Conversion of ab-initio force fields and structures to molecular mechanics energy functions

The rapid development of computers in recent years has brought increasingly complex compounds into the range of high level ab-initio calculations. Such calculations produce valuable results which in many cases would be difficult or even impossible to obtain, with comparable accuracy, in any other way (Fogarasi & Pulay, Annu. Rev. Phys. Chem. 35, 191, 1984). Thus, it is highly desirable to be able to utilize these results in the construction of potential energy functions used in molecular mechanics (MM), molecular dynamics and Monte-Carlo calculations. For instance, the significance of quadratic cross terms in MM energy functions is still insufficiently explored (Lii & Allinger, J. Am. Chem. Soc. 111, 8566, 1989). In order to make possible the complete utilization of ab-initio results in MM calculations, we have developed a method by which scaled ab-initio (or empirical) force fields and structures can be directly converted to MM potential energy parameters, without sacrificing any of the original accuracy with regard to vibrational frequencies or structure. Here we briefly outline the conversion procedure, a more complete analysis being published separately.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29587/1/0000676.pd

Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be $18.3\pm 3.5$ kcal mol$^{-1}$ for MP2/cc-pVDZ and $19.3\pm 3.6$ for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.Comment: SI not attache

First principles view on chemical compound space: Gaining rigorous atomistic control of molecular properties

A well-defined notion of chemical compound space (CCS) is essential for gaining rigorous control of properties through variation of elemental composition and atomic configurations. Here, we review an atomistic first principles perspective on CCS. First, CCS is discussed in terms of variational nuclear charges in the context of conceptual density functional and molecular grand-canonical ensemble theory. Thereafter, we revisit the notion of compound pairs, related to each other via "alchemical" interpolations involving fractional nuclear chargens in the electronic Hamiltonian. We address Taylor expansions in CCS, property non-linearity, improved predictions using reference compound pairs, and the ounce-of-gold prize challenge to linearize CCS. Finally, we turn to machine learning of analytical structure property relationships in CCS. These relationships correspond to inferred, rather than derived through variational principle, solutions of the electronic Schr\"odinger equation

CARBON-BASED COMPLEX STRUCTURE AND MODEL DEVELOPMENT

Growing concerns about the environment and energy crisis prompt a search for effective carbon-based materials due to their low cost, renewability, sustainability, easy accessibility and excellent properties. We study the model development, structure and properties of graphene oxide, cellulose and their nanocomposites in order to obtain a better fundamental understanding of carbon complex materials and construct a structure-property relationship via reactive molecular dynamics simulations. In chapter 3, the model development of GO is studied. Theoretical GO models developed so far present a good description of its chemical structure. However, when it comes to the structural properties, such as the size and distribution of vacancy defects, the curvature (or roughness), there exist significant gaps between computational models and experimentally synthesized GO materials. We carry out reactive molecular dynamics simulations and use experimental characteristics to fine tune theoretical GO models. Attentions have been paid to the vacancy defects, the distribution and hybridization of carbon atoms, and the overall C/O ratio of GO. The GO models proposed in this work have been significantly improved to represent quantitative structural details of GO materials synthesized via the modified Hummers method. The temperature-programmed protocol and the computational post analyses of Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, vacancy size and curvature distribution, are of general interest to a broad audience working on GO structures from other synthesis methods and other two-dimensional materials and their composites. In Chapter 4, we outline the state-of-the-art understanding of cellulose structures, and discuss in details cellulose interactions, dissolutions and decompositions via computational methods of molecular dynamics (MD) and reactive molecular dynamics (RxMD) simulations. In addition, cellulose characterizations, beneficial to validate and support computational results, are also briefly summarized. Such a state-of-the-art account of atomistic computational studies could inspire interdisciplinary collaborations, optimize process design, promote cellulose-based materials for emerging important applications and shed a light on fundamental understandings of similar systems of biomolecules, polymers and surfactants. In Chapter 5, we investigate the fundamental mechanism of how cellulose structure transforms under pyrolysis conditions and the practical guideline of how cellulose properties are fined tuned accordingly. A series of reactive molecular dynamics calculations has been designed to reveal the structural evolution of crystalline cellulose under pyrolysis treatments. Through the detailed analysis of cellulose configuration change, hydrogen bonding network variation, reaction and redistribution of carbon, oxygen and hydrogen elements, and Young’s modulus, a molecule level insight of crystalline cellulose and its structural evolution under pyrolysis conditions has been constructed via reactive molecular dynamics simulations. We anticipate those theoretical results could effectively promote the design, the manufacture, and the optimization of cellulose based materials for relevant emerging applications. In Chapter 6, we combined the results from previous chapters and explore a new composite material that incorporating amorphous cellulose chains on GO surface, which is barely reported by recent publications. A series of RxMD simulations have been carried out to reveal the mechanical properties of pure GO and cellulose-GO nanocomposites. Two different cellulose-GO composites are constructed, namely, cellulose (monolayer)-GO model and cellulose (multilayer)-GO model. The tensile deformation, Young’s modulus and mechanical strength of GO and cellulose-GO composites have been recorded and calculated under the temperature of 300, 500 800 K, with two strain rates of 10-4/fs and 10-5/fs. We hope the GO model with the simultaneously description to both structural and chemical properties can provide a new fundamental understanding of the mechanical performance of GO and cellulose-GO composites, and could add some advancement to existing knowledge of carbon-based materials

Hydrogen adsorption in metal-organic frameworks: the role of nuclear quantum effects

The role of nuclear quantum effects on the adsorption of molecular hydrogen in metal-organic frameworks (MOFs) has been investigated on grounds of Grand-Canonical Quantized Liquid Density-Functional Theory (GC-QLDFT) calculations. For this purpose, we have carefully validated classical H2 -host interaction potentials that are obtained by fitting Born-Oppenheimer ab initio reference data. The hydrogen adsorption has first been assessed classically using Liquid Density-Functional Theory (LDFT) and the Grand-Canonical Monte Carlo (GCMC) methods. The results have been compared against the semi-classical treatment of quantum effects by applying the Feynman-Hibbs correction to the Born-Oppenheimer-derived potentials, and by explicit treatment within the Grand-Canonical Quantized Liquid Density-Functional Theory (GC-QLDFT). The results are compared with experimental data and indicate pronounced quantum and possibly many-particle effects. After validation calculations have been carried out for IRMOF-1 (MOF-5), GC-QLDFT is applied to study the adsorption of H2 in a series of MOFs, including IRMOF-4, -6, -8, -9, -10, -12, -14, -16, -18 and MOF-177. Finally, we discuss the evolution of the H2 quantum fluid with increasing pressure and lowering temperature

Challenges in simulating light-induced processes in DNA

© 2016 by the authors; licensee MDPI, Basel, Switzerland. In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments