Iyengar, 2 6/8/2006
Srinivasan S. Iyengar
Molecular structure and motion determines properties including spectroscopy and reactivity. We study properties of fundamental chemical systems[1],[2],[3],[4] of interest in atmospheric4 and biological[5],[6] chemistry, and nano-technology using theoretical and computational chemistry. We also specialize in the development of new computational methods[7],[8],[9],[10],[11] and tools to facilitate efficient and accurate study of chemical dynamics in such large systems. This puts our research efforts on the interface of chemistry, computational physics and applied mathematics.
Simulating the dynamics of large biological and chemical systems using computational chemistry has a long history. It is worthwhile to briefly overview this area here, before we embark into a detailed exposition of our specific research interests. We start with describing a computational tool known as molecular dynamics. Here, the molecular geometry (or conformation) is allowed to naturally evolve in time using the inter-atomic forces between the various constituents of the system. The physical law that governs such a dynamics is given by the Schrödinger equation. However, this equation is very difficult to solve even on today’s ultra-fast computers. This has lead researchers in the past to develop models to describe the inter-atomic potential energy for large systems, and these models, being easier to compute as compared to the Schrödinger equation, have been used to study the structure and dynamics of molecules and determine their properties. However, these models have a number of limitations that severely restrict their applicability to systems where chemical reactions do not occur. Since studying chemical reactions and their feasibility is an important part of understanding chemistry, the applicability of such methods is rather limited.
We specialize in using the Schrödinger equation, and more specifically the concepts of quantum mechanics, to computationally perform molecular dynamics. Such approaches that use the Schrödinger equation in their development are called ab initio molecular dynamics (AIMD) approaches. (The words ab initio are derived from Latin: ab stands for ‘from’ and initio means ‘first-principles’; thus the term ab initio is used to characterize computational methods that are derived from first-principles.) And due to the rather intricate and computationally expensive methodology involved in solving the Schrödinger equation, we develop approximations and alternate approaches to facilitate the study of large systems. Specifically, our group has recently developed a new approach to ab initio molecular dynamics.7-9
Our computational methodology7-11 provides a computationally efficient framework to accurately model chemical reaction dynamics in large systems. In quantum mechanics, the wavefunction describing the electrons and the state of the nuclear degrees of freedom, which could be described using the Cartesian coordinates of the nuclei or quantum description of the same, together represent the structure of the molecular system. Our approach helps propagate in time the complete state of a molecular system, in a computationally efficient fashion and hence makes the treatment of large,5,6,9,10,[12] have been successfully treated using this approach. This approach is called Quantum Wavepacket Ab Initio Molecular Dynamics (QWAIMD). The approach allows a massively parallel-computational implementation; computational treatment of simultaneous dynamics of electrons and nuclei in medium sized chemical systems can now be treated over 100s of computer processors leading to an efficient computational methodology. Furthermore, our approach allows the flexibility to treat a subset of the nuclei in a quantum mechanical fashion while simultaneously studying the dynamical evolution of the electrons with the majority of nuclei treated in a classical fashion. (See Refs. 1-3 for details on the theoretical aspects.)
Why would one want to treat "some nuclei using quantum mechanics"? It turns out that this problem is of relevance in many biological enzyme problems and also in atmospheric chemical problems, the study of which we are now actively pursuing. As an example, of our current study, Figure 1 the represents the active site of the enzyme "lipoxygenase" where the quantum mechanical nature of a transferring hydrogen atom dictates the kinetics. Such interesting chemistry is also found in many atmospheric chemical problems as a result we are currently applying this methodology to problems in biological chemistry and atmospheric chemistry. In addition, for problems where a quantum mechanical treatment of nuclei is not necessary, as part of a collaborative effort we have invented another powerful new ab initio molecular dynamics approach that enables the study of chemical dynamics in medium-to-large size systems. Systems with more than 100 atoms can be routinely handled within this scheme at an accurate level of theory. The approach is based on the simultaneous dynamics of the electronic degrees of freedom along with the nuclear degrees of freedom (treated classically). The method is called Atom-centered Density Matrix Propagation (ADMP). (See for example Refs. 10-13 for details on the theoretical aspects.) The atom-centered density matrix propagation (ADMP) approach[13],10 is a new (and already established) approach to ab initio molecular dynamics that was pioneered by us and is being used by a number of groups around the world. In our group, we work on further development of such approaches to facilitate the study of cutting-edge chemical problems as described in the following sections.
We are also currently modifying and generalizing the Quantum Wavepacket Ab Initio Molecular Dynamics (QWAIMD) approach described above to treat the transport of excess electrons and flux of electron densities through molecular wires and other nano-scale devices. Key theoretical challenges remain here which we are currently in the process of surmounting. Some of the important issues that we are currently focusing our attention on here, include the accurate description of an electronic flux through a molecular wire subjected to open system boundary conditions.
The QWAIMD also presents many interesting problems from a scientific computing point of view which allows graduate students and post-doc in our group to become familiar with state of the art ideas in numerical analysis.We develop our own numerical methodologies and associated computational models.
Another active area of research in our group involves the use of ab initio molecular dynamics (with and without nuclear quantum effects) to study the spectroscopic properties of small molecular clusters. As part of a team of collaborators we have recently noted that the hydrated proton in a water cluster has an amphiphillic (hydrophobic+hydrophillic) character. These results were obtained originally from ab initio and empirical molecular dynamics and later confirmed by experiment. These will lead to profound implications in biological and atmospheric problems where proton transfer plays a critical role. We have also shown that dynamics can play a critical role in determining the vibrational spectra of such small "in-flux" clusters.
Thus, in our group, a graduate student will have the opportunity to learn and understand many different aspects of theoretical chemistry, including quantum mechanics, classical mechanics, molecular dynamics, applied mathematics and computational algorithm development. Many of the projects that are described below surmount traditional boundaries of chemistry and physics, and will expose the student to important concepts in theoretical/computational physics and applied mathematics. You will also learn to apply these important concepts to develop new computational and theoretical methods resulting in state-of-the-art computational tools. Below a mixed set of fundamental and applied projects are provided.
1. Quantum Dynamical Effects in Biological Enzyme kinetics: The complete and accurate study of enzyme reactions is an important problem in biological sciences. As noted in the introductory section above, the quantum mechanical nature of nuclei can contribute significantly to the kinetics. Experimentally, this is seen through an unexpectedly large primary and secondary kinetic isotope effect[14],[15],[16] and these have been thought to be due to nuclear quantum effects, such as hydrogen tunneling.14 What does all this mean? General chemistry tells us that there exists an exponential relation between temperature and the reaction rate constant. The so-called Arrhenius rate expression. In some enzymes, such as the one in Figure 1 above, what is experimentally found is that the rate constant does not depend on temperature at all. The hydrogen atom is an extremely light atom and shows the propensity to display quantum behavior, more so than any other atom, and it is believed that this might be the reason for this experimental result. However, the sheer size of enzyme systems makes time-dependent quantum dynamical studies impossible. Hence, approximate methods to examine such critical problems are essential. Our preliminary results indicate that indeed quantum mechanical nature of the hydrogen atom can contribute to this result and we find that “proton orbitals” such as the one in Figure 3 do exists. These orbitals facilitate “hydrogen tunneling” thus leading to unexpected experimental results. The student will have the opportunity to study this problem using our newly developed QWAIMD approach and its variations. The computational method is based on a partitioning scheme and will involve QM/MM (quantum mechanics/molecular mechanics) generalization of our procedure. This involves the seamless extension of our current formalism into the QM/MM scheme and will involve understanding the current formalism followed by appropriate generalization to treat large systems.
2. Molecular electronics through quantum dynamics: The possibility of silicon based electronic chip technology coming close to its inherent physical limitations has given rise to the new area of molecular electronics. Here single molecules are connected across electrodes and treated as potential transistors, capacitors and molecular switches, that is potential components of a novel, futuristic quantum computer. As part of a C500 project the student will have the opportunity to make important contributions and participate in critical steps required to calculate the conductivity of electrons across molecular wires, connected across electrodes using generalizations of our QWAIMD approach.
3. Quantum dynamical and ab initio dynamical effects in critical atmospheric chemical problems: Topics on ozone control: The projects discussed below are fundamental in atmospheric chemistry and are related to ozone production. These projects are in collaboration with the Philip Stevens Group and the Caroline Jarrold Group. As part of the C500 project, the students will have the opportunity to study fundamental atmospheric chemistry problems using state of the art theory.7,8,10,11
The problem of photochemical air pollution remains a serious threat to human health and welfare. Ozone, the primary component of photochemical smog, forms from chemical reactions involving nitrogen oxides (NOx) and volatile organic compounds (VOCs) emitted from transportation, energy production, and industrial activities. Despite years of control legislation, many areas in the United States have consistently exceeded the National Ambient Air Quality Standard for ozone. Hence, recent strategies on ozone control are focusing on regional ozone production. The dominant natural emission of isoprene from trees can contribute significantly to the production of ozone through its high reactivity with the hydroxyl radical (OH), the main oxidant in the atmosphere. Ozone reduction strategies depend on an accurate understanding of isoprene chemistry under a variety of conditions. As part of this C500 project the reactivity and spectroscopy of OH radical with isoprene in the presence of water will be studied in detail using QWAIMD. A side-project that automatically arises here is as follows:
a) Treatment of hydroxide water clusters: This project deals with the structure, stability energetics and spectroscopic properties of hydroxide water clusters. We have recently found that the hydroxide ion can display non-standard bond arrangements when surrounded by water molecules. The central oxygen atom displays an anamolous propensity to be pentavalent. However, we also find that properties such as the vibrational frequencies which can be determined experimentally, are susceptible to the fact that there exists many other geometries (with similar energetics) that support a central tetrahedral oxygen; hence the measurable spectrum is an average of all these “similar” geometries. Dynamics plays an important role in this spectral averaging process. We are in the midst of predicting the spectroscopic properties of such clusters and make important connections to experiment. The student will have an opportunity to investigate this further using ab initio dynamics.
4. Quantum dynamical effects on spectroscopy: NMR and IR spectroscopy: As noted in the introductory section, we have recently discovered1-3 that the protonated species in water (that is, the hydronium ion) has “hydrophobic” and “hydrophilic” sites. The hydrophobic end of the hydronium is close to its lone pairs. Due to this reason, we have found that a hydroniuim ion tends to reside on the surface of a cluster of water molecules and the surface of a water/vacuum interface. This is in contrast to conventional chemical wisdom where the protonated species is expected to be solvated at the center of a cluster of water molecules. Figure 2 shows a 21-water protonated cluster that is found in upper stratosphere. The protonated species here is an H2O-H3O+ that is a solvated hydronium and is called a Zundel ion. Note that this protonated species is on the surface of the cluster. As one can imagine this is an extremely fundamental observation and has important implications which has lead to many experiments (by other groups) designed to test this phenomenon.
In addition, we are one of the first groups to point out that this system has unique spectroscopic properties1 which are essentially dictated by the dynamics of the water molecules. As part of the C500 project, the student will have the opportunity to conduct similar studies on NMR coupling constants. NMR is an extremely fundamental tool in chemistry and in biochemistry. Do quantum nuclear effects and dynamical effects play a critical role in NMR coupling constants? Specific systems that will be considered are DNA base pairs and protein anti-parallel beta sheets.
5. Non-adiabatic Reaction Dynamics of Complex Systems. In many biological and chemical systems, reactions can involve multiple electronic states. This is particularly the case for photochemical reaction. For example, in rhodopsin (Figure 5), which is found in the mammalian eye, the cis-trans isomerization of a protonated Schiff base called retinal causes a conformational change leading to vision. This is among the fastest known chemical reactions. Detailed quantum mechanical study of such processes constitutes an unsolved problem in computational biophysical chemistry. The incoming graduate student will have the opportunity here to first fully understand the concepts behind our quantum ab initio dynamics formalism. This project is a development project and will involve training in computation, mathematics and chemical-physics.