Quantum Mechanical Electronic Structure Calculations Research Articles

MolTwister – a molecular systems construction, manipulation and statistical mechanical calculation tool

To perform molecular dynamics (MD) simulations, Monte Carlo (MC) simulations, quantum mechanical (QM) electronic structure calculations, or similar atomistic calculations, it is necessary to first construct and define the molecular system of interest. This involves creating an initial configuration of atoms, where MD and MC simulations require forcefield assignments, for example in the form of non-bonded, bonded, angular and dihedral potentials. Once simulations or calculations have been performed, large sets of data are available (often several gigabytes). These contain atomic trajectories and other relevant static or dynamic information, from which static and dynamic properties (such as density profiles, vibrational density of states and velocity autocorrelation functions) can be obtained through statistical mechanical calculations. MolTwister is an open source software platform that addresses the construction of molecular systems, basic 3D visualization of these, the generation of input files for selected MD packages, as well as calculation of properties from atomistic simulation data. It also contains a GPU accelerated MD simulator suited for smaller tasks such as molecular thermalization. The software package is written in C++14 and can be used as a basis for further development, where efforts have been made to make access to underlying functionality easy. Moreover, it supports Python, where scripts have access to the majority of program functionality. Program summaryProgram Title: MolTwisterCPC Library link to program files:https://doi.org/10.17632/ph6pwst9mn.1Developer's repository link:http://moltwister.comLicensing provisions: GPLv3 or laterProgramming language: C++14Nature of problem: Lack of SW tools for easy construction of complex molecular systems, as well as tools enabling analysis of long molecular trajectories.Solution method: Developed command line tool with associated 3D view, where molecular construction commands can be executed in complex manners through a Python interface. The program also has commands for analysis of molecular data that process one molecular time-frame at a time, thus enabling analysis of long molecular trajectories. Moreover, the program structure is designed for easy implementation of new commands by other researchers.Additional comments including restrictions and unusual features: Supported file formats: xyz, pdb, mtt (MolTwister trajectory), dcd, xtc, qepos, python, script (MolTwister scripts)Supported MD engines: HOOMD-blue, LAMMPS, MolTwister internal (moldyn)

Correcting Rate Constants from Anharmonic Molecular Dynamics for Quantum Effects.

Anharmonicity can greatly affect rate constants. One or even several orders of magnitude of deviation are found for obtaining rate constants using the standard rigid-rotor harmonic-oscillator model. In turn, reactive molecular dynamics (MD) simulations are a powerful way to explore chemical reaction networks and calculate rate constants from the fully anharmonic potential energy surface. However, the classical nature of the dynamics and the required numerical efficiency of the force field limit the accuracy of the resulting kinetics. We combine the best of both worlds by presenting an approximation that pairs anharmonic information intrinsic to classical MD with high-accuracy energies and frequencies from quantum-mechanical electronic structure calculations. The proposed scheme is applied to hydrogen abstractions in the methane system, which allows for the benchmarking of rate constants corrected by our approach against experimental rate constants. This comparison reveals a standard deviation of factor 2.6. Two archetypes of possible failure are identified in the course of a detailed investigation of the CH3• + H• → CH22• + H2 reaction. From this follows the application range of the method, within which the method shows a standard deviation of factor 2.1. The computational efficiency and beneficial scaling of the method allow for application to larger systems, as shown for hydrogen abstraction from 2-butanone by HO2•.

Proton-transfer in 1,1,3,3 tetramethyl guanidine by means of ultrasonic relaxation and Raman spectroscopies and molecular orbital calculations.

In this work, we report on the structure and dynamics of the 1,1,3,3 tetramethyl guanidine (TMG) aqueous solutions in a wide concentration and temperature range by combining vibrational and ultrasonic spectroscopies. The experimental Raman spectra have been compared with the corresponding spectra obtained by ab initio quantum mechanical and density functional theory electronic structure calculations. This comparison indicated that only a single mechanism occurs when dissolving TMG in water and this is the proton transfer reaction, while the formation of byproducts during hydrolysis of TMG is dubious. This observation is further supported by the concentration dependence of the Raman spectra. The analysis of the ultrasonic relaxation data also revealed that the system exhibits a single relaxation process associated with this proton transfer reaction. It has been also observed that both relaxation amplitude and frequency exhibit a clear monotonous increase with increasing amine concentration in the solutions supporting the concept of the proton transfer reaction. The corresponding activation enthalpy was estimated directly from the temperature dependence of the acoustic data and found equal to ΔH*=5.56±0.34kcal/mol, which seems to be reasonable for hydrogen-bond formation. Furthermore, the concentration dependence of the acoustic parameters and kinematic viscosity data has been used as a probe for the molecular association in these solutions. The results have been discussed in relation to the ability or inability of water molecules to form stable clathrates after the addition of amine molecules in the solutions.

Linear programming applied to polarized Raman spectroscopy for elucidating molecular structure at surfaces

We present a framework for using linear programming to solve a challenging problem in surface science, the elucidation of the structure and composition of adsorbed molecules from a mixture, using simulated data from polarized Raman experiments. In the past, methods applied in order to interpret such spectroscopic information were combinatorial approaches that are limited in scalability or accuracy. Quantum mechanical electronic structure calculations yield the optical response of a single molecule, from which spectra of a mixture can be determined by appropriate weighting. Furthermore, spectral obtained in different beam polarizations provide projections of the signal in the laboratory frame. We demonstrate that linear programming is an ideal tool for utilizing all of this information in order to provide the sought structural picture.

Revealing the Sequence-Structure-Electronic Property Relation of Self-Assembling π-Conjugated Oligopeptides by Molecular and Quantum Mechanical Modeling.

Self-assembled nanoaggregates of π-conjugated synthetic peptides present a biocompatible and highly tunable alternative to silicon-based optical and electronic materials. Understanding the relationship between structural morphology and electronic properties of these assemblies is critical for understanding and controlling their mechanical, optical, and electronic responses. In this work, we combine all-atom classical molecular simulations with quantum mechanical electronic structure calculations to ascertain the sequence-structure-electronic property relationship within a family of Asp-X-X-quaterthiophene-X-X-Asp (DXX-OT4-XXD) oligopeptides in which X is one of the five amino acids {Ala, Phe, Gly, Ile, Val} ({A, F, G, I, V}). Molecular dynamics simulations reveal that smaller amino acid substituents (A, G) favor linear stacking within a peptide dimer, whereas larger groups (F, I, V) induce larger twist angles between the peptides. Density functional theory calculations on the dimer show the absorption spectrum to be dominated by transitions between carbon and sulfur p orbitals. Although the absorption spectrum is largely insensitive to the relative twist angle, the highest occupied molecular orbital strongly localizes onto one molecule within the dimer at large twist angles, impeding the efficiency of transport between molecules. Our results provide a fundamental understanding of the relation between peptide orientation and electronic structure and offer design precepts for rational engineering of these systems.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc.

Adsorbate-Induced Changes in Magnetic Interactions in Fe2(dobdc) with Adsorbed Hydrocarbon Molecules

Metal–organic frameworks, which are a special case of coordination polymers, form a class of materials with numerous applications due to their high porosities and large internal surface areas and in some cases also due to paramagnetic metal ions. A family of such materials of general formula M2(dobdc) (where M is a divalent metal ion, and dobdc4– is 2,5-dioxido-1,4-benzenedicarboxylate) has attracted considerable attention for gas separation, catalysis, and magnetism. In this work, we explore the magnetic properties of a member of this family, Fe2(dobdc), both in the activated form (bare MOF after solvent removal) and when hydrocarbons are bound to the open coordination sites of the metal. We report quantum mechanical electronic structure calculations using both cluster models and periodic models, and we compare our results to previously reported theoretical studies. We find that hydrocarbon adsorption only mildly affects the isotropic couplings but that the isotropic magnetic couplings obtained with hybrid exchange–correlation functionals for the cluster models were found to be in good agreement with the experimental values, and the ones obtained using local exchange–correlation functionals with empirical Coulomb and exchange integrals for the periodic models were also found to agree well with experiments. Furthermore, local density functionals with empirical Coulomb and exchange integrals for periodic models are found to give good agreement with the experimental result that the adsorption of ethylene changes the magnetic ordering. We also used second-order n-electron valence state perturbation theory and contracted spin–orbit configuration interaction to study the role of adsorption on the crystal-field splitting of the quintet manifold and on the single-ion anisotropy of the iron center.

Atomic Oxygen Recombination at Surface Defects on Reconstructed (0001) α-Quartz Exposed to Atomic and Molecular Oxygen

The surface chemistry of silica is strongly affected by the nature of chemically active sites (or defects) occurring on the surface. Here, we employ quantum mechanical electronic structure calculations to study an uncoordinated silicon defect, a non-bridging oxygen defect, and a peroxyl defect on the reconstructed (0001) surface of α-quartz. We characterized the spin states and energies of the defects, and calculated the reaction profiles for atomic oxygen recombination at the defects. We elucidated the diradical character by analyzing the low-lying excited states using multireference wave function methods. We show that the diradical defects consist of weakly coupled doublet radicals, and the atomic oxygen recombination can take place through a barrierless process at defects. We have delineated the recombination mechanism and computed the formation energy of the peroxyl and non-bridging oxygen defects. We found that key recombination reaction paths are barrierless. In addition, we characterize the electro...

Dynamical, spectroscopic and computational imaging of bond breaking in photodissociation: roaming and role of conical intersections.

Recent experimental and theoretical advances in the study of the dissociation of excited molecules are revealing unexpected mechanisms, when their outcomes are tackled by combining (i) space-time ion imaging of translational features, with (ii) spectroscopic probing of rotational and vibrational distributions; crucial is the assistance of (iii) the quantum chemistry of structural investigations of rearrangements of chemical bonds, and of (iv) the simulations of molecular dynamics to follow the evolution of selective bond stretching and breaking. Here we present results of such an integrated approach to methyl formate, HCOOCH3, the simplest of esters; the main focus is on the rotovibrationally excited CO (v=1) product and in general on the energy distribution in the fragments. Previous laser studies of dissociation into CO and CH3OH at a sequence of various wavelengths discovered signatures of a roaming mechanism by the late arrival of CO (v=0) products in time-of-flight ion imaging. Subsequent detailed investigations as a function of excitation energy provided the assessment of the threshold, which opens for triple breakdown into CO and further fragments H and CH3O, as spectroscopically characterized by ion imaging and FTIR respectively. Accompanying quantum mechanical electronic structure calculations and classical molecular dynamics simulations clarify the origin of these fragments through "roaming" pathways involving incipient radical intermediates at energies below the triple fragmentation threshold: a specific role is played by nonadiabatic transitions at a conical intersection between ground and excited states; alternative pathways focalize our attention to regions of the potential energy surfaces other than those in the neighbourhoods of saddle points along minimum energy paths: eventually this leads us to look for avenues in reaction kinetics beyond those of venerable transition state theories.

On the quantum theory of molecules

Transition state theory was introduced in 1930s to account for chemical reactions. Central to this theory is the idea of a potential energy surface (PES). It was assumed that such a surface could be constructed using eigensolutions of the Schrödinger equation for the molecular (Coulomb) Hamiltonian but at that time such calculations were not possible. Nowadays quantum mechanical ab initio electronic structure calculations are routine and from their results PESs can be constructed which are believed to approximate those assumed derivable from the eigensolutions. It is argued here that this belief is unfounded. It is suggested that the potential energy surface construction is more appropriately regarded as a legitimate and effective modification of quantum mechanics for chemical purposes.

Is there an exact potential energy surface?

Transition state theory was introduced in the 1930s to account for chemical reactions. Central to this theory is the idea of a potential energy surface (PES). It was assumed that quantum mechanical computation, when it became possible, would yield such surfaces, but for the time being they would have to be constructed empirically. The approach was very successful. Nowadays, quantum mechanical ab initio electronic structure calculations are possible and from their results PESs can be constructed. Such surfaces are now widely used in the explanation of chemical reactions in place of the traditional empirical ones. It is argued here that theoretical basis of such PESs is not quite as clear as is usually assumed and that, from a quantum mechanical perspective, certain puzzles remain.

Polarity-Sensitive Fluorescent Probes in Lipid Bilayers: Bridging Spectroscopic Behavior and Microenvironment Properties

We have studied the emission features of the fluorescent polarity-sensitive probes known as Prodan and Laurdan in a liquid-crystalline DPPC bilayer. To this purpose, we have combined high-level quantum mechanical electronic structure calculations with a molecular field theory for the positional-orientational-conformational distribution of the probes, in their ground and excited states, inside of the lipid bilayer, taking into account at both levels the nonuniformity and anisotropy of the environment. Thus, we can interpret the features of the fluorescence spectra of Prodan and Laurdan in relation to the position and orientation of their chromophore in the bilayer. We have found that the environment polarity is not sufficient to explain the large red shifts experimentally observed and that specific effects due to hydrogen bonding must be considered. We show that the orientation of the probe is important in determining the accessibility to water of the H-bond-acceptor group; in the case of Laurdan interesting conformational effects are highlighted.

Simulation of Nanostructured Materials for Solar Energy Conversion

In the last half of the 20th century, computation has become an indispensible tool in science. Enormous progress in high-performance computational capabilities allow us to solve highly complex mathematical equations with ever-increasing accuracy, providing detailed scientific understanding. The role of quantum-mechanical electronic structure calculations in advancing nano-technology is greatly expanding in recent years, and such computational research has started to play an important role not only in understanding but also for designing new functional materials. In this article, we highlight how such computational methods are being employed for improving upon existing and predicting novel nano-materials for photovoltaic applications.

Conformational Dependence of Electronic Coupling Across Peptide Bonds: A Ramachandran Map

Electronic coupling across peptide bonds has been determined throughout the peptide bond conformational space. Using the side chains of tyrosine (Tyr) and tryptophan (Trp) as donors (D) and acceptors (A), respectively, a plot of the electronic coupling matrix element HDA versus (ϕ,ψ) torsional angles has been constructed for Trp-peptide-Tyr molecules. The HDA values were obtained using the generalized Mulliken−Hush approach with electronic transition energies, permanent and transition dipole parameters derived from semiempirical quantum mechanical electronic structure calculations (INDO/S). The computed HDA values and the corresponding electron transfer (ET) rates show that specific helical peptide conformations situated in a narrow ϕ region of the full HDA-(ϕ,ψ) map play a significant role in developing strong electronic coupling for promoting ET. The HDA-(ϕ,ψ) map clearly defines the angular regions in space, where strong Trp-peptide-Tyr coupling occurs and peptide-mediated ET results, as well as regions of weak peptide coupling where the presence of the peptide has only marginal effects on electronic coupling.

Electronic and molecular structure of M-DNA fragments

To study M-DNA molecular structure (such DNA with transition metal ions placed between the nucleic bases is able to conduct the electric current) and its conductivity mechanisms, we carried out ab initio quantum-mechanical calculations of electronic and spatial structures, thermodynamic characteristics of adenine-thymine (АТ) and guanine-cytosine (GC) base pair complexes with Zn(2+) and Ni(2+). To take into account the influence of the alkaline environment, calculations for these complexes were also carried out with hydroxyl and two water molecules. Computations were performed at MP2 level of theory using 6-31+G* basis set. Analogous calculations were carried out for (AC)(TG) stacking dimer of nucleic acid base pairs with two Zn(2+). The calculation of the interaction energy in complexes has shown the preference of locating the metal ion (instead of the imino proton) between bases in M-DNA. The electronic transition energy calculation has revealed the reduction of the first singlet transition energy in АТ and GC complexes with Ni(2+) from 4.5eV to 0.4 - 0.6eV. Ni(2+) orbitals take part in the formation of HOMO and LUMO on the complexes investigated. It was shown that charges of metal ions incorporated into complexes with nucleic bases and in dimer decrease significantly.

Theory and Simulation of Nanostructured Materials for Photovoltaic Applications

Quantum mechanical electronic structure calculations are playing an ever-expanding role in advancing nanotechnology as well as in advancing our understanding and design of new functional materials. Recent research utilizing quantum mechanical electronic structure calculations is helping to improve upon our understanding of existing nanomaterials-and predict new nanomaterials-for photovoltaic applications.

Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach

Charge transport through a short DNA oligomer (Dickerson dodecamer (DD)) in the presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics (MD) simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations, arising either from the solvent fluctuations or from base-pair vibrational modes, can be taken into account in a straightforward way through the time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the on-site energies along the DNA wire.

The Minnesota Density Functionals and their Applications to Problems in Mineralogy and Geochemistry

Quantum mechanical electronic structure calculations are playing an increasingly useful role in many areas of mineralogy and geochemistry. This review introduces the density functional method for such calculations, gives an overview of the density functionals developed at the University of Minnesota, and summarizes selected applications using these density functionals that are relevant to mineralogy and geochemistry. A key reason for the importance of computational methods in mineralogy is the ability to explore problems that cannot easily be studied in the laboratory. For example, it is very difficult to carry out laboratory studies under the real conditions of the Earth’s mantle and core because the temperature of the Earth’s core ranges up to 6000 K, and the pressure ranges up to 360 GPa. In the past decade, applications of quantum mechanical methods to understanding the properties of minerals and melts in the Earth’s interior have become increasingly important (Warren and Ackland 1996; Oganov and Brodholt 2000; Stixrude and Peacor 2002; Brodholt and Vocadlo 2006; Gillan et al. 2006; Tsuchiya et al. 2006). Some specific examples of problems in solid-state geochemistry where electronic structure calculations can be particularly useful are phase equilibria (Tsuchiya et al. 2004; Lay et al. 2005; Schwegler et al. 2008), equations of state, elastic constants, bulk and shear moduli (Li et al. 2006), hydrogen, proton, and water diffusion in minerals (Sakamura et al. 2003; Belonoshko et al. 2004; Pohlmann et al. 2004), the character and structural properties of hydroxyl groups in minerals and structures of hydrous minerals (Winkler et al. 1994, 1995; Nobes et al. 2000; Brodholt and Refson 2000; Churakov et al. 2003; Walker et al. 2006; Ockwig et al. 2009), hydrolysis and dissolution mechanisms (Strandh et al. 1997, Criscenti et …

The role of transiton-state bond-order on structure-reactivity relationships: the case of pericyclic and pseudo-pericyclic reactions

The importance of the transition-state bond-order (n) in the interpretation of chemical reactivity, in complement to the effect of reaction energy, for decarbonylation pericyclic and pseudopericyclic reactions of 3-cyclopentenone and related molecules is demonstrated through the intersecting-state model and quantum-mechanical electronic structure calculations. Both types of methodology reveal that n is strongly related to transition state geometry.

Decomposition of the Factors That Govern Binding Site Preference in a Multiple Rotaxane

A particularly interesting class of multiple rotaxanes consists of complexes where one long shaft threads two rings. If the shaft contains three or more potential binding sites for the rings, multiple co-conformations are possible. Such a complex is a molecular topological analogue to an abacus. Here we address the question, how does strength of ring binding to the shaft vary with respect to position on the shaft? Previous studies have found that a shaft with three binding sites exhibits strongest ring binding at the center site. Here a five-binding-site shaft is studied. We employ a novel method to partition the total energy of the system into contributions from intercomponent binding and intracomponent distortion. The method uses the output of quantum mechanical electronic structure calculations to determine fitting parameters in a set of coupled equations. The solution of the equations yields the energy partitioning and reveals the influence of long-range intercomponent interactions.