Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
      MacKerell, Alexander D., Jr.; Feig, Michael; Brooks, Charles L., III
      Journal of Computational Chemistry (2004), 25 (11), 1400-1415CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an at. level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone is crucial to achieve representative conformational distributions in simulation studies. To improve the treatment of the peptide backbone, quantum mech. (QM) and mol. mech. (MM) calcns. were undertaken on the alanine, glycine, and proline dipeptides, and the results from these calcns. were combined with mol. dynamics (MD) simulations of proteins in crystal and aq. environments. QM potential energy maps of the alanine and glycine dipeptides at the LMP2/cc-pVxZ/MP2/6-31G* levels, where x = D, T, and Q, were detd., and are compared to available QM studies on these mols. The LMP2/cc pVQZ//MP2/6-31G* energy surfaces for all three dipeptides were then used to improve the MM treatment of the dipeptides. These improvements included addnl. parameter optimization via Monte Carlo simulated annealing and extension of the potential energy function to contain peptide backbone .vphi., ψ dihedral crossterms or a .vphi., ψ grid-based energy correction term. Simultaneously, MD simulations of up to seven proteins in their cryst. environments were used to validate the force field enhancements. Comparison with QM and crystallog. data showed that an addnl. optimization of the .vphi., ψ dihedral parameters along with the grid-based energy correction were required to yield significant improvements over the CHARMM22 force field. However, systematic deviations in the treatment of .vphi. and ψ in the helical and sheet regions were evident. Accordingly, empirical adjustments were made to the grid-based energy correction for alanine and glycine to account for these systematic differences. These adjustments lead to greater deviations from QM data for the two dipeptides but also yielded improved agreement with exptl. crystallog. data. These improvements enhance the quality of the CHARMM force field in treating proteins. This extension of the potential energy function is anticipated to facilitate improved treatment of biol. macromols. via MM approaches in general.
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    54. 54
      Kalé, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. NAMD2: Greater scalability for parallel molecular dynamics. J. Comput. Phys. 1999, 151, 283– 312,  DOI: 10.1006/jcph.1999.6201
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      NAMD2: Greater Scalability for Parallel Molecular Dynamics
      Kale, Laxmikant; Skeel, Robert; Bhandarkar, Milind; Brunner, Robert; Gursoy, Attila; Krawetz, Neal; Phillips, James; Shinozaki, Aritomo; Varadarajan, Krishnan; Schulten, Klaus
      Journal of Computational Physics (1999), 151 (1), 283-312CODEN: JCTPAH; ISSN:0021-9991. (Academic Press)
      Mol. dynamics programs simulate the behavior of biomol. systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by application-domain programmers. The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decompn. combined with force decompn. to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability. It uses a combination of numerical techniques and algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calcns. NAMD2 uses a portable run-time framework called Converse that also supports interoperability among multiple parallel paradigms. As a result, different components of applications can be written in the most appropriate parallel paradigms. NAMD2 runs on most parallel machines including workstation clusters and has yielded speedups in excess of 180 on 220 processors. This paper also describes the performance obtained on some benchmark applications. (c) 1999 Academic Press.
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    55. 55
      Pearlman, D. A.; Case, D. A.; Caldwell, J.; Ross, W. R.; Cheatham, T. E., III; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comput. Phys. Commun. 1995, 91, 1– 41,  DOI: 10.1016/0010-4655(95)00041-D
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      "AMBER", a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to stimulate the structural and energetic properties of molecules
      Pearlman, David A.; Case, David A.; Caldwell, James W.; Ross, Wilson S.; Cheatham, Thomas E. III; DeBolt, Steve; Ferguson, David; Seibel, George; Kollman, Peter
      Computer Physics Communications (1995), 91 (1-3), 1-42CODEN: CPHCBZ; ISSN:0010-4655. (Elsevier)
      We describe the development, current features, and some directions for future development of the AMBER package of computer programs. This package has evolved from a program that was constructed to do Assisted Model Building and Energy Refinement to a group of programs embodying a no. of the powerful tools of modern computational chem.-mol. dynamics and free energy calcns.
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      Brown, W. M.; Petersen, M. K.; Plimpton, S. J.; Grest, G. S. Liquid crystal nanodroplets in solution. J. Chem. Phys. 2009, 130, 044901,  DOI: 10.1063/1.3058435
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      Liquid crystal nanodroplets in solution
      Brown, W. Michael; Petersen, Matt K.; Plimpton, Steven J.; Grest, Gary S.
      Journal of Chemical Physics (2009), 130 (4), 044901/1-044901/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The aggregation of liq. crystal nanodroplets from a homogeneous soln. is studied by mol. dynamics simulations. The liq. crystal particles are modeled as elongated ellipsoidal Gay-Berne particles while the solvent is modeled as spherical Lennard-Jones particles. Extending previous studies of , we find that liq. crystal nanodroplets are not stable and that after sufficiently long times the nanodroplets always aggregate into a single large droplet. Results describing the droplet shape and orientation for different temps. and shear rates are presented. The implementation of the Gay-Berne potential for biaxial ellipsoidal particles in a parallel mol. dynamics code is also briefly discussed. (c) 2009 American Institute of Physics.
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    57. 57
      Durrant, J. D.; Kochanek, S. E.; Casalino, L.; Ieong, P. U.; Dommer, A. C.; Amaro, R. E. Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ACS Cent. Sci. 2020, 6, 189– 196,  DOI: 10.1021/acscentsci.9b01071
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      Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism
      Durrant, Jacob D.; Kochanek, Sarah E.; Casalino, Lorenzo; Ieong, Pek U.; Dommer, Abigail C.; Amaro, Rommie E.
      ACS Central Science (2020), 6 (2), 189-196CODEN: ACSCII; ISSN:2374-7951. (American Chemical Society)
      Influenza virus circulates in human, avian, and swine hosts, causing seasonal epidemic and occasional pandemic outbreaks. Influenza neuraminidase, a viral surface glycoprotein, has two sialic acid binding sites. The catalytic (primary) site, which also binds inhibitors such as oseltamivir carboxylate, is responsible for cleaving the sialic acid linkages that bind viral progeny to the host cell. In contrast, the functional annotation of the secondary site remains unclear. Here, we better characterize these two sites through the development of an all-atom, explicitly solvated, exptl. based integrative model of the pandemic influenza A H1N1 2009 viral envelope, contg. ∼160 million atoms and spanning ∼115 nm in diam. Mol. dynamics simulations of this crowded subcellular environment, coupled with Markov state model theory, provide a novel framework for studying realistic mol. systems at the mesoscale and allow us to quantify the kinetics of the 150-loop transition between the open and closed states. An anal. of chloride ion occupancy along the neuraminidase surface implies a potential new role for the neuraminidase secondary site, wherein the terminal sialic acid residues of the linkages may bind before transfer to the primary site where enzymic cleavage occurs. Altogether, our work breaks new ground for mol. simulation in terms of the size, complexity, and methodol. analyses of the simulated components, as well as provides fundamental insights into the understanding of substrate recognition processes for this vital influenza drug target, suggesting a new strategy for the development of anti-influenza therapeutics.
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    58. 58
      Hagy, M. C.; Hernandez, R. Dynamical simulation of dipolar Janus colloids: Dynamical properties. J. Chem. Phys. 2013, 138, 184903,  DOI: 10.1063/1.4803864
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      58
      Dynamical simulation of dipolar Janus colloids: Dynamical properties
      Hagy, Matthew C.; Hernandez, Rigoberto
      Journal of Chemical Physics (2013), 138 (18), 184903/1-184903/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The dynamical properties of dipolar Janus particles are studied through simulation using our previously-developed detailed pointwise (PW) model and an isotropically coarse-grained (CG) model. The CG model is found to have accelerated dynamics relative to the PW model over a range of conditions for which both models have near identical static equil. properties. Phys., this suggests dipolar Janus particles have slower transport properties (such as diffusion) in comparison to isotropically attractive particles. Time rescaling and damping with Langevin friction are explored to map the dynamics of the CG model to that of the PW model. Both methods map the diffusion const. successfully and improve the velocity autocorrelation function and the mean squared displacement of the CG model. Neither method improves the distribution of reversible bond durations f(tb) obsd. in the CG model, which is found to lack the longer duration reversible bonds obsd. in the PW model. We attribute these differences in f(tb) to changes in the energetics of multiple rearrangement mechanisms. This suggests a need for new methods that map the coarse-grained dynamics of such systems to the true time scale. (c) 2013 American Institute of Physics.
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    59. 59
      Downey-Mavromatis, A.; Widener, A. Chemistry faculty’s diversity has changed little since 2011. Chem. Eng. News 2020, 98, 22– 25,  DOI: 10.1021/cen-09843-feature2
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      Chemistry faculty's diversity has changed little since 2011
      Downey-Mavromatis, Arminda
      Chemical & Engineering News (2020), 98 (43), 22-25CODEN: CENEAR; ISSN:1520-605X. (American Chemical Society)
      For the past decade, C&EN has worked with the Open Chem. Collaborative in Diversity Equity (OXIDE) to publish statistics on gender and racial and ethnic diversity of US chem. faculty. OXIDE collects the data, a task that's not as easy as it might sound, its leaders say. Nevertheless, it's important work, esp. with the increased focus from universities on campus diversity efforts after protests about racism and police brutality against Black people this year. "This is definitely a moment of reflection for our nation-and one cannot effectively reflect without knowing the facts," says Dontarie Stallings, assoc. director of OXIDE and a teaching professor of chem. at the University of California San Diego. The current facts: the racial and ethnic diversity of US chem. faculty has changed little since 2011. OXIDE began documenting diversity among chem. faculty because although some universities survey their faculty and students to understand their diversity and OXIDE hopes data will help departments improve faculty's diversity, inclusion, and equity 10.47287/cen-09843-feature2-meeting-gr1Rigoberto Hernandez (left) and Dontarie Stallings at an American Chem. Society meeting in 2016 (Credit: Courtesy of Rigoberto Hernandez) oxidesurveyRigoberto HernandezDontarie StallingsA photo of Rigoberto Hernandez and Dontarie Stallings.
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    60. 60
      Hernandez, R. The private sector’s role in chemistry’s future. Chem. Eng. News 2015, 93, 33,  DOI: 10.1021/cen-09337-comment
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      Hernandez, R. OneChemistry in the marketplace of ideas. Chem. Eng. News 2017, 95, 41,  DOI: 10.1021/cen-09517-comment
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      There is no corresponding record for this reference.
    62. 62
      Craven, G. T.; Junginger, A.; Hernandez, R. Lagrangian descriptors of driven chemical reaction manifolds. Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2017, 96, 022222,  DOI: 10.1103/PhysRevE.96.022222
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    63. 63
      Schraft, P.; Junginger, A.; Feldmaier, M.; Bardakcioglu, R.; Main, J.; Wunner, G.; Hernandez, R. Neural network approach to time-dependent dividing surfaces in classical reaction dynamics. Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2018, 97, 042309,  DOI: 10.1103/PhysRevE.97.042309
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      There is no corresponding record for this reference.
    64. 64
      Feldmaier, M.; Reiff, J.; Benito, R. M.; Borondo, F.; Main, J.; Hernandez, R. Influence of external driving on decays in the geometry of the LiCN isomerization. J. Chem. Phys. 2020, 153, 084115,  DOI: 10.1063/5.0015509
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      Influence of external driving on decays in the geometry of the LiCN isomerization
      Feldmaier, Matthias; Reiff, Johannes; Benito, Rosa M.; Borondo, Florentino; Main, Joerg; Hernandez, Rigoberto
      Journal of Chemical Physics (2020), 153 (8), 084115CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The framework of transition state theory relies on the detn. of a geometric structure identifying reactivity. It replaces the laborious exercise of following many trajectories for a long time to provide chem. reaction rates and pathways. In this paper, recent advances in constructing this geometry even in time-dependent systems are applied to the LiCN .dblharw. LiNC isomerization reaction driven by an external field. We obtain decay rates of the reactant population close to the transition state by exploiting local properties of the dynamics of trajectories in and close to it. We find that the external driving has a large influence on these decay rates when compared to the non-driven isomerization reaction. This, in turn, provides renewed evidence for the possibility of controlling chem. reactions, like this one, through external time-dependent fields. (c) 2020 American Institute of Physics.
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    65. 65
      Bureau, H.; Quirk, S.; Hernandez, R. The relative stability of trpzip1 and its mutants determined by computation and experiment. RSC Adv. 2020, 10, 6520,  DOI: 10.1039/D0RA00920B
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      65
      The relative stability of trpzip1 and its mutants determined by computation and experiment
      Bureau, Hailey R.; Quirk, Stephen; Hernandez, Rigoberto
      RSC Advances (2020), 10 (11), 6520-6535CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
      Six mutants of the tryptophan zipper peptide trpzip1 have been computationally and exptl. characterized. We det. the varying roles in secondary structure stability of specific residues through a mutation assay. Four of the mutations directly effect the Trp-Trp interactions and two of the mutations target the salt bridge between Glu5 and Lys8. CD spectra and thermal unfolding are used to det. the secondary structure and stability of the mutants compared to the wildtype peptide. Adaptive steered mol. dynamics has been used to obtain the energetics of the unfolding pathways of the mutations. The hydrogen bonding patterns and side-chain interactions over the course of unfolding have also been calcd. and compared to wildtype trpzip1. The key finding from this work is the importance of a stabilizing non-native salt bridge pair present in the K8L mutation.
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    66. 66
      Zhuang, Y.; Bureau, H.; Quirk, S.; Hernandez, R. Adaptive Steered Molecular Dynamics of Biomolecules. Mol. Simul. 2021, 47, 408,  DOI: 10.1080/08927022.2020.1807542
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      Adaptive steered molecular dynamics of biomolecules
      Zhuang, Yi; Bureau, Hailey R.; Quirk, Stephen; Hernandez, Rigoberto
      Molecular Simulation (2021), 47 (5), 408-419CODEN: MOSIEA; ISSN:0892-7022. (Taylor & Francis Ltd.)
      Adaptive steered mol. dynamics (ASMD) is a variant of steered mol. dynamics (SMD) in which the driving of the auxiliary - viz steered - particle is performed in stages. In SMD, many nonequil. trajectories are generated allowing for fast sampling of the ensemble space and access to rare events. Equil. observables, such as the potential of mean force along the pathway, result from averaging over these trajectories using Jarzynski's Equality (JE). Unfortunately, in SMD, a large no. of trajectories are needed to cover all possible configurations in order to obtain converged quantities in the exponential av. of the JE, and this is computationally expensive. ASMD reduces the no. of trajectories that must be sampled by discarding those trajectories that have deviated far from the equil. path in stages. At the end of a stage, one chooses - or contracts - one (in naive ASMD) or some (in multi-branched ASMD or MB-ASMD) of the configurations produced from the previous stage to initiate the trajectories in the next stage. Alternatively, in full-relaxation ASMD (FR-ASMD), all generated structures are relaxed under the constraint of a fixed auxiliary particle exerting no net work on the system. We provide a direct comparison of the energetics and other observables obtained from these approaches. We find that FR-ASMD is preferred when the unfolding pathways follow up along a single funnel and the system is sufficiently small that computational resources are not a limiting concern. It gives the highest accuracy in such cases while avoiding the inefficiencies of SMD. However, for complex energy landscapes typical of most multi-domain proteins, MB-ASMD is preferred because it provides a mechanism to sample alternative pathways while suffering only a modest loss in accuracy compared to FR-ASMD.
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    67. 67
      Zhuang, Y.; Bureau, H. R.; Lopez, C.; Bucher, R.; Quirk, S.; Hernandez, R. Energetics and structure of alanine-rich _-helices via Adaptive Steered Molecular Dynamics (ASMD). Biophys. J. 2021, 120, 2009,  DOI: 10.1016/j.bpj.2021.03.017
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      67
      Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics
      Zhuang, Yi; Bureau, Hailey R.; Lopez, Christine; Bucher, Ryan; Quirk, Stephen; Hernandez, Rigoberto
      Biophysical Journal (2021), 120 (10), 2009-2018CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
      The energetics and hydrogen bonding profiles of the helix-to-coil transition were found to be an additive property and to increase linearly with chain length, resp., in alanine-rich α-helical peptides. A model system of polyalanine repeats was used to establish this hypothesis for the energetic trends and hydrogen bonding profiles. Numerical measurements of a synthesized polypeptide Ac-Y(AEAAKA)kF-NH2 and a natural α-helical peptide a2N (1-17) provide evidence of the hypothesis's generality. Adaptive steered mol. dynamics was employed to investigate the mech. unfolding of all of these alanine-rich polypeptides. We found that the helix-to-coil transition is primarily dependent on the breaking of the intramol. backbone hydrogen bonds and independent of specific side-chain interactions and chain length. The mech. unfolding of the α-helical peptides results in a turnover mechanism in which a 310-helical structure forms during the unfolding, remaining at a near const. population and thereby maintaining additivity in the free energy. The intermediate partially unfolded structures exhibited polyproline II helical structure as previously seen by others. In summary, we found that the av. force required to pull alanine-rich α-helical peptides in between the endpoints-namely the native structure and free coil-is nearly independent of the length or the specific primary structure.
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    68. 68
      Mahala, B.; Hernandez, R. Solvent softness effects on unimolecular chemical reaction rate constants. Chem. Phys. Lett. 2020, 744, 137182,  DOI: 10.1016/j.cplett.2020.137182
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      68
      Solvent softness effects on unimolecular chemical reaction rate constants
      Mahala, Benjamin D.; Hernandez, Rigoberto
      Chemical Physics Letters (2020), 744 (), 137182CODEN: CHPLBC; ISSN:0009-2614. (Elsevier B.V.)
      The stochastic hard collision (SHC) model for a coarse-grained solvent has been used to solvate a class of model chem. reactions. Although there is precedent from our prior work that the use of nondeterministic interaction potentials can lead to accurate dynamics at long-enough time scales, this work provides evidence that this model has dynamical consistency specifically in the response to the reactant motion. That is, the agreement between the theor. rate consts. and those obtained from the stochastic simulations provides support for the SHC solvent without sacrificing the correlations in the dynamics of the reacting solutes.
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    69. 69
      Murphy, C. J.; Vartanian, A. M.; Geiger, F. M.; Hamers, R. J.; Pedersen, J.; Cui, Q.; Haynes, C. L.; Carlson, E. E.; Hernandez, R.; Klaper, R. D.; Orr, G.; Rosenzweig, Z. Biological responses to engineered nanomaterials: Needs for the next decade. ACS Cent. Sci. 2015, 1, 117,  DOI: 10.1021/acscentsci.5b00182
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      Biological Responses to Engineered Nanomaterials: Needs for the Next Decade
      Murphy, Catherine J.; Vartanian, Ariane M.; Geiger, Franz M.; Hamers, Robert J.; Pedersen, Joel; Cui, Qiang; Haynes, Christy L.; Carlson, Erin E.; Hernandez, Rigoberto; Klaper, Rebecca D.; Orr, Galya; Rosenzweig, Ze'ev
      ACS Central Science (2015), 1 (3), 117-123CODEN: ACSCII; ISSN:2374-7951. (American Chemical Society)
      A review. The interaction of nanomaterials with biomols., cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biol. and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chem. nature of nanomaterials in dynamic, complex aq. environments; (ii) real-time measurements of nanomaterial-biol. interactions with chem. specificity; (iii) delineation of mol. modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.
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      Wu, M.; Vartanian, A. M.; Chong, G.; Pandiakumar, A. K.; Hamers, R. J.; Hernandez, R.; Murphy, C. J. Solution NMR analysis of ligand environment in quaternary ammonium-terminated self-assembled monolayers on gold nanoparticles: The effect of surface curvature and ligand structure. J. Am. Chem. Soc. 2019, 141, 4316,  DOI: 10.1021/jacs.8b11445
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      Solution NMR Analysis of Ligand Environment in Quaternary Ammonium-Terminated Self-Assembled Monolayers on Gold Nanoparticles: The Effect of Surface Curvature and Ligand Structure
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      Journal of the American Chemical Society (2019), 141 (10), 4316-4327CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      We report a soln. NMR-based anal. of (16-mercaptohexadecyl)trimethylammonium bromide (MTAB) self-assembled monolayers on colloidal gold nanospheres (AuNSs) with diams. from 1.2 to 25 nm and gold nanorods (AuNRs) with aspect ratios from 1.4 to 3.9. The chem. shift anal. of the proton signals from the solvent-exposed headgroups of bound ligands suggests that the headgroups are satd. on the ligand shell as the sizes of the nanoparticles increase beyond ∼10 nm. Quant. NMR shows that the ligand d. of MTAB-AuNSs is size-dependent. Ligand d. ranges from ∼3 mols. per nm2 for 25 nm particles to up to 5-6 mols. per nm2 in ∼10 nm and smaller particles for in situ measurements of bound ligands; after I2/I- treatment to etch away the gold cores, ligand d. ranges from ∼2 mols. per nm2 for 25 nm particles to up to 4-5 mols. per nm2 in ∼10 nm and smaller particles. T2 relaxation anal. shows greater hydrocarbon chain ordering and less headgroup motion as the diam. of the particles increases from 1.2 nm to ∼13 nm. Mol. dynamics simulations of 4, 6, and 8 nm (11-mercaptoundecyl)trimethylammonium bromide-capped AuNSs confirm greater hydrophobic chain packing order and satn. of charged headgroups within the same spherical ligand shell at larger nanoparticle sizes and higher ligand densities. Combining the NMR studies and MD simulations, we suggest that the headgroup packing limits the ligand d., rather than the sulfur packing on the nanoparticle surface, for ∼10 nm and larger particles. For MTAB-AuNRs, no chem. shift data nor ligand d. data suggest that two populations of ligands that might correspond to side-ligands and end-ligands exist; yet T2 relaxation dynamics data suggest that headgroup mobility depends on aspect ratio and abs. nanoparticle dimensions.
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    71. 71
      Daly, C. A., Jr.; Allen, C. R.; Rozanov, N. D.; Chong, G.; Melby, E. S.; Kuech, T. R.; Lohse, S. E.; Murphy, C. J.; Pedersen, J. A.; Hernandez, R. Surface Coating Structure and Its Interaction with Cytochrome c in EG6-Coated Nanoparticles Varies with Surface Curvature. Langmuir 2020, 36, 5030– 5039,  DOI: 10.1021/acs.langmuir.0c00681
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      Surface Coating Structure and Its Interaction with Cytochrome c in EG6-Coated Nanoparticles Varies with Surface Curvature
      Daly, Clyde A.; Allen, Caley; Rozanov, Nikita; Chong, Gene; Melby, Eric S.; Kuech, Thomas R.; Lohse, Samuel E.; Murphy, Catherine J.; Pedersen, Joel A.; Hernandez, Rigoberto
      Langmuir (2020), 36 (18), 5030-5039CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      The compn., orientation, and conformation of proteins in biomol. coronas acquired by nanoparticles in biol. media contribute to how they are identified by a cell. While numerous studies have investigated protein compn. in biomol. coronas, relatively little detail is known about how the nanoparticle surface influences the orientation and conformation of the proteins assocd. with them. The authors previously showed that the peripheral membrane protein cytochrome c adopts preferred poses relative to neg. charged 3-mercaptopropionic acid (MPA)-gold nanoparticles (AuNPs). Here, the authors employ mol. dynamics simulations and complementary expts. to establish that cytochrome c also assumes preferred poses upon assocn. with nanoparticles functionalized with an uncharged ligand, specifically ω-(1-mercaptounde-11-cyl)hexa(ethylene glycol) (EG6). The authors find that the display of the EG6 ligands is sensitive to the curvature of the surface-and, consequently, the effective diam. of the nearly spherical nanoparticle core-which in turn affects the preferred poses of cytochrome c.
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      Bathe, M.; Hernandez, R.; Komiyama, T.; Machiraju, R.; Neogi, S. Autonomous computing materals. ACS Nano 2021, 15, 3586– 3592,  DOI: 10.1021/acsnano.0c09556
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      Autonomous Computing Materials
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      ACS Nano (2021), 15 (3), 3586-3592CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      A review. Conventional materials are reaching their limits in computation, sensing, and data storage capabilities, ushered in by the end of Moore's law, myriad sensing applications, and the continuing exponential rise in worldwide data storage demand. Conventional materials are also limited by the controlled environments in which they must operate, their high energy consumption, and their limited capacity to perform simultaneous, integrated sensing, computation, and data storage and retrieval. In contrast, the human brain is capable of multimodal sensing, complex computation, and both short- and long-term data storage simultaneously, with near instantaneous rate of recall, seamless integration, and minimal energy consumption. Motivated by the brain and the need for revolutionary new computing materials, we recently proposed the data-driven materials discovery framework, autonomous computing materials. This framework aims to mimic the brain's capabilities for integrated sensing, computation, and data storage by programming excitonic, phononic, photonic, and dynamic structural nanoscale materials, without attempting to mimic the unknown implementational details of the brain. If realized, such materials would offer transformative opportunities for distributed, multimodal sensing, computation, and data storage in an integrated manner in biol. and other nonconventional environments, including interfacing with biol. sensors and computers such as the brain itself.
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      The ACS Georgia Section celebrates the 75th awarding of the Charles Holmes Herty Medal for the year 2009. Craig L. Hill, a professor at Emory University, received the award for his contributions in catalytic oxidn. In particular, he is being recognized for his development of the most reactive known catalysts for removal of environmental pollutants, odors, and toxics from air; prepn. of terminal noble-metal oxo compds.; and creation of the only stable and sol. catalysts for oxidn. of water.
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    Cited By

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    This article is cited by 4 publications.

    1. Rigoberto Hernandez. Discipline-Based Diversity Research in Chemistry. Accounts of Chemical Research 2023, 56 (7) , 787-797. https://doi.org/10.1021/acs.accounts.2c00797
    2. Vicki H. Grassian. Physical Chemistry of Environmental Interfaces and the Environment in Physical Chemistry─A Career Perspective. The Journal of Physical Chemistry A 2022, 126 (30) , 4874-4880. https://doi.org/10.1021/acs.jpca.2c04098
    3. Vicki H. Grassian. Physical Chemistry of Environmental Interfaces and the Environment in Physical Chemistry─A Career Perspective. The Journal of Physical Chemistry B 2022, 126 (30) , 5598-5604. https://doi.org/10.1021/acs.jpcb.2c04099
    4. Vicki H. Grassian. Physical Chemistry of Environmental Interfaces and the Environment in Physical Chemistry─A Career Perspective. The Journal of Physical Chemistry C 2022, 126 (30) , 12320-12326. https://doi.org/10.1021/acs.jpcc.2c04100
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    • Figure 1

      Figure 1. Then and now. At left, Hernandez is pictured in his high school yearbook in a stylish cotton suit, gray leather shoes, and open collar which was on trend if different from the fashion of polos and tweed that would be the norm just a few months later upon teleporting to Princeton (photo by Mark Maynard). At right, Hernandez is pictured in his current work uniform featuring a tie, white dress shirt, and a jacket (photo by Robert R. Felt).

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      Figure 2

      Figure 2. A selected snapshot of Hernandez’s research efforts shown (clockwise from top left) through journal covers spanning across transition state theory (reprinted with permission from ref (1), copyright 2010 Elsevier), Janus and striped particles (reprinted with permission from ref (2), copyright 2014 AIP Publishing), diffusion through complex environments (reprinted with permission from ref (3), copyright 2010 American Chemical Society), stochastic hard collisions (reprinted with permission from ref (4), copyright 2018 Elsevier), sustainable nanoparticles (reprinted with permission from ref (5), copyright 2016 American Chemical Society), and diversity equity (reprinted with permission from ref (6), copyright 2018 American Chemical Society).

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    • References

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      This article references 89 other publications.

      1. 1
        Hernandez, R.; Bartsch, T.; Uzer, T. Transition State Theory in Liquids Beyond Planar Dividing Surfaces. Chem. Phys. 2010, 370, 270– 276,  DOI: 10.1016/j.chemphys.2010.01.016
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        1
        Transition state theory in liquids beyond planar dividing surfaces
        Hernandez, Rigoberto; Uzer, T.; Bartsch, Thomas
        Chemical Physics (2010), 370 (1-3), 270-276CODEN: CMPHC2; ISSN:0301-0104. (Elsevier B.V.)
        The success of transition state theory (TST) in describing the rates of chem. reactions has been less-than-perfect in soln. (and sometimes even in the gas phase) because conventional dividing surfaces are only approx. free of recrossings between reactants and products. Recent advances in dynamical systems theory have helped to identify the interconnected manifolds-"superhighways"-leading from reactants to products. The existence of these manifolds has been proven rigorously, and explicit algorithms are available for their calcn. We now show that these extended structures can be used to obtain reaction rates directly in dissipative systems. We also suggest a treatment for the substantially more general case in which the mol. solvent is fully specified by the positions of all its atoms. Specifically, we can construct effective solvent configurations for which the exact TST manifolds can be constructed and used to sample the rates of an open system.
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      2. 2
        Hagy, M. C.; Hernandez, R. Dynamical simulation of electrostatic striped colloidal particles. J. Chem. Phys. 2014, 140, 034701,  DOI: 10.1063/1.4859855
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        2
        Dynamical simulation of electrostatic striped colloidal particles
        Hagy, Matthew C.; Hernandez, Rigoberto
        Journal of Chemical Physics (2014), 140 (3), 034701/1-034701/13CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        The static and dynamic properties of striped colloidal particles are obtained using mol. dynamics computer simulations. Striped particles with n = 2 to n = 7 stripes of alternating elec. charge are modeled at a high level of detail through a pointwise (PW) representation of the particle surface. We also consider the extent to which striped particles are similar to comparable isotropically attractive particles-such as depletion attracting colloids-by modeling striped particles with an isotropic pair interaction computed by coarse-graining (CG) over orientations at a pair level. Surprisingly, the CG models reproduce the static structure of the PW models for a range of vol. fractions and interaction strengths consistent with the fluid region of the phase diagram for all n. As a corollary, different n-striped particle systems with comparable pair affinities (e.g., dimer equil. const.) have similar static structure. Stronger pair interactions lead to a collapsed structure in simulation as consistent with a glass-like phase. Different n-striped particle systems are found to have different phase boundaries and for certain n's no glass-like state is obsd. in any of our simulations. The CG model is found to have accelerated dynamics relative to the PW model for the same range of fluid conditions for which the models have identical static structure. This suggests striped electrostatic particles have slower dynamics than comparable isotropically attractive colloids. The slower dynamics result from a larger no. of long-duration reversible bonds between pairs of striped particles than seen in isotropically attractive systems. Higher n-striped particles systems generally have slower dynamics than lower n-striped systems with comparable pair affinities. (c) 2014 American Institute of Physics.
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      3. 3
        Tucker, A. K.; Hernandez, R. Observation of a trapping transition in the diffusion of a thick needle through fixed point scatterers. J. Phys. Chem. A 2010, 114, 9628– 9634,  DOI: 10.1021/jp100111y
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        3
        Observation of a Trapping Transition in the Diffusion of a Thick Needle through Fixed Point Scatterers
        Tucker, Ashley K.; Hernandez, Rigoberto
        Journal of Physical Chemistry A (2010), 114 (36), 9628-9634CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
        The long-time correlation functions of an infinitesimally thin needle moving through stationary point scatterers--a so-called Lorentz model--exhibits surprisingly long-time tails. These long-time tails are now seen to persist in a two-dimensional model even when the needle has a finite thickness. If the needles are too thick, then the needles are effectively trapped at all nontrivial densities of the scatterers. At needle widths approx. equal to or smaller than σ = ε/20 where ε is the av. spacing between scatterers, the needle diffuses and exhibits the crossover transition from the expected Enskog behavior to the enhanced translation diffusion seen earlier by Hofling, Frey and Franosch. At this needle width, an increase in its center-of-mass diffusion with respect to increasing d. is seen after a crossover d. of n* ≈ 5 is reached. (The reduced d. n* is defined as n* = nL2 where n is the no. d. of particles and L is the needle length.). The crossover transition for needles with finite thickness is spread over a range of densities exhibiting intermediate behavior. The asymptotic divergence of the center of mass diffusion is suppressed compared to that of infinitely thin needles. Finally, a new diminished diffusion regime, apparently due to the increased importance of head-on collisions, now appears at high scattering densities.
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      4. 4
        Singh, R. S.; Hernandez, R. Modeling soft core-shell colloids using stochastic hard collision dynamics. Chem. Phys. Lett. 2018, 708, 233– 240,  DOI: 10.1016/j.cplett.2018.08.032
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        4
        Modeling soft core-shell colloids using stochastic hard collision dynamics
        Singh, Rakesh S.; Hernandez, Rigoberto
        Chemical Physics Letters (2018), 708 (), 233-240CODEN: CHPLBC; ISSN:0009-2614. (Elsevier B.V.)
        The equil. structure and thermodn. behavior of a soft matter suspension of hard-core soft-shell (HCSS) colloids have been modeled using stochastic hard collision (SHC) dynamics [Craven et al., J. Chem. Phys. 2013, 138, 244901]. SHC dynamics includes the effects of inter-penetrability of soft particles while retaining the computational efficiency of hard collision dynamics. The HCSS colloids are characterized using two parameters: softness parameter (a measure of the propensity toward interpenetration), and core-to-shell ratio. In both, mol. dynamics and Monte-Carlo simulations, the softness parameter is seen to profoundly affect the effective packing fraction and the thermodn. behavior of the system. Once we accounted for the trivial effects from changes in the reduced vol. fraction on changing softness, we found that the inter-particle penetration continues to affect this thermodn. behavior. The structural origin of this nontrivial effect likely lies in the loss of translational order upon increasing softness.
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      5. 5
        Cui, Q.; Hernandez, R.; Mason, S. E.; Frauenheim, T.; Pedersen, J. A.; Geiger, F. Mini-review. Sustainable nanotechnology: Opportunities and challenges for theoretical/computational studies. J. Phys. Chem. B 2016, 120, 7297– 7306,  DOI: 10.1021/acs.jpcb.6b03976
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        Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies
        Cui, Qiang; Hernandez, Rigoberto; Mason, Sara E.; Frauenheim, Thomas; Pedersen, Joel A.; Geiger, Franz
        Journal of Physical Chemistry B (2016), 120 (30), 7297-7306CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
        For assistance in the design of the next generation of nanomaterials that are functional and have minimal health and safety concerns, it is imperative to establish causality, rather than correlations, in how properties of nanomaterials det. biol. and environmental outcomes. Due to the vast design space available and the complexity of nano/bio interfaces, theor. and computational studies are expected to play a major role in this context. In this minireview, we highlight opportunities and pressing challenges for theor. and computational chem. approaches to explore the relevant physicochem. processes that span broad length and time scales. We focus discussions on a bottom-up framework that relies on the detn. of correct intermol. forces, accurate mol. dynamics, and coarse-graining procedures to systematically bridge the scales, although top-down approaches are also effective at providing insights for many problems such as the effects of nanoparticles on biol. membranes.
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        Analysis by gender of the doctoral and postdoctoral institutions of faculty members at the top-fifty ranked chemistry departments
        Kuck, Valerie J.; Marzabadi, Cecilia H.; Nolan, Susan A.; Buckner, Janine P.
        Journal of Chemical Education (2004), 81 (3), 356-363CODEN: JCEDA8; ISSN:0021-9584. (Journal of Chemical Education, Dept. of Chemistry)
        There is no expanded citation for this reference.
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      10. 10
        Miller, W. H.; Hernandez, R.; Moore, C. B.; Polik, W. F. A transition state theory-based statistical distribution of unimolecular decay rates, with application to unimolecular decomposition of formaldehyde. J. Chem. Phys. 1990, 93, 5657– 5666,  DOI: 10.1063/1.459636
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        10
        A transition state theory-based statistical distribution of unimolecular decay rates with application to unimolecular decomposition of formaldehyde
        Miller, William H.; Hernandez, Rigoberto; Moore, C. Bradley; Polik, William F.
        Journal of Chemical Physics (1990), 93 (8), 5657-66CODEN: JCPSA6; ISSN:0021-9606.
        A statistical distribution of state-specific unimol. decay rates is derived (within the framework of random matrix theory) that is detd. completely by the transition state properties of the potential energy surface. It includes the std. χ-square distributions as a special case. Model calcns. are presented to show the extent to which it can differ from the χ-square distribution, and specific application is made to the state-specific unimol. decay rate data for D2CO → D2 + CO.
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      11. 11
        Hernandez, R.; Miller, W. H.; Moore, C. B.; Polik, W. F. A Random Matrix/Transition State Theory for the Probability Distribution of State-Specific Unimolecular Decay Rates: Generalization to Include Total Angular Momentum Conservation and Other Dynamical Symmetries. J. Chem. Phys. 1993, 99, 950– 962,  DOI: 10.1063/1.465360
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        11
        A random matrix/transition state theory for the probability distribution of state-specific unimolecular decay rates: generalization to include total angular momentum conservation and other dynamical symmetries
        Hernandez, Rigoberto; Miller, William H.; Moore, C. Bradley; Polik, William F.
        Journal of Chemical Physics (1993), 99 (2), 950-62CODEN: JCPSA6; ISSN:0021-9606.
        A previously developed random matrix/transition state theory (RM/TST) model for the probability distribution of state-sp. unimol. decay rates was generalized to incorporate total angular momentum conservation and other dynamic symmetries. The model is made into a predictive theory by using a semiclassical method to det. the transmission probabilities of a nonseparable rovibrational Hamiltonian at the transition state. The overall theory gives a good description of the state-sp. rates for the D2CO → D2 + CO unimol. decay; in particular, it describes the dependence of the distribution of rates on total angular momentum J. Comparison of the exptl. values with results of the RM/TST theory suggests that there is mixing among the rovibrational states.
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      12. 12
        Miller, W. H. Autobiographical Sketch of William Hughes Miller. J. Phys. Chem. A 2001, 105, 2487– 2489,  DOI: 10.1021/jp0101920
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      13. 13
        Miller, W. H. Semi-classical theory for non-separable systems:. Construction of “good” action-angle variables for reaction rate constants. Faraday Discuss. Chem. Soc. 1977, 62, 40,  DOI: 10.1039/DC9776200040
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        13
        Semiclassical theory for non-separable systems: construction of good action-angle variables for reaction rate constants
        Miller, William H.
        Faraday Discussions of the Chemical Society (1977), 62 (Potential Energy Surf.), 40-6CODEN: FDCSB7; ISSN:0301-7249.
        A semiclassical expression for bimol. rate consts. for reactions which have a single activation barrier is obtained in terms of the good action variables of the classical Hamiltonian which are assocd. with the saddle point region of the potential energy surface. The formulas apply to nonseparable and separable saddle points.
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      14. 14
        Miller, W. H.; Hernandez, R.; Handy, N. C.; Jayatilaka, D.; Willetts, A. Ab initio calculation of anharmonic constants for a transition state, with application to semiclassical transition state tunneling probabilities. Chem. Phys. Lett. 1990, 172, 62– 68,  DOI: 10.1016/0009-2614(90)87217-F
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        14
        Ab initio calculation of anharmonic constants for a transition state, with application to semiclassical transition state tunneling probabilities
        Miller, William H.; Hernandez, Rigoberto; Handy, Nicholas C.; Jayatilaka, Dylan; Willetts, Andrew
        Chemical Physics Letters (1990), 172 (1), 62-8CODEN: CHPLBC; ISSN:0009-2614.
        "Good" (i.e. conserved) action variables exist in the vicinity of a saddle point (i.e. transition state) of a potential energy surface in complete analogy to those related to a min. on the surface. Transition state theory tunneling (or transmission) probabilities can be expressed semiclassically in terms of these "good" action variables, including the effects of non-separable coupling of all degrees of freedom with each other. This paper shows how ab initio quantum chem. methods recently developed for calcg. anharmonic consts. about a potential min. (i.e. for ordinary vibrational energy levels) can be readily adapted to obtain those related to a transition state, thus providing a rigorous and practical way to apply this non-separable transition state theory. Application is made to the transition state for the reaction D2CO → D2 + CO.
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      15. 15
        Cohen, M. J.; Handy, N. C.; Hernandez, R.; Miller, W. H. Cumulative reaction probabilities for H + H2 → H2 + H from a knowledge of the anharmonic force field. Chem. Phys. Lett. 1992, 192, 407– 416,  DOI: 10.1016/0009-2614(92)85491-R
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        15
        Cumulative reaction probabilities for atomic hydrogen + molecular hydrogen → molecular hydrogen + atomic hydrogen from a knowledge of the anharmonic force field
        Cohen, Michael J.; Handy, Nicholas C.; Hernandez, Rigoberto; Miller, William H.
        Chemical Physics Letters (1992), 192 (4), 407-16CODEN: CHPLBC; ISSN:0009-2614.
        In an earlier publication, the authors showed how knowledge of a quartic force field expanded about a transition state can be used to obtain transition-state-theory tunneling probabilities. Thus coupling between the reaction mode and other modes is included in this second-order perturbation theory approach. The authors study the very anharmonic reaction H+H2→H2+H and show that even in this extreme case, there is reasonable agreement between the cumulative reaction probabilities calcd. by this semiclassical approach, and full quantum calcns.
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      16. 16
        Hernandez, R.; Miller, W. H. Semiclassical Transition State Theory. A New Perspective. Chem. Phys. Lett. 1993, 214, 129– 136,  DOI: 10.1016/0009-2614(93)90071-8
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        16
        Semiclassical transition state theory. A new perspective
        Hernandez, Rigoberto; Miller, William H.
        Chemical Physics Letters (1993), 214 (2), 129-36CODEN: CHPLBC; ISSN:0009-2614.
        The semiclassical transition state theory (SCTST) introduced by W. H. Miller et al. (1990) requires the inversion of an (effectively integrable) Hamiltonian with respect to the action of the reactive coordinate. The inversion may be avoided in computing the thermal rate const.; the resulting expression provides an appealing link to conventional transition state theory. This reformulation of the SCTST rate is illustrated by application to the bimol. reaction, H + H2 → H2 + H, and to the unimol. dissocn., D2CO → D2 + CO.
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      17. 17
        Hernandez, R. A Combined Use of Perturbation Theory and Diagonalization: Application to Bound Energy Levels and Semiclassical Rate Theory. J. Chem. Phys. 1994, 101, 9534– 9547,  DOI: 10.1063/1.467985
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        17
        A combined use of perturbation theory and diagonalization: application to bound energy levels and semiclassical rate theory
        Hernandez, Rigoberto
        Journal of Chemical Physics (1994), 101 (11), 9534-47CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        A new method, mixed diagonalization, is introduced in which an effective Hamiltonian operator acting on a reduced dimensional space is constructed using the similarity transformations of canonical Van Vleck perturbation theory (CVPT). This construction requires the characterization of modes into two categories, global and local, which in the bound vibrational problem are tantamount to the large and small amplitude vibrations, resp. The local modes in the Hamiltonian are projected out by CVPT, and the resulting Hamiltonian operator acts only on the space of global modes. The method affords the treatment of energy levels of bound systems in which some vibrational assignments are possible. It systematically provides a reduced dimensional Hamiltonian which is more amenable to exact numerical soln. that the original full-dimensional Hamiltonian. In recent work, a semiclassical transition state theory (SCTST) rate expression was written in terms of a Hamiltonian operator parameterized by the imaginary action along the local reaction path in the transition state region [Chem. Phys. Lett. 214, 129(1993)]. The Hamiltonian constructed by mixed diagonalization has this form, and can be used to obtain more accurate semiclassical rate expressions.
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      18. 18
        Nguyen, T. L.; Stanton, J. F.; Barker, J. R. Ab Initio Reaction Rate Constants Computed Using Semiclassical Transition-State Theory: HO + H2 → H2O + H and Isotopologues. J. Phys. Chem. A 2011, 115, 5118– 5126,  DOI: 10.1021/jp2022743
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        18
        Ab Initio Reaction Rate Constants Computed Using Semiclassical Transition-State Theory: HO + H2 → H2O + H and Isotopologues
        Nguyen, Thanh Lam; Stanton, John F.; Barker, John R.
        Journal of Physical Chemistry A (2011), 115 (20), 5118-5126CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
        A new algorithm for the semiclassical transition-state theory (SCTST) formulated by W.H. Miller and co-workers is used to compute rate consts. for the isotopologues of the title reaction, with no empirical adjustments. The SCTST and relevant results from second-order vibrational perturbation theory (VPT2) are summarized. VPT2 is used at the CCSD(T) level of electronic structure theory to compute the anharmonicities of the fully coupled vibrational modes (including the reaction coordinate) of the transition structure. The anharmonicities are used in SCTST to compute the rate consts. over the temp. range from 200 to 2500 K. The computed rate consts. are compared to exptl. data and theor. calcns. from the literature. The SCTST results for abs. rate consts. and for both primary and secondary isotope effects are in excellent agreement with the exptl. data for this reaction over the entire temp. range. The sensitivity of SCTST to various parameters is investigated by using a set of simplified models. The results show that multidimensional tunneling along the curved reaction path is important at low temps. and the anharmonic coupling among the vibrational modes is important at high temps. The theor. kinetics data are also presented as fitted empirical algebraic expressions.
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      19. 19
        Barker, J. R.; Nguyen, T. L.; Stanton, J. F. Kinetic Isotope Effects for Cl + CH4 → HCl + CH3 Calculated Using ab Initio Semiclassical Transition State Theory. J. Phys. Chem. A 2012, 116, 6408– 6419,  DOI: 10.1021/jp212383u
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        19
        Kinetic Isotope Effects for Cl + CH4 .dblharw. HCl + CH3 Calculated Using ab Initio Semiclassical Transition State Theory
        Barker, John R.; Nguyen, Thanh Lam; Stanton, John F.
        Journal of Physical Chemistry A (2012), 116 (24), 6408-6419CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
        Calcns. were carried out for 25 isotopologues of the title reaction for various combinations of 35Cl, 37Cl, 12C, 13C, 14C, H, and D. The computed rate consts. are based on harmonic vibrational frequencies calcd. at the CCSD(T)/aug-cc-pVTZ level of theory and Xij vibrational anharmonicity coeffs. calcd. at the CCSD(T) /aug-cc-pVDZ level of theory. For some reactions, anharmonicity coeffs. were also computed at the CCSD(T)/aug-cc-pVTZ level of theory. The classical reaction barrier was taken from Eskola et al. [J. Phys. Chem. A 2008, 112, 7391-7401], who extrapolated CCSD(T) calcns. to the complete basis set limit. Rate consts. were calcd. for temps. from ∼100 to ∼2000 K. The computed ab initio rate const. for the normal isotopologue is in good agreement with expts. over the entire temp. range (∼10% lower than the recommended exptl. value at 298 K). The ab initio H/D kinetic isotope effects (KIEs) for CH3D, CH2D2, CHD3, and CD4 are in very good agreement with literature exptl. data. The ab initio 12C/13C KIE is in error by ∼2% at 298 K for calcns. using Xij coeffs. computed with the aug-cc-pVDZ basis set, but the error is reduced to ∼1% when Xij coeffs. computed with the larger aug-cc-pVTZ basis set are used. Systematic improvements appear to be possible. The present SCTST results are found to be more accurate than those from other theor. calcns. Overall, this is a very promising method for computing ab initio kinetic isotope effects.
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      20. 20
        Nguyen, T. L.; Stanton, J. F. Ab Initio Thermal Rate Calculations of HO + HO → O(3P) + H2O Reaction and Isotopologues. J. Phys. Chem. A 2013, 117, 2678– 2686,  DOI: 10.1021/jp312246q
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        20
        Ab Initio Thermal Rate Calculations of HO + HO = O(3P) + H2O Reaction and Isotopologues
        Nguyen, Thanh Lam; Stanton, John F.
        Journal of Physical Chemistry A (2013), 117 (13), 2678-2686CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
        The forward and reverse reactions, HO + HO .dblharw. O(3P) + H2O, which play roles in both combustion and lab. studies, were theor. characterized with a master equation approach to compute thermal reaction rate consts. at both the low and high pressure limits. Our ab initio k(T) results for the title reaction and two isotopic variants agree very well with expts. (within 15%) over a wide temp. range. The calcd. reaction rate shows a distinctly non-Arrhenius behavior and a strong curvature consistent with the expt. This characteristic behavior is due to effects of pos. barrier height and quantum mech. tunneling. Tunneling is very important and contributes more than 70% of total reaction rate at room temp. A prereactive complex is also important in the overall reaction scheme.
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      21. 21
        Komatsuzaki, T.; Berry, R. S. Regularity in chaotic reaction paths. I. Ar6. J. Chem. Phys. 1999, 110, 9160– 9173,  DOI: 10.1063/1.478838
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        21
        Regularity in chaotic reaction paths. I. Ar6
        Komatsuzaki, Tamiki; Berry, R. Stephen
        Journal of Chemical Physics (1999), 110 (18), 9160-9173CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        We scrutinize the saddle crossings of a simple cluster of six atoms to show (a) that it is possible to choose a coordinate system in which the transmission coeff. for the classical reaction path is unity at all energies up to a moderately high energy, above which the transition state is chaotic; (b) that at energies just more than sufficient to allow passage across the saddle, all or almost all the degrees of freedom of the system are essentially regular in the region of the transition state; and (c) that the degree of freedom assocd. with the reaction coordinate remains essentially regular through the region of the transition state, even to moderately high energies. Microcanonical mol. dynamics simulation of Ar6 bound by pairwise Lennard-Jones potentials reveals the mechanics of passage. We use Lie canonical perturbation theory to construct the nonlinear transformation to a hyperbolic coordinate system which reveals these regularities. This transform "rotates away" the recrossings and nonregular behavior, esp. of the motion along the reaction coordinate, leaving a coordinate and a corresponding dividing surface in phase space which minimize recrossings and mode-mode mixing in the transition state region. The action assocd. with the reactive mode tends to be an approx. invariant of motion through the saddle crossings throughout a relatively wide range of energy. Only at very low energies just above the saddle could any other approx. invariants of motion be found for the other, nonreactive modes. No such local invariants appeared at energies at which the modes are all chaotic and coupled to one another.
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      22. 22
        Komatsuzaki, T.; Berry, R. S. Regularity in chaotic reactions paths II: Ar6. Energy dependence and visualization of the reaction bottleneck. Phys. Chem. Chem. Phys. 1999, 1, 1387– 1397,  DOI: 10.1039/a809424a
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        22
        Regularity in chaotic reaction paths II: Ar6. Energy dependence and visualization of the reaction bottleneck
        Komatsuzaki, Tamiki; Stephen Berry, R.
        Physical Chemistry Chemical Physics (1999), 1 (6), 1387-1397CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
        Reaction trajectories reveal regular behavior in the reactive degree of freedom and unit transmission coeffs. as the system crosses the saddle region sepg. reactants and products. The regularity persists up to moderately high energies, even when all other degrees of freedom are chaotic. This behavior is apparent in a representation obtained by transformation with Lie canonical perturbation theory. The dividing surface in this representation is analogous to the conventional dividing surface in the sense that it is the point set for which the reaction coordinate has the const. value it has at the saddle-point singularity. However the nonlinear, full phase-space character of the transformation makes the new crossing surface a complicated, abstr. object whose interpretation and visualization, the objective of this paper, can be realized by cataloging the recrossings as they disappear in successively higher orders of perturbation, and by projection into spaces of only a few dimensions. The result is a conceptual interpretation of how regular behavior persists in a reactive degree of freedom.
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      23. 23
        Komatsuzaki, T.; Berry, R. S. Local regularity and non-recrossing path in transition state—a new strategy in chemical reaction theories. J. Mol. Struct.: THEOCHEM 2000, 506, 55– 70,  DOI: 10.1016/S0166-1280(00)00402-4
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        23
        Local regularity and non-recrossing path in transition state - a new strategy in chemical reaction theories
        Komatsuzaki, T.; Berry, R. S.
        Journal of Molecular Structure: THEOCHEM (2000), 506 (), 55-70CODEN: THEODJ; ISSN:0166-1280. (Elsevier Science B.V.)
        We analyze local regularities in the regions of transition states of a 6-atom Lennard-Jones cluster to demonstrate how one can choose a non-recrossing reaction path in phase space along which the transmission coeff. for the classical reaction path is unity from threshold up to a moderately high energy, above which the transition state is chaotic, and how one can picture the nonlinear, full-phase-space character of the dividing hypersurface by projecting it into spaces of only a few dimensions. These overcome one of the long-standing ambiguities in chem. reaction theories, the recrossing problem, up to moderately high energies, and make transition state theory more generalized, applicable even in cases in which apparent recrossings spoil the conventional theory.
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      24. 24
        Komatsuzaki, T.; Berry, R. S. Regularity in chaotic reaction paths III: Ar6 local invariances at the reaction bottleneck. J. Chem. Phys. 2001, 115, 4105– 4117,  DOI: 10.1063/1.1385152
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        24
        Regularity in chaotic reaction paths III: Ar6 local invariances at the reaction bottleneck
        Komatsuzaki, Tamiki; Berry, R. Stephen
        Journal of Chemical Physics (2001), 115 (9), 4105-4117CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        We recently developed a new method to ext. a many-body phase-space dividing surface, across which the transmission coeff. for the classical reaction path is unity. The example of isomerization of a 6-atom Lennard-Jones cluster showed that the action assocd. with the reaction coordinate is an approx. invariant of motion through the saddle regions, even at moderately high energies, at which most or all the other modes are chaotic [J. Chem. Phys. 105, 10838 (1999); Phys. Chem. Chem. Phys. 1, 1387 (1999)]. In the present article, we propose a new algorithm to analyze local invariances about the transition state of N-particle Hamiltonian systems. The approx. invariants of motion assocd. with a reaction coordinate in phase space densely distribute in the sea of chaotic modes in the region of the transition state. Using projections of distributions in only two principal coordinates, one can grasp and visualize the stable and unstable invariant manifolds to and from a hyperbolic point of a many-body nonlinear system, like those of the one-dimensional, integrable pendulum. This, in turn, reveals a new type of phase space bottleneck in the region of a transition state that emerges as the total energy increases, which may trap a reacting system in that region.
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      25. 25
        Komatsuzaki, T.; Berry, R. S. Dynamical hierarchy in transition states: Why and how does a system climb over the mountain?. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 7666– 7671,  DOI: 10.1073/pnas.131627698
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        25
        Dynamical hierarchy in transition states: why and how does a system climb over the mountain?
        Komatsuzaki, Tamiki; Berry, R. Stephen
        Proceedings of the National Academy of Sciences of the United States of America (2001), 98 (14), 7666-7671CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
        How a reacting system climbs through a transition state during a reaction was an intriguing subject for decades. Here the authors present and quantify a technique to identify and characterize local invariance about the transition state of an N-particle Hamiltonian system, using Lie canonical perturbation theory combined with microcanonical mol. dynamics simulation. At least three distinct energy regimes of dynamical behavior occur in the region of the transition state, distinguished by the extent of their local dynamical invariance and regularity. Isomerization of a six-atom Lennard-Jones cluster illustrates this: up to energies high enough to make the system manifestly chaotic, approx. invariants of motion assocd. with a reaction coordinate in phase space imply a many-body dividing hypersurface in phase space that is free of recrossings even in a sea of chaos. The method makes it possible to visualize the stable and unstable invariant manifolds leading to and from the transition state, i.e., the reaction path in phase space, and how this regularity turns to chaos with increasing total energy of the system. This, in turn, illuminates a new type of phase space bottleneck in the region of a transition state that emerges as the total energy and mode coupling increase, which keeps a reacting system increasingly trapped in that region.
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        Pollak, E.; Pechukas, P. Unified statistical model for “complex” and “direct” reaction mechanisms: A test on the collinear H + H2 exchange reaction. J. Chem. Phys. 1979, 70, 325– 333,  DOI: 10.1063/1.437194
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        26
        Unified statistical model for "complex" and "direct" reaction mechanisms: a test on the collinear atomic hydrogen + molecular hydrogen exchange reaction
        Pollak, Eli; Pechukad, Philip
        Journal of Chemical Physics (1979), 70 (1), 325-33CODEN: JCPSA6; ISSN:0021-9606.
        Miller's unified statistical theory for bimol. chem. reactions is tested on the collinear H + H2 exchange reaction, treated classically. The reaction probability calcd. from unified statistical theory is more accurate than that calcd. from ordinary transition state theory or from variational transition state theory; in particular, unified statistical theory predicts the high-energy falloff of the reaction probability, which transition state theory does not. A derivation of unified statistical theory emphasizes the dynamical and statistical assumptions that are the foundation of the theory. These assumptions unambiguously define the "collision complex" in unified statistical theory and are tested in detail on the H + H2 reaction. Finally, a lower bound on the reaction probability is derived; this bound complements the upper bound provided by transition state theory and is significantly more accurate, for the H + H2 reaction, than either transition state theory or unified statistical theory.
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        Pollak, E. In Theory of Chemical Reaction Dynamics; Baer, M., Ed.; CRC Press: Boca Raton, FL, 1985; Vol. 3; p 123.
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        Grobgeld, D.; Pollak, E.; Zakrzewski, J. A Numerical Method for Locating Stable Periodic Orbits in Chaotic Systems. Phys. D 1992, 56, 368– 380,  DOI: 10.1016/0167-2789(92)90176-N
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        Moix, J. M.; Hernandez, R.; Pollak, E. Momentum and velocity autocorrelation functions of a diatomic molecule are not necessarily proportional to each other. J. Phys. Chem. B 2008, 112, 213– 218,  DOI: 10.1021/jp0730951
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        29
        Momentum and Velocity Autocorrelation Functions of a Diatomic Molecule Are Not Necessarily Proportional to Each Other
        Moix, Jeremy M.; Hernandez, Rigoberto; Pollak, Eli
        Journal of Physical Chemistry B (2008), 112 (2), 213-218CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
        We present a computation of the classical momentum and velocity correlation functions of Br2 considered as an idealized mol. wire connecting dissipated lead atoms at each end of the dimer. It is demonstrated that coupling of the diat. relative momentum to the leads may result in momenta that are not equal to the mass-weighted velocity. These differences show up in numerical simulations of both the av. value and time correlations of the bond momentum and velocity. These observations are supported by anal. predictions for the av. temp. of the diat. They imply that the "std. recipes" for modeling the system with a generalized Langevin equation are insufficient.
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      30. 30
        Hernandez, R.; Cao, J.; Voth, G. A. On the Feynman path centroid density as a phase space distribution in quantum statistical mechanics. J. Chem. Phys. 1995, 103, 5018– 5026,  DOI: 10.1063/1.470588
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        30
        On the Feynman path centroid density as a phase space distribution in quantum statistical mechanics
        Hernandez, Rigoberto; Cao, Jianshu; Voth, Gregory A.
        Journal of Chemical Physics (1995), 103 (12), 5018-26CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        The phase space formulation of quantum statistical mechanics using the Feynman path centroid d. offers an alternative perspective to the std. Wigner prescription for the classical-like evaluation of equil. and/or dynamical quantities of statistical systems. The use of this formulation has been implicit in recent work on quantum rate theories, for example, in which the centroid d. distribution replaces the classical Boltzmann distribution. In order to further understand the approxns. involved in this and similar transcriptions, the present work elaborates and clarifies the issue of operator ordering in a rigorous centroid-based formulation. In particular, through the use of the Weyl correspondence, a precise definition of the centroid symbol of operators and their products is presented. Though we fall short of finding the algebraic structure tantamount to that found in the Weyl symbols-of which the Wigner distribution is an example- the resulting expressions have internal consistency and are amenable to approx. evaluation through cumulant expansions.
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        Hernandez, R.; Voth, G. A. Quantum time correlation functions and classical coherence. Chem. Phys. 1998, 233, 243– 255,  DOI: 10.1016/S0301-0104(98)00027-5
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        31
        Quantum time correlation functions and classical coherence
        Hernandez, Rigoberto; Voth, Gregory A.
        Chemical Physics (1998), 233 (2,3), 243-255CODEN: CMPHC2; ISSN:0301-0104. (Elsevier Science B.V.)
        Quantum time correlation functions for electronically adiabatic and nonadiabatic processes have recently been evaluated directly using the semiclassical initial value representation [J. Cao and G.A. Voth, J. Chem. Phys. 104 (1996) 271]. In this paper, the approach to the classical limit of this theory is analyzed and the nature of coherence in such limits is explored.
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      32. 32
        Verashchagina, A.; Bettio, F. Gender segregation in the labour market; Directorate-General for Employment, Social Affairs and Inclusion (European Commission), 2009.
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        Hernandez, R.; Somer, F. L. Stochastic dynamics in irreversible nonequilibrium environments. 1. The fluctuation-dissipation relation. J. Phys. Chem. B 1999, 103, 1064– 1069,  DOI: 10.1021/jp983625g
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        Stochastic Dynamics in Irreversible Nonequilibrium Environments. 1. The Fluctuation-Dissipation Relation
        Hernandez, Rigoberto; Somer, Frank L.,Jr.
        Journal of Physical Chemistry B (1999), 103 (7), 1064-1069CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
        A generalization of the generalized Langevin equation (stochastic dynamics) is introduced in order to model chem. reactions which take place in changing environments. The friction kernel representing the solvent response is given a nonstationary form with respect to which the instantaneous random solvent force satisfies a natural generalization of the fluctuation-dissipation relation. Theor. considerations, as well as numerical simulations, show that the dynamics of this construction satisfy the equipartition theorem beyond its equil. limits.
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      34. 34
        Hernandez, R.; Somer, F. L. Stochastic dynamics in irreversible nonequilibrium environments. 2. A model for thermosetting polymerization. J. Phys. Chem. B 1999, 103, 1070– 1077,  DOI: 10.1021/jp9836269
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        Stochastic Dynamics in Irreversible Nonequilibrium Environments. 2. A Model for Thermosetting Polymerization
        Hernandez, Rigoberto; Somer, Frank L. Jr.
        Journal of Physical Chemistry B (1999), 103 (7), 1070-1077CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
        A generalization of the generalized Langevin equation (GLE), the so-called irreversible GLE (iGLE) [Hernandez, R.; Somer, F. L. J. Phys. Chem. 1999, 103, XXXX], is further extended to describe non-stationary environments in which the non-stationarity is induced by the macroscopic behavior of the ensemble itself, rather than an external force. Such a formalism lends itself to the dynamical study of the length distributions of growing polymers.
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        Hernandez, R. The projection of a mechanical system onto the irreversible generalized Langevin equation (iGLE). J. Chem. Phys. 1999, 111, 7701– 7704,  DOI: 10.1063/1.480160
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        The projection of a mechanical system onto the irreversible generalized Langevin equation
        Hernandez, Rigoberto
        Journal of Chemical Physics (1999), 111 (17), 7701-7704CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        The so-called irreversible generalized Langevin equation [R. Hernandez and F. L. Somer, J. Phys. Chem. B 103, 1064 (1999)], which extends the generalized Langevin equation (stochastic dynamics) to include irreversible changes (nonstationarity) in the solvent response, is shown to be the projection of an explicit time-dependent Hamiltonian system.
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      36. 36
        Locker, C. R.; Hernandez, R. A minimalist model protein with multiple folding funnels. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 9074– 9079,  DOI: 10.1073/pnas.161438898
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        36
        A minimalist model protein with multiple folding funnels
        Locker, C. Rebecca; Hernandez, Rigoberto
        Proceedings of the National Academy of Sciences of the United States of America (2001), 98 (16), 9074-9079CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
        Kinetic and structural studies of wild-type proteins such as prions and amyloidogenic proteins provide suggestive evidence that proteins may adopt multiple long-lived states in addn. to the native state. All of these states differ structurally because they lie far apart in configuration space, but their stability is not necessarily caused by cooperative (nucleation) effects. In this study, a minimalist model protein is designed to exhibit multiple long-lived states to explore the dynamics of the corresponding wild-type proteins. The minimalist protein is modeled as a 27-monomer sequence confined to a cubic lattice with three different monomer types. An order parameter-the winding index-is introduced to characterize the extent of folding. The winding index has several advantages over other commonly used order parameters like the no. of native contacts. It can distinguish between enantiomers, its calcn. requires less computational time than the no. of native contacts, and reduced-dimensional landscapes can be developed when the native state structure is not known a priori. The results for the designed model protein prove by existence that the rugged energy landscape picture of protein folding can be generalized to include protein "misfolding" into long-lived states.
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        Servos, J. W. Physical Chemistry from Ostwald to Pauling: The Making of a Science in America; Princeton University Press, 1990.
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        Hernandez, R. 6. Blurring of Physical Chemistry and Chemical Physics. 2013; http://everywherechemistry.blogspot.com/2013/08/6-blurring-of-physical-chemistry-and.html, accessed January 15, 2021.
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        Schatz, G. C. Celebrating Our 120th Anniversary. J. Phys. Chem. A 2016, 120, 9679– 9681,  DOI: 10.1021/acs.jpca.6b10935
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        Celebrating Our 120th Anniversary
        Schatz, George C.
        Journal of Physical Chemistry A (2016), 120 (49), 9679-9681CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
        There is no expanded citation for this reference.
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      40. 40
        Bartsch, T.; Hernandez, R.; Uzer, T. Transition state in a noisy environment. Phys. Rev. Lett. 2005, 95, 058301,  DOI: 10.1103/PhysRevLett.95.058301
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        40
        Transition State in a Noisy Environment
        Bartsch, Thomas; Hernandez, Rigoberto; Uzer, T.
        Physical Review Letters (2005), 95 (5), 058301/1-058301/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
        Transition state theory overestimates reaction rates in soln. because conventional dividing surfaces between reagents and products are crossed many times by the same reactive trajectory. We describe a recipe for constructing a time-dependent dividing surface free of such recrossings in the presence of noise. The no-recrossing limit of transition state theory thus becomes generally available for the description of reactions in a fluctuating environment.
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      41. 41
        Shukla, C.; Hallett, J. P.; Popov, A. V.; Hernandez, R.; Liotta, C.; Eckert, C. Molecular Dynamics Simulation of the Cybotactic Region in Gas-Expanded Methanol-Carbon Dioxide and Acetone-Carbon Dioxide Mixtures. J. Phys. Chem. B 2006, 110, 24101– 24111,  DOI: 10.1021/jp0648947
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        41
        Molecular Dynamics Simulation of the Cybotactic Region in Gas-Expanded Methanol-Carbon Dioxide and Acetone-Carbon Dioxide Mixtures
        Shukla, Charu L.; Hallett, Jason P.; Popov, Alexander V.; Hernandez, Rigoberto; Liotta, Charles L.; Eckert, Charles A.
        Journal of Physical Chemistry B (2006), 110 (47), 24101-24111CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
        Local solvation and transport effects in gas-expanded liqs. (GXLs) are reported based on mol. simulation. GXLs were found to exhibit local d. enhancements similar to those seen in supercrit. fluids, although less dramatic. This approach was used as an alternative to a multiphase atomistic model for these mixts. by utlilizing exptl. results to describe the necessary fixed conditions for a locally (quasi-) stable mol. dynamics model of the (single) GXL phase. The local anisotropic pair correlation function, orientational correlation functions, and diffusion rates are reported for two systems: CO2-expanded methanol and CO2-expanded acetone at 298 K and pressures up to 6 MPa.
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      42. 42
        Hallett, J. P.; Kitchens, C. L.; Hernandez, R.; Liotta, C.; Eckert, C. Probing the Cybotactic Region in Gas-Expanded Liquids (GXLs). Acc. Chem. Res. 2006, 39, 531– 538,  DOI: 10.1021/ar0501424
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        42
        Probing the Cybotactic Region in Gas-Expanded Liquids (GXLs)
        Hallett, Jason P.; Kitchens, Christopher L.; Hernandez, Rigoberto; Liotta, Charles L.; Eckert, Charles A.
        Accounts of Chemical Research (2006), 39 (8), 531-538CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
        Gas-expanded liqs. (GXLs) are a new and benign class of liq. solvents, which may offer many advantages for sepns., reactions, and advanced materials. GXLs are intermediate in properties between normal liqs. and supercrit. fluids, both in solvating power and in transport properties. Other advantages include benign nature, low operating pressures, and highly tunable properties by simple pressure variations. The chem. community has only just begun to exploit the advantages of these GXLs for industrial applications. This account focuses on the synergism of exptl. techniques with theor. modeling resulting in a powerful combination for exploring chem. structure and transport in the cybotactic region of GXLs (at the nanometer lengthscale).
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      43. 43
        Stockard, J.; Rohlfing, C. M.; Richmond, G. L. Equity for women and underrepresented minorities in STEM: Graduate experiences and career plans in chemistry. Proc. Natl. Acad. Sci. U. S. A. 2021, 118, e2020508118,  DOI: 10.1073/pnas.2020508118
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        Equity for women and underrepresented minorities in STEM: Graduate experiences and career plans in chemistry
        Stockard, Jean; Rohlfing, Celeste M.; Richmond, Geraldine L.
        Proceedings of the National Academy of Sciences of the United States of America (2021), 118 (4), e2020508118CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
        Recent events prompted scientists in the United States and throughout the world to consider how systematic racism affects the scientific enterprise. This paper provides evidence of inequities related to race-ethnicity and gender in graduate school experiences and career plans of PhD students in the top 100 ranked departments in one science, technol., engineering, and math (STEM) discipline, chem. Mixed-model regression analyses were used to examine factors that might moderate these differences. The results show that graduate students who identified as a member of a racial/ethnic group traditionally underrepresented in chem. (underrepresented minorities, URM) were significantly less likely than other students to report that their financial support was sufficient to meet their needs. They were also less likely to report having supportive relationships with peers and postdocs. Women, and esp. URM women, were significantly less likely to report supportive relationships with advisors. Despite their more neg. experiences in graduate school, students who identified as URM expressed greater commitment to finishing their degree and staying in the field. When there was at least one faculty member within their departments who also identified as URM they were also more likely than other students to aspire to a university professorship with an emphasis on research. Men were significantly more likely than women to express strong commitment to finishing the PhD and remaining in chem., but this difference was stronger in top-ranked departments. Men were also more likely than women to aspire to a professorship with an emphasis on research, and this difference remained when individual and departmental-level variables were controlled.
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        Bowman, J. M. Autobiography of Joel M. Bowman. J. Phys. Chem. A 2013, 117, 6907– 6909,  DOI: 10.1021/jp405529p
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        Tucker, S. C. Solvent Density Inhomogeneities in Supercritical Fluids. Chem. Rev. 1999, 99, 391– 418,  DOI: 10.1021/cr9700437
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        Solvent Density Inhomogeneities in Supercritical Fluids
        Tucker, Susan C.
        Chemical Reviews (Washington, D. C.) (1999), 99 (2), 391-418CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
        A review, with ∼184 refs., where fundamentals, evidence of local d. inhomogeneities, and addnl. characteristics of local d. inhomogeneities were discussed.
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        Locker, C. R.; Hernandez, R. Folding behavior of model proteins with weak energetic frustration. J. Chem. Phys. 2004, 120, 11292– 11303,  DOI: 10.1063/1.1751394
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        Folding behavior of model proteins with weak energetic frustration
        Locker, C. Rebecca; Hernandez, Rigoberto
        Journal of Chemical Physics (2004), 120 (23), 11292-11303CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        The native structure of fast-folding proteins, albeit a deep local free-energy min., may involve a relatively small energetic penalty due to nonoptimal, though favorable, contacts between amino acid residues. The weak energetic frustration that such contacts represent varies among different proteins and may account for folding behavior not seen in unfrustrated models. Minimalist model proteins with heterogeneous contacts-as represented by lattice heteropolymers consisting of three types of monomers-also give rise to weak energetic frustration in their corresponding native structures, and the present study of their equil. and nonequil. properties reveals some of the breadth in their behavior. In order to capture this range within a detailed study of only a few proteins, four candidate protein structures (with their cognate sequences) have been selected according to a figure of merit called the winding index-a characteristic of the no. of turns the protein winds about an axis. The temp.-dependent heat capacities reveal a high-temp. collapse transition, and an infrequently obsd. low-temp. rearrangement transition that arises because of the presence of weak energetic frustration. Simulation results motivate the definition of a new measure of folding affinity as a sequence-dependent free energy-a function of both a reduced stability gap and high accessibility to non-native structures-that correlates strongly with folding rates.
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        Leite, V. B. P.; Alonso, L. C. P.; Newton, M.; Wang, J. Single Molecule Electron Transfer Dynamics in Complex Environments. Phys. Rev. Lett. 2005, 95, 118301,  DOI: 10.1103/PhysRevLett.95.118301
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        Single Molecule Electron Transfer Dynamics in Complex Environments
        Leite, Vitor B. P.; Alonso, Luciana C. P.; Newton, Marshall; Wang, Jin
        Physical Review Letters (2005), 95 (11), 118301/1-118301/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
        We propose a new theor. approach to study the kinetics of the electron transfer (ET) under the dynamical influence of the complex environments with the first passage times (FPT) of the reaction events. By measuring the mean and high order moments of FPT and their ratios, the full kinetics of ET, esp. the dynamical transitions across different temp. zones, is revealed. The potential applications of the current results to single mol. electron transfer are discussed.
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        Sension, R.; Tokmakoff, A. Proceedings of “Optical Probes of Dynamics in Complex Environments”; OSTI, 2008; https://www.osti.gov/servlets/purl/1062182, accessed January 15, 2021.
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        Virshup, A. M.; Punwong, C.; Pogorelov, T. V.; Lindquist, B. A.; Ko, C.; Martínez, T. J. Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics. J. Phys. Chem. B 2009, 113, 3280– 3291,  DOI: 10.1021/jp8073464
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        Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics
        Virshup, Aaron M.; Punwong, Chutintorn; Pogorelov, Taras V.; Lindquist, Beth A.; Ko, Chaehyuk; Martinez, Todd J.
        Journal of Physical Chemistry B (2009), 113 (11), 3280-3291CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
        Our picture of reactions on electronically excited states has evolved considerably in recent years, due to advances in our understanding of points of degeneracy between different electronic states, termed "conical intersections" (CIs). CIs serve as funnels for population transfer between different electronic states, and play a central role in ultrafast photochem. Because most practical photochem. occurs in soln. and protein environments, it is important to understand the role complex environments play in directing excited-state dynamics generally, as well as specific environmental effects on CI geometries and energies. In order to model such effects, we employ the full multiple spawning (FMS) method for multistate quantum dynamics, together with hybrid quantum mech./mol. mech. (QM/MM) potential energy surfaces using both semiempirical and ab initio QM methods. In this article, we present an overview of these methods, and a comparison of the excited-state dynamics of several biol. chromophores in solvent and protein environments. Aq. solvation increases the rate of quenching to the ground state for both the photoactive yellow protein (PYP) and green fluorescent protein (GFP) chromophores, apparently by energetic stabilization of their resp. CIs. In contrast, solvation in methanol retards the quenching process of the retinal protonated Schiff base (RPSB), the rhodopsin chromophore. Protein environments serve to direct the excited-state dynamics, leading to higher quantum yields and enhanced reaction selectivity.
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      50. 50
        Hernandez, R.; Popov, A. Molecular dynamics out of equilibrium: Mechanics and measurables. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2014, 4, 541– 561,  DOI: 10.1002/wcms.1190
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        Molecular dynamics out of equilibrium: mechanics and measurables
        Hernandez, Rigoberto; Popov, Alexander V.
        Wiley Interdisciplinary Reviews: Computational Molecular Science (2014), 4 (6), 541-561CODEN: WIRCAH; ISSN:1759-0884. (Wiley-Blackwell)
        Mol. dynamics is fundamentally the integration of the equations of motion over a representation of an at. and mol. system. The most rigorous choice for performing mol. dynamics entails the use of quantum-mech. equations of motion and a representation of the mol. system through all of its electrons and atoms. For most mol. problems involving at least hundreds of atoms, but generally many more, this is simply computationally prohibitive. Thus the art of mol. dynamics lies in choosing the representation and the appropriate equations of motion capable of addressing the requisite measurables. When used adroitly, it can provide both equil. (averaged) and time-dependent properties of a mol. system. Many computational packages now exist that perform mol. dynamics simulations. They generally include force fields to represent the interactions between atoms and mols. (smoothing out electrons through the Born-Oppenheimer approxn.) and integrate the remaining particles classically. Despite these simplifications, all-atom mol. dynamics remains computationally inaccessible if one includes the no. of atoms required to simulate mesoscopic solvents. Here we use anal. models to demonstrate how mol. dynamics can be used to limit the solvent size in systems experiencing either equil. or nonequil. conditions. It is equally important to address the measurables (such as reaction rates) that are to be obtained prior to the generation of the data-intensive trajectories. WIREs Comput Mol Sci 2014, 4:541-561. doi: 10.1002/wcms.1190 For further resources related to this article, please visit the . Conflict of interest: The authors have declared no conflicts of interest for this article.
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        Press release: Nobel Prize in Chemistry 2013. https://www.nobelprize.org/prizes/chemistry/2013/press-release/, accessed January 15, 2021.
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        MacKerell, A. D., Jr. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586– 3616,  DOI: 10.1021/jp973084f
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        All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
        MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.
        Journal of Physical Chemistry B (1998), 102 (18), 3586-3616CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
        New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used exptl. gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the at. charges, were detd. by fitting ab initio interaction energies and geometries of complexes between water and model compds. that represented the backbone and the various side chains. In addn., dipole moments, exptl. heats and free energies of vaporization, solvation and sublimation, mol. vols., and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in a crystal. A detailed anal. of the relationship between the alanine dipeptide potential energy surface and calcd. protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in soln. and in crystals. Extensive comparisons between mol. dynamics simulation and exptl. data for polypeptides and proteins were performed for both structural and dynamic properties. Calcd. data from energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with exptl. crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of mols. of biol. interest.
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        Mackerell, A. D., Jr.; Feig, M.; Brooks, C. L., III Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 2004, 25, 1400– 1415,  DOI: 10.1002/jcc.20065
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        Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
        MacKerell, Alexander D., Jr.; Feig, Michael; Brooks, Charles L., III
        Journal of Computational Chemistry (2004), 25 (11), 1400-1415CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
        Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an at. level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone is crucial to achieve representative conformational distributions in simulation studies. To improve the treatment of the peptide backbone, quantum mech. (QM) and mol. mech. (MM) calcns. were undertaken on the alanine, glycine, and proline dipeptides, and the results from these calcns. were combined with mol. dynamics (MD) simulations of proteins in crystal and aq. environments. QM potential energy maps of the alanine and glycine dipeptides at the LMP2/cc-pVxZ/MP2/6-31G* levels, where x = D, T, and Q, were detd., and are compared to available QM studies on these mols. The LMP2/cc pVQZ//MP2/6-31G* energy surfaces for all three dipeptides were then used to improve the MM treatment of the dipeptides. These improvements included addnl. parameter optimization via Monte Carlo simulated annealing and extension of the potential energy function to contain peptide backbone .vphi., ψ dihedral crossterms or a .vphi., ψ grid-based energy correction term. Simultaneously, MD simulations of up to seven proteins in their cryst. environments were used to validate the force field enhancements. Comparison with QM and crystallog. data showed that an addnl. optimization of the .vphi., ψ dihedral parameters along with the grid-based energy correction were required to yield significant improvements over the CHARMM22 force field. However, systematic deviations in the treatment of .vphi. and ψ in the helical and sheet regions were evident. Accordingly, empirical adjustments were made to the grid-based energy correction for alanine and glycine to account for these systematic differences. These adjustments lead to greater deviations from QM data for the two dipeptides but also yielded improved agreement with exptl. crystallog. data. These improvements enhance the quality of the CHARMM force field in treating proteins. This extension of the potential energy function is anticipated to facilitate improved treatment of biol. macromols. via MM approaches in general.
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      54. 54
        Kalé, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. NAMD2: Greater scalability for parallel molecular dynamics. J. Comput. Phys. 1999, 151, 283– 312,  DOI: 10.1006/jcph.1999.6201
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        54
        NAMD2: Greater Scalability for Parallel Molecular Dynamics
        Kale, Laxmikant; Skeel, Robert; Bhandarkar, Milind; Brunner, Robert; Gursoy, Attila; Krawetz, Neal; Phillips, James; Shinozaki, Aritomo; Varadarajan, Krishnan; Schulten, Klaus
        Journal of Computational Physics (1999), 151 (1), 283-312CODEN: JCTPAH; ISSN:0021-9991. (Academic Press)
        Mol. dynamics programs simulate the behavior of biomol. systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by application-domain programmers. The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decompn. combined with force decompn. to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability. It uses a combination of numerical techniques and algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calcns. NAMD2 uses a portable run-time framework called Converse that also supports interoperability among multiple parallel paradigms. As a result, different components of applications can be written in the most appropriate parallel paradigms. NAMD2 runs on most parallel machines including workstation clusters and has yielded speedups in excess of 180 on 220 processors. This paper also describes the performance obtained on some benchmark applications. (c) 1999 Academic Press.
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      55. 55
        Pearlman, D. A.; Case, D. A.; Caldwell, J.; Ross, W. R.; Cheatham, T. E., III; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comput. Phys. Commun. 1995, 91, 1– 41,  DOI: 10.1016/0010-4655(95)00041-D
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        55
        "AMBER", a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to stimulate the structural and energetic properties of molecules
        Pearlman, David A.; Case, David A.; Caldwell, James W.; Ross, Wilson S.; Cheatham, Thomas E. III; DeBolt, Steve; Ferguson, David; Seibel, George; Kollman, Peter
        Computer Physics Communications (1995), 91 (1-3), 1-42CODEN: CPHCBZ; ISSN:0010-4655. (Elsevier)
        We describe the development, current features, and some directions for future development of the AMBER package of computer programs. This package has evolved from a program that was constructed to do Assisted Model Building and Energy Refinement to a group of programs embodying a no. of the powerful tools of modern computational chem.-mol. dynamics and free energy calcns.
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      56. 56
        Brown, W. M.; Petersen, M. K.; Plimpton, S. J.; Grest, G. S. Liquid crystal nanodroplets in solution. J. Chem. Phys. 2009, 130, 044901,  DOI: 10.1063/1.3058435
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        56
        Liquid crystal nanodroplets in solution
        Brown, W. Michael; Petersen, Matt K.; Plimpton, Steven J.; Grest, Gary S.
        Journal of Chemical Physics (2009), 130 (4), 044901/1-044901/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        The aggregation of liq. crystal nanodroplets from a homogeneous soln. is studied by mol. dynamics simulations. The liq. crystal particles are modeled as elongated ellipsoidal Gay-Berne particles while the solvent is modeled as spherical Lennard-Jones particles. Extending previous studies of , we find that liq. crystal nanodroplets are not stable and that after sufficiently long times the nanodroplets always aggregate into a single large droplet. Results describing the droplet shape and orientation for different temps. and shear rates are presented. The implementation of the Gay-Berne potential for biaxial ellipsoidal particles in a parallel mol. dynamics code is also briefly discussed. (c) 2009 American Institute of Physics.
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      57. 57
        Durrant, J. D.; Kochanek, S. E.; Casalino, L.; Ieong, P. U.; Dommer, A. C.; Amaro, R. E. Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ACS Cent. Sci. 2020, 6, 189– 196,  DOI: 10.1021/acscentsci.9b01071
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        57
        Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism
        Durrant, Jacob D.; Kochanek, Sarah E.; Casalino, Lorenzo; Ieong, Pek U.; Dommer, Abigail C.; Amaro, Rommie E.
        ACS Central Science (2020), 6 (2), 189-196CODEN: ACSCII; ISSN:2374-7951. (American Chemical Society)
        Influenza virus circulates in human, avian, and swine hosts, causing seasonal epidemic and occasional pandemic outbreaks. Influenza neuraminidase, a viral surface glycoprotein, has two sialic acid binding sites. The catalytic (primary) site, which also binds inhibitors such as oseltamivir carboxylate, is responsible for cleaving the sialic acid linkages that bind viral progeny to the host cell. In contrast, the functional annotation of the secondary site remains unclear. Here, we better characterize these two sites through the development of an all-atom, explicitly solvated, exptl. based integrative model of the pandemic influenza A H1N1 2009 viral envelope, contg. ∼160 million atoms and spanning ∼115 nm in diam. Mol. dynamics simulations of this crowded subcellular environment, coupled with Markov state model theory, provide a novel framework for studying realistic mol. systems at the mesoscale and allow us to quantify the kinetics of the 150-loop transition between the open and closed states. An anal. of chloride ion occupancy along the neuraminidase surface implies a potential new role for the neuraminidase secondary site, wherein the terminal sialic acid residues of the linkages may bind before transfer to the primary site where enzymic cleavage occurs. Altogether, our work breaks new ground for mol. simulation in terms of the size, complexity, and methodol. analyses of the simulated components, as well as provides fundamental insights into the understanding of substrate recognition processes for this vital influenza drug target, suggesting a new strategy for the development of anti-influenza therapeutics.
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      58. 58
        Hagy, M. C.; Hernandez, R. Dynamical simulation of dipolar Janus colloids: Dynamical properties. J. Chem. Phys. 2013, 138, 184903,  DOI: 10.1063/1.4803864
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        58
        Dynamical simulation of dipolar Janus colloids: Dynamical properties
        Hagy, Matthew C.; Hernandez, Rigoberto
        Journal of Chemical Physics (2013), 138 (18), 184903/1-184903/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        The dynamical properties of dipolar Janus particles are studied through simulation using our previously-developed detailed pointwise (PW) model and an isotropically coarse-grained (CG) model. The CG model is found to have accelerated dynamics relative to the PW model over a range of conditions for which both models have near identical static equil. properties. Phys., this suggests dipolar Janus particles have slower transport properties (such as diffusion) in comparison to isotropically attractive particles. Time rescaling and damping with Langevin friction are explored to map the dynamics of the CG model to that of the PW model. Both methods map the diffusion const. successfully and improve the velocity autocorrelation function and the mean squared displacement of the CG model. Neither method improves the distribution of reversible bond durations f(tb) obsd. in the CG model, which is found to lack the longer duration reversible bonds obsd. in the PW model. We attribute these differences in f(tb) to changes in the energetics of multiple rearrangement mechanisms. This suggests a need for new methods that map the coarse-grained dynamics of such systems to the true time scale. (c) 2013 American Institute of Physics.
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      59. 59
        Downey-Mavromatis, A.; Widener, A. Chemistry faculty’s diversity has changed little since 2011. Chem. Eng. News 2020, 98, 22– 25,  DOI: 10.1021/cen-09843-feature2
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        Chemistry faculty's diversity has changed little since 2011
        Downey-Mavromatis, Arminda
        Chemical & Engineering News (2020), 98 (43), 22-25CODEN: CENEAR; ISSN:1520-605X. (American Chemical Society)
        For the past decade, C&EN has worked with the Open Chem. Collaborative in Diversity Equity (OXIDE) to publish statistics on gender and racial and ethnic diversity of US chem. faculty. OXIDE collects the data, a task that's not as easy as it might sound, its leaders say. Nevertheless, it's important work, esp. with the increased focus from universities on campus diversity efforts after protests about racism and police brutality against Black people this year. "This is definitely a moment of reflection for our nation-and one cannot effectively reflect without knowing the facts," says Dontarie Stallings, assoc. director of OXIDE and a teaching professor of chem. at the University of California San Diego. The current facts: the racial and ethnic diversity of US chem. faculty has changed little since 2011. OXIDE began documenting diversity among chem. faculty because although some universities survey their faculty and students to understand their diversity and OXIDE hopes data will help departments improve faculty's diversity, inclusion, and equity 10.47287/cen-09843-feature2-meeting-gr1Rigoberto Hernandez (left) and Dontarie Stallings at an American Chem. Society meeting in 2016 (Credit: Courtesy of Rigoberto Hernandez) oxidesurveyRigoberto HernandezDontarie StallingsA photo of Rigoberto Hernandez and Dontarie Stallings.
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      60. 60
        Hernandez, R. The private sector’s role in chemistry’s future. Chem. Eng. News 2015, 93, 33,  DOI: 10.1021/cen-09337-comment
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        There is no corresponding record for this reference.
      61. 61
        Hernandez, R. OneChemistry in the marketplace of ideas. Chem. Eng. News 2017, 95, 41,  DOI: 10.1021/cen-09517-comment
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        There is no corresponding record for this reference.
      62. 62
        Craven, G. T.; Junginger, A.; Hernandez, R. Lagrangian descriptors of driven chemical reaction manifolds. Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2017, 96, 022222,  DOI: 10.1103/PhysRevE.96.022222
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        There is no corresponding record for this reference.
      63. 63
        Schraft, P.; Junginger, A.; Feldmaier, M.; Bardakcioglu, R.; Main, J.; Wunner, G.; Hernandez, R. Neural network approach to time-dependent dividing surfaces in classical reaction dynamics. Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2018, 97, 042309,  DOI: 10.1103/PhysRevE.97.042309
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        There is no corresponding record for this reference.
      64. 64
        Feldmaier, M.; Reiff, J.; Benito, R. M.; Borondo, F.; Main, J.; Hernandez, R. Influence of external driving on decays in the geometry of the LiCN isomerization. J. Chem. Phys. 2020, 153, 084115,  DOI: 10.1063/5.0015509
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        64
        Influence of external driving on decays in the geometry of the LiCN isomerization
        Feldmaier, Matthias; Reiff, Johannes; Benito, Rosa M.; Borondo, Florentino; Main, Joerg; Hernandez, Rigoberto
        Journal of Chemical Physics (2020), 153 (8), 084115CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
        The framework of transition state theory relies on the detn. of a geometric structure identifying reactivity. It replaces the laborious exercise of following many trajectories for a long time to provide chem. reaction rates and pathways. In this paper, recent advances in constructing this geometry even in time-dependent systems are applied to the LiCN .dblharw. LiNC isomerization reaction driven by an external field. We obtain decay rates of the reactant population close to the transition state by exploiting local properties of the dynamics of trajectories in and close to it. We find that the external driving has a large influence on these decay rates when compared to the non-driven isomerization reaction. This, in turn, provides renewed evidence for the possibility of controlling chem. reactions, like this one, through external time-dependent fields. (c) 2020 American Institute of Physics.
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      65. 65
        Bureau, H.; Quirk, S.; Hernandez, R. The relative stability of trpzip1 and its mutants determined by computation and experiment. RSC Adv. 2020, 10, 6520,  DOI: 10.1039/D0RA00920B
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        65
        The relative stability of trpzip1 and its mutants determined by computation and experiment
        Bureau, Hailey R.; Quirk, Stephen; Hernandez, Rigoberto
        RSC Advances (2020), 10 (11), 6520-6535CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
        Six mutants of the tryptophan zipper peptide trpzip1 have been computationally and exptl. characterized. We det. the varying roles in secondary structure stability of specific residues through a mutation assay. Four of the mutations directly effect the Trp-Trp interactions and two of the mutations target the salt bridge between Glu5 and Lys8. CD spectra and thermal unfolding are used to det. the secondary structure and stability of the mutants compared to the wildtype peptide. Adaptive steered mol. dynamics has been used to obtain the energetics of the unfolding pathways of the mutations. The hydrogen bonding patterns and side-chain interactions over the course of unfolding have also been calcd. and compared to wildtype trpzip1. The key finding from this work is the importance of a stabilizing non-native salt bridge pair present in the K8L mutation.
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      66. 66
        Zhuang, Y.; Bureau, H.; Quirk, S.; Hernandez, R. Adaptive Steered Molecular Dynamics of Biomolecules. Mol. Simul. 2021, 47, 408,  DOI: 10.1080/08927022.2020.1807542
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        66
        Adaptive steered molecular dynamics of biomolecules
        Zhuang, Yi; Bureau, Hailey R.; Quirk, Stephen; Hernandez, Rigoberto
        Molecular Simulation (2021), 47 (5), 408-419CODEN: MOSIEA; ISSN:0892-7022. (Taylor & Francis Ltd.)
        Adaptive steered mol. dynamics (ASMD) is a variant of steered mol. dynamics (SMD) in which the driving of the auxiliary - viz steered - particle is performed in stages. In SMD, many nonequil. trajectories are generated allowing for fast sampling of the ensemble space and access to rare events. Equil. observables, such as the potential of mean force along the pathway, result from averaging over these trajectories using Jarzynski's Equality (JE). Unfortunately, in SMD, a large no. of trajectories are needed to cover all possible configurations in order to obtain converged quantities in the exponential av. of the JE, and this is computationally expensive. ASMD reduces the no. of trajectories that must be sampled by discarding those trajectories that have deviated far from the equil. path in stages. At the end of a stage, one chooses - or contracts - one (in naive ASMD) or some (in multi-branched ASMD or MB-ASMD) of the configurations produced from the previous stage to initiate the trajectories in the next stage. Alternatively, in full-relaxation ASMD (FR-ASMD), all generated structures are relaxed under the constraint of a fixed auxiliary particle exerting no net work on the system. We provide a direct comparison of the energetics and other observables obtained from these approaches. We find that FR-ASMD is preferred when the unfolding pathways follow up along a single funnel and the system is sufficiently small that computational resources are not a limiting concern. It gives the highest accuracy in such cases while avoiding the inefficiencies of SMD. However, for complex energy landscapes typical of most multi-domain proteins, MB-ASMD is preferred because it provides a mechanism to sample alternative pathways while suffering only a modest loss in accuracy compared to FR-ASMD.
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      67. 67
        Zhuang, Y.; Bureau, H. R.; Lopez, C.; Bucher, R.; Quirk, S.; Hernandez, R. Energetics and structure of alanine-rich _-helices via Adaptive Steered Molecular Dynamics (ASMD). Biophys. J. 2021, 120, 2009,  DOI: 10.1016/j.bpj.2021.03.017
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        Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics
        Zhuang, Yi; Bureau, Hailey R.; Lopez, Christine; Bucher, Ryan; Quirk, Stephen; Hernandez, Rigoberto
        Biophysical Journal (2021), 120 (10), 2009-2018CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
        The energetics and hydrogen bonding profiles of the helix-to-coil transition were found to be an additive property and to increase linearly with chain length, resp., in alanine-rich α-helical peptides. A model system of polyalanine repeats was used to establish this hypothesis for the energetic trends and hydrogen bonding profiles. Numerical measurements of a synthesized polypeptide Ac-Y(AEAAKA)kF-NH2 and a natural α-helical peptide a2N (1-17) provide evidence of the hypothesis's generality. Adaptive steered mol. dynamics was employed to investigate the mech. unfolding of all of these alanine-rich polypeptides. We found that the helix-to-coil transition is primarily dependent on the breaking of the intramol. backbone hydrogen bonds and independent of specific side-chain interactions and chain length. The mech. unfolding of the α-helical peptides results in a turnover mechanism in which a 310-helical structure forms during the unfolding, remaining at a near const. population and thereby maintaining additivity in the free energy. The intermediate partially unfolded structures exhibited polyproline II helical structure as previously seen by others. In summary, we found that the av. force required to pull alanine-rich α-helical peptides in between the endpoints-namely the native structure and free coil-is nearly independent of the length or the specific primary structure.
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      68. 68
        Mahala, B.; Hernandez, R. Solvent softness effects on unimolecular chemical reaction rate constants. Chem. Phys. Lett. 2020, 744, 137182,  DOI: 10.1016/j.cplett.2020.137182
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        68
        Solvent softness effects on unimolecular chemical reaction rate constants
        Mahala, Benjamin D.; Hernandez, Rigoberto
        Chemical Physics Letters (2020), 744 (), 137182CODEN: CHPLBC; ISSN:0009-2614. (Elsevier B.V.)
        The stochastic hard collision (SHC) model for a coarse-grained solvent has been used to solvate a class of model chem. reactions. Although there is precedent from our prior work that the use of nondeterministic interaction potentials can lead to accurate dynamics at long-enough time scales, this work provides evidence that this model has dynamical consistency specifically in the response to the reactant motion. That is, the agreement between the theor. rate consts. and those obtained from the stochastic simulations provides support for the SHC solvent without sacrificing the correlations in the dynamics of the reacting solutes.
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      69. 69
        Murphy, C. J.; Vartanian, A. M.; Geiger, F. M.; Hamers, R. J.; Pedersen, J.; Cui, Q.; Haynes, C. L.; Carlson, E. E.; Hernandez, R.; Klaper, R. D.; Orr, G.; Rosenzweig, Z. Biological responses to engineered nanomaterials: Needs for the next decade. ACS Cent. Sci. 2015, 1, 117,  DOI: 10.1021/acscentsci.5b00182
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        69
        Biological Responses to Engineered Nanomaterials: Needs for the Next Decade
        Murphy, Catherine J.; Vartanian, Ariane M.; Geiger, Franz M.; Hamers, Robert J.; Pedersen, Joel; Cui, Qiang; Haynes, Christy L.; Carlson, Erin E.; Hernandez, Rigoberto; Klaper, Rebecca D.; Orr, Galya; Rosenzweig, Ze'ev
        ACS Central Science (2015), 1 (3), 117-123CODEN: ACSCII; ISSN:2374-7951. (American Chemical Society)
        A review. The interaction of nanomaterials with biomols., cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biol. and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chem. nature of nanomaterials in dynamic, complex aq. environments; (ii) real-time measurements of nanomaterial-biol. interactions with chem. specificity; (iii) delineation of mol. modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.
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      70. 70
        Wu, M.; Vartanian, A. M.; Chong, G.; Pandiakumar, A. K.; Hamers, R. J.; Hernandez, R.; Murphy, C. J. Solution NMR analysis of ligand environment in quaternary ammonium-terminated self-assembled monolayers on gold nanoparticles: The effect of surface curvature and ligand structure. J. Am. Chem. Soc. 2019, 141, 4316,  DOI: 10.1021/jacs.8b11445
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        Solution NMR Analysis of Ligand Environment in Quaternary Ammonium-Terminated Self-Assembled Monolayers on Gold Nanoparticles: The Effect of Surface Curvature and Ligand Structure
        Wu, Meng; Vartanian, Ariane M.; Chong, Gene; Pandiakumar, Arun Kumar; Hamers, Robert J.; Hernandez, Rigoberto; Murphy, Catherine J.
        Journal of the American Chemical Society (2019), 141 (10), 4316-4327CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
        We report a soln. NMR-based anal. of (16-mercaptohexadecyl)trimethylammonium bromide (MTAB) self-assembled monolayers on colloidal gold nanospheres (AuNSs) with diams. from 1.2 to 25 nm and gold nanorods (AuNRs) with aspect ratios from 1.4 to 3.9. The chem. shift anal. of the proton signals from the solvent-exposed headgroups of bound ligands suggests that the headgroups are satd. on the ligand shell as the sizes of the nanoparticles increase beyond ∼10 nm. Quant. NMR shows that the ligand d. of MTAB-AuNSs is size-dependent. Ligand d. ranges from ∼3 mols. per nm2 for 25 nm particles to up to 5-6 mols. per nm2 in ∼10 nm and smaller particles for in situ measurements of bound ligands; after I2/I- treatment to etch away the gold cores, ligand d. ranges from ∼2 mols. per nm2 for 25 nm particles to up to 4-5 mols. per nm2 in ∼10 nm and smaller particles. T2 relaxation anal. shows greater hydrocarbon chain ordering and less headgroup motion as the diam. of the particles increases from 1.2 nm to ∼13 nm. Mol. dynamics simulations of 4, 6, and 8 nm (11-mercaptoundecyl)trimethylammonium bromide-capped AuNSs confirm greater hydrophobic chain packing order and satn. of charged headgroups within the same spherical ligand shell at larger nanoparticle sizes and higher ligand densities. Combining the NMR studies and MD simulations, we suggest that the headgroup packing limits the ligand d., rather than the sulfur packing on the nanoparticle surface, for ∼10 nm and larger particles. For MTAB-AuNRs, no chem. shift data nor ligand d. data suggest that two populations of ligands that might correspond to side-ligands and end-ligands exist; yet T2 relaxation dynamics data suggest that headgroup mobility depends on aspect ratio and abs. nanoparticle dimensions.
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      71. 71
        Daly, C. A., Jr.; Allen, C. R.; Rozanov, N. D.; Chong, G.; Melby, E. S.; Kuech, T. R.; Lohse, S. E.; Murphy, C. J.; Pedersen, J. A.; Hernandez, R. Surface Coating Structure and Its Interaction with Cytochrome c in EG6-Coated Nanoparticles Varies with Surface Curvature. Langmuir 2020, 36, 5030– 5039,  DOI: 10.1021/acs.langmuir.0c00681
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        Surface Coating Structure and Its Interaction with Cytochrome c in EG6-Coated Nanoparticles Varies with Surface Curvature
        Daly, Clyde A.; Allen, Caley; Rozanov, Nikita; Chong, Gene; Melby, Eric S.; Kuech, Thomas R.; Lohse, Samuel E.; Murphy, Catherine J.; Pedersen, Joel A.; Hernandez, Rigoberto
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        The compn., orientation, and conformation of proteins in biomol. coronas acquired by nanoparticles in biol. media contribute to how they are identified by a cell. While numerous studies have investigated protein compn. in biomol. coronas, relatively little detail is known about how the nanoparticle surface influences the orientation and conformation of the proteins assocd. with them. The authors previously showed that the peripheral membrane protein cytochrome c adopts preferred poses relative to neg. charged 3-mercaptopropionic acid (MPA)-gold nanoparticles (AuNPs). Here, the authors employ mol. dynamics simulations and complementary expts. to establish that cytochrome c also assumes preferred poses upon assocn. with nanoparticles functionalized with an uncharged ligand, specifically ω-(1-mercaptounde-11-cyl)hexa(ethylene glycol) (EG6). The authors find that the display of the EG6 ligands is sensitive to the curvature of the surface-and, consequently, the effective diam. of the nearly spherical nanoparticle core-which in turn affects the preferred poses of cytochrome c.
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