Combined Quantum Mechanics Research Articles

A QM/MM study of the catalytic mechanism of succinic semialdehyde dehydrogenase from Synechococcus sp. PCC 7002 and Salmonella typhimurium

The catalytic mechanism of succinic semialdehyde dehydrogenase (SSADH) has been studied using a combined quantum mechanics and molecular mechanics (QM/MM) approach.

QM/MM investigation of the concentration effects on the second-order nonlinear optical responses of solutions.

A multiscale approach combining quantum mechanics (QM) and molecular mechanics methods has been employed to investigate the effects of solute-solute interactions and therefore of concentration on the first hyperpolarizability of solutions of nitrobenzene in benzene. First, spatial distributions of solute and solvent molecules are generated using Monte Carlo simulations where the intermolecular interactions are described using the Lennard-Jones potentials and Coulomb terms. Then, a reduced number of statistically-uncorrelated configurations are sampled and submitted to time-dependent Hartree-Fock calculations of the first hyperpolarizability. When only one molecule is described quantum-mechanically and is embedded in the electrostatic polarization field of the solution described by point charges, βHRS and β// as well as the depolarization ratio increase in parallel with the concentration in nitrobenzene. This effect is attributed to the increase of the polarization field associated with the presence of polar nitrobenzene molecules in the surrounding. Then, the first solvation shell is considered explicitly in the QM calculation to address solute-solute interactions effects. When the number of nitrobenzenes in the first solvation shell increases, βHRS and β// normalized to the number of nitrobenzene molecules decrease and this decrease attains roughly 50% when there are 3 nitrobenzene molecules in the first solvation shell. These drastic reductions of the first hyperpolarizability result from (partial) centro-symmetric arrangements between the nitrobenzene molecules, as supported by the relationship between β and the angle between the nitrobenzene charge transfer axes. Moreover, these β decreases originate mostly from the reduction of the dipolar β component, whereas the octupolar one is rather constant as a function of the nitrobenzene concentration.

Effects of carbon chain on hole-transport properties in naphtho[2,1-b:6,5-b′]difuran derivatives: Remarkable anisotropic mobilities

Theoretical investigations of hole-transport properties in two naphtho[2,1-b:6,5-b′]difuran derivatives as novel p-type organic semiconductor based on the Marcus–Hush theory combining quantum mechanics are carried out. This work focuses on the effects of carbon chain on molecular orbitals, partial charge difference, ionization potential, internal energy relaxation, and hole-transport behaviors. Through computational modeling, we are shedding light on the favorable function of C8-DPNDF single crystal as p-type organic material. With the introduction of octyl group, C8-DPNDF single crystal possesses high hole-transfer mobilites (1.589cm2V−1s−1) and remarkable anisotropic behavior. The simulated anisotropic mobility curve of C8-DPNDF demonstrates the maximum value of the mobility appears when the measuring conducting channel is along the b-axis of the single crystal. The adiabatic ionization potential (AIP) and vertical ionization potential (VIP) of C8-DPNDF are about 6.312 and 6.399eV, that is, slightly smaller than those of DPNDF. The relatively small IP values can ensure effective hole injection from the source electrode. The data obtained from the present work can be used to prove that C8-DPNDF molecule has the potential to develop into high-efficient p-type organic semiconductor materials, whose hole-transport mobility can be further improved when the measuring transistor channel is controlled carefully.

Multiscale molecular modeling can be an effective tool to aid the development of biomass conversion technology: A perspective

Lignocellulosic biomass is an alternate and renewable source of carbon. However, due to high oxygen content and diverse functionality, its conversion to fuels and chemicals is technologically challenging. Since physico-chemical characteristics of biomass and its derived components are very different from petroleum, fundamental understanding of their interactions with catalysts and solvents and of their behavior during thermochemical processing needs to be developed. In the present paper, we provide a perspective on how multiscale molecular modeling can assist in developing the science of biomass processing. The scope of this paper is limited to liquid phase catalytic and pyrolytic conversion of biomass. Car–Parrinello molecular dynamics (CPMD), a multiscale method that combines quantum mechanics and classical molecular dynamics and is an excellent choice to simulate biomass interactions in the condensed phase, is discussed. An overview of metadynamics, a method to accelerate CPMD dynamics, is also given. Revealing the chemistry of biomass pyrolysis, identifying liquid phase catalytic reaction mechanisms and developing a fundamental understanding of the role of solvents in biomass processing are the three main areas highlighted in this paper. Molecular modeling based investigations in these areas are reviewed and key findings are summarized. Limitations of the current approaches are discussed and the relevance of multiscale methods like CPMD and metadynamics is discussed. Potential studies that could implement multiscale molecular modeling methods to solve some of the challenging problems in developing biomass conversion technology are elaborated and an outlook is provided.

The Fenna-Matthews-Olson protein revisited: a fully polarizable (TD)DFT/MM description.

We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analysis of the excitonic properties of the Fenna-Matthews-Olson (FMO) protein by using a polarizable MM model combined with a time-dependent density functional theory description. Overall, our results indicate that structural fluctuations, electrostatic interactions, and short-range quantum effects can significantly modulate the model Hamiltonian parameters (site energies and couplings). We find that the specific interactions with the axial ligand and the hydrogen-bonded residues are responsible for the energy ladder, with their effects being mainly due to electrostatic interactions, but with short-range quantum contributions that are not negligible. In addition, a striking modulation of the screening effects experienced by the BChl pairs, due to the heterogeneous polarizability of the FMO and solvent environment, is observed. Finally, we find that the exciton model gives a reliable description of the delocalized excited states in the complex.

The development and validation of a pseudoatoms approach for combined quantum mechanics and molecular mechanics calculations of polypeptide

A pseudoatoms approach was proposed for combined quantum mechanics and molecular mechanics (QM/MM) calculations of polypeptide to ensure that each amino acid residue was an indivisible unit in the partitioning of the polypeptide into QM and MM subsystems. The pseudoatoms approach broke the QM/MM boundary peptide bonds as follow: the pseudoatom Ops(sp3) replacing the QM frontier amine N(sp3), and the pseudoatoms Nps(sp2)Oca(sp2) replacing the QM frontier C(sp2)O(sp2) carbonyl group. Conventional ab initio effective core potential (ECP) were constructed on the pseudoatoms to duplicate the all-electron molecular structure and charge distribution. The pseudoatoms’ ECP parameters were optimized using a genetic algorithm method, and consequently validated by a test set of 19 amino acids. The pseudoatoms approach was further validated by simulating an oligopeptide involved reaction with QM/MM and full-QM methods, respectively. The results from the QM/MM simulations are similar to those from the corresponding full-QM simulations. In summary, the pseudoatoms approach may be useful for QM/MM calculations of polypeptide. Additionally, it can be implemented without program modifications due to the use of conventional ECP.

Unraveling the differences of the hydrolytic activity of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase: a quantum mechanics-molecular mechanics modeling study.

Chagas’ disease, also known as American trypanosomiasis, is a lethal, chronic disease that currently affects more than 10 million people in Central and South America. The trans-sialidase from Trypanosoma cruzi (T. cruzi, TcTS) is a crucial enzyme for the survival of this parasite: sialic acids from the host are transferred to the cell surface glycoproteins of the trypanosome, thereby evading the host’s immune system. On the other hand, the sialidase of T. rangeli (TrSA), which shares 70% sequence identity with TcTS, is a strict hydrolase and shows no trans-sialidase activity. Therefore, TcTS and TrSA represent an excellent framework to understand how different catalytic activities can be achieved with extremely similar structures. By means of combined quantum mechanics–molecular mechanics (QM/MM, SCC-DFTB/Amberff99SB) calculations and umbrella sampling simulations, we investigated the hydrolysis mechanisms of TcTS and TrSA and computed the free energy profiles of these reactions. The results, together with our previous computational investigations, are able to explain the catalytic mechanism of sialidases and describe how subtle differences in the active site make TrSA a strict hydrolase and TcTS a more efficient trans-sialidase.

Understanding bacterial bioluminescence: a theoretical study of the entire process, from reduced flavin to light emission.

Bacterial bioluminescence (BL) has been successfully applied in water-quality monitoring and in vivo imaging. The attention of researchers has been attracted for several decades, but the mechanism of bacterial BL is still largely unknown due to the complexity of the multistep reaction process. Debates mainly focus on three key questions: How is the bioluminophore produced? What is the exact chemical form of the bioluminophore? How does the protein environment affect the light emission? Using quantum mechanics (QM), combined QM and molecular mechanics (QM/MM) and molecular dynamic (MD) calculations in gas-phase, solvent and protein environments, the entire process of bacterial BL was investigated, from flavin reduction to light emission. This investigation revealed that: 1) the chemiluminescent decomposition of flavin peroxyhemiacetal does not occur through the intramolecular chemical initiated electron exchange luminescence (CIEEL) or the "dioxirane" mechanism, as suggested in the literature. Instead, the decomposition occurs according to the charge-transfer initiated luminescence (CTIL) mechanism for the thermolysis of dioxetanone. 2) The first excited state of 4a-hydroxy-4a,5-dihydroFMN (HFOH) was affirmed to be the bioluminophore of bacterial BL. This study provides details regarding the mechanism by which bacterial BL is produced and is helpful in understanding bacterial BL in general.

Nucleation of Conformational Polymorphs: A Computational Study of Tolfenamic Acid by Explicit Solvation

The nucleation mechanism of polymorph formation remains poorly understood. For conformational polymorphism, the nature and strength of molecular interactions influence the conformation of a molecule, and such interplay between conformation and intermolecular interaction likely plays out through the self-assembling process of nucleation governing the outcome of resultant crystal structures. This study investigates molecular interactions and structural properties of a conformationally flexible molecule, tolfenamic acid, in explicit solvent by means of molecular dynamics and combined quantum mechanics and molecular mechanics methods. The results point out that tolfenamic acid prefers to take a relatively flat conformation, stabilized by intermolecular interactions between the solute and solvent molecules. Tolfenamic acid molecules can also adopt a more twisted conformation in a homodimeric state which exhibits lower solvation energy but greater stability. The computational work unravels the important influence by intermolecular interactions—between the solute and solvent or between the solute and solute—on stabilizing the conformation of solute molecules and, thus, highlights the underlying cooperation between a molecule’s conformation and its intermolecular interaction leading to the nucleation of distinct polymorphic structures.

Experimental Unconditionally Secure Bit Commitment

Quantum physics allows for unconditionally secure communication between parties that trust each other. However, when the parties do not trust each other such as in the bit commitment scenario, quantum physics is not enough to guarantee security unless extra assumptions are made. Unconditionally secure bit commitment only becomes feasible when quantum physics is combined with relativistic causality constraints. Here we experimentally implement a quantum bit commitment protocol with relativistic constraints that offers unconditional security. The commitment is made through quantum measurements in two quantum key distribution systems in which the results are transmitted via free-space optical communication to two agents separated with more than 20 km. The security of the protocol relies on the properties of quantum information and relativity theory. In each run of the experiment, a bit is successfully committed with less than 5.68×10(-2) cheating probability. This demonstrates the experimental feasibility of quantum communication with relativistic constraints.

Bivariate normal distribution of coherent state in parameterized phase space

Combining quantum mechanics and the normal distribution in statistics we study the coherent state from the point of view of statistics and by using the integration method within ordered product of operators. We find that the pure coherent state |z >z| exhibits a bivariate normal distribution of randon variables in (q,p) phase space, z=(q+ip)/√2, with a real k-parameter which is related to the quantization scheme, and the correlation coefficient is ik. For k=±1, |z >z| respectively is arranged as P-ordering (all P stand on the left of all Q) and Q-ordering (all Q stand on the left of all P), while in the case of k=0, |z >z| is arranged as the Weyl-ordering. In the cases of P-ordering and Q-ordering, in the classical correspondence function of |z >z||z=(q+ip)/√2 the bivariates (q,p) are correlated, only in the case of Weyl correspondece, (q,p) are independent. In other words, the Weyl ordering of operators is liable to decouple the correlation in bivariates.

Hydrogen storage on silicon, carbon, and silicon carbide nanotubes: A combined quantum mechanics and grand canonical Monte Carlo simulation study

Grand canonical Monte Carlo (GCMC) simulation combined with ab initio quantum mechanics calculations were employed to study hydrogen storage in homogeneous armchair open-ended single walled silicon nanotubes (SWSiNTs), single walled carbon nanotubes (SWCNTs), and single walled silicon carbide nanotubes (SWSiCNTs) in triangular arrays. Two different groups of nanotubes were studied: the first were (12,12) SiNTs, (19,19) CNTs, and (15,15) SiCNTs and the second were (7,7) SiNTs, (11,11) CNTs, and (9,9) SiCNTs with the diameters of ∼26 and ∼15 Å for the first and second groups, respectively. The simulations were carried out for different thermodynamic states. The potential energy functions (PEFs) were calculated using ab initio quantum mechanics and then fitted with (12,6) Lennard-Jones (LJ) potential model as a bridge between first principles calculations and GCMC simulations. The absolute, excess, and delivery adsorption isotherms of hydrogen were calculated for two groups of nanotubes. The isosteric heat of adsorption and the radial distribution functions (RDFs) for the adsorbed molecules on different nanotubes were also computed. Different isotherms were fitted with the simulation adsorption data and the model parameters were correlated. According to the results, the hydrogen uptake values in (19,19) CNT array exceeded the US DOE (Department of Energy) target of 6.0 wt% (FY 2010) at 77 K and 1.0 and 2.0 MPa for absolute and excess uptakes, respectively. The results also show that SiNTs and SiCNTs are not more useful materials compared with corresponding CNTs for hydrogen storage.

2013 Nobel Prize In Chemistry

Theoretical chemistry doesn’t always get the respect it deserves. This is not one of those times, as the Royal Swedish Academy of Sciences has awarded the 2013 Nobel Prize in Chemistry to three theoretical chemists— Martin Karplus of the University of Strasbourg, in France, and Harvard University; Michael Levitt of Stanford University School of Medicine; and Arieh Warshel of the University of Southern California. The trio is being recognized “for the development of multiscale models for complex chemical systems.” Beginning some 40 years ago, Karplus, Levitt, and Warshel helped develop computational techniques for modeling processes such as chemical reactions and protein folding. The Nobel citation refers to their success in combining quantum mechanics and molecular mechanics into a technique called QM/MM, which is now a state-of-the-art approach for simulating processes in biomolecular systems. “The beauty of QM/MM is that it overcomes the size restriction of quantum mechanics so you can ...

Quantum mechanical modeling: a tool for the understanding of enzyme reactions.

Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods.

Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins

We have examined the effect of geometry optimization on energies calculated with the quantum mechanical (QM) cluster, combined QM and molecular mechanics (QM/MM), and big-QM approaches (very large single-point QM calculations taken from QM/MM-optimized structures, including all atoms within 4.5 Å of the minimal active site, all buried charged groups in the protein, and truncations moved at least three residues away from the active site). We studied a simple proton-transfer reaction between His-79 and Cys-546 in the active site of [Ni,Fe] hydrogenase and optimize QM systems of 50 different sizes (56-362 atoms). Geometries optimized with QM/MM are stable and reliable, whereas QM-cluster optimizations give larger changes in the structures and sometimes lead to large distortions in the active site if some hydrogen-bond partners to the metal ligands are omitted. Keeping 2-3 atoms for each truncated residue (rather than one) fixed in the optimization improves the results but does not solve all problems for the QM-cluster optimizations. QM-cluster energies in vacuum and a continuum solvent are insensitive to the geometry optimizations with a mean absolute change upon the optimizations of only 4-7 kJ/mol. This shows that geometry optimizations do not decrease the dependence of QM-cluster energies on how the QM system is selected; there is still a ∼60 kJ/mol difference between calculations in which groups have been added to the QM system according to their distance to the active site or based on QM/MM free-energy components. QM/MM energies do not show such a difference, but they converge rather slowly with respect to the size of the QM system, although the convergence is improved by moving truncations away from the active site. The big-QM energies are stable over the 50 different optimized structures, 57 ± 1 kJ/mol, although some smaller trends can be discerned. This shows that both QM-cluster geometries and energies should be interpreted with caution. Instead, we recommend QM/MM for geometry optimizations and energies calculated by the big-QM approach.

Electron-Hole Transfer in G-Quadruplexes with Different Tetrad Stacking Geometries: A Combined QM and MD Study

G-quadruplex nucleic acids represent a unique avenue for the building of electrically conductive wires. These four-stranded structures are formed through the stacking of multiple planar guanine assemblies termed G-tetrads. The diverse folding patterns of G-quadruplexes allow for several geometries to be adopted by stacked guanine bases within the core and at the dimeric interface of these structures. It is currently not clear how different G-tetrad stacking arrangements affect electron hole mobility through a G-quadruplex wire. Using a combined quantum mechanics and molecular dynamics approach, we demonstrate that the electron-hole transfer rates within the G-tetrad stacks vary greatly for different stacking geometries. We identify a distinguished structure that allows for strong electronic coupling and thus enhanced molecular electric conductance. We also demonstrate the importance of sampling a large number of geometries when considering the bulk properties of such systems. Hole hopping within single G-tetrads is slower by at least two orders of magnitude than between stacked guanines; therefore, hole jumping within individual tetrads should not affect the hole mobility in G-quadruplexes. The results of this study suggest engineering G-tetrads with continuous 5/6-ring stacking from an assembly of single guanosine analogs or through modification of the backbone in G-rich DNA sequences.

Structure and thermodynamics of H3O+(H2O)8 clusters: A combined molecular dynamics and quantum mechanics approach

We have studied the structure and stability of H3O+(H2O)8 clusters using a combination of molecular dynamics sampling and high-level ab initio calculations. 20 distinct oxygen frameworks are found within 2kcal/mol of the electronic or standard Gibbs free energy minimum. The impact of quantum zero-point vibrational corrections on the relative stability of these isomers is quite significant. The box-like isomers are favored in terms of electronic energy, but with the inclusion of zero-point vibrational corrections and entropic effects tree-like isomers are favored at higher temperatures. Under conditions from 0 to 298.15K, the global minimum is predicted to be a tree-like structure with one dangling singly coordinated water molecule. Above 298.15K, higher entropy tree-like isomers with two or more singly coordinated water molecules are favored. These assignments are generally consistent with experimental IR spectra of (H3O+)(H2O)8 obtained at ∼150K.

Combined Molecular Dynamics and Quantum Mechanics Study of Oil Droplet Adsorption on Different Self-Assembly Monolayers in Aqueous Solution

In this paper, the dodecane is selected as the oil phase, and the adsorption behavior of an oil droplet on six self-assembled monolayer (SAM) surfaces in aqueous solution is investigated by a combined molecular dynamics and quantum mechanics method. First, the adsorption configuration of an oil droplet on these six surfaces is investigated, which indicates that the oil droplets spread on SAMs of −CH3, −OCH3, and −COOCH3 and detach from SAMs of −NH2, −OH, and −COOH. After that, the interactions of oil–SAM and water–SAM are calculated to rationalize the driving force controlling the conformational change of the oil droplet on various SAMs. Researched results suggest that the conformational change of the oil droplet is mainly driven by the interaction between water and SAMs. Finally, the mechanism of oil spreading or detachment behavior is discussed from the aspect of water property near the SAM, and calculated results show that the adsorption capability and dynamic property of interfacial water have a profo...

DPT tautomerization of the long A∙A* Watson-Crick base pair formed by the amino and imino tautomers of adenine: combined QM and QTAIM investigation

Combining quantum-mechanical (QM) calculations with quantum theory of atoms in molecules (QTAIM) and using the methodology of sweeps of the energetic, electron-topological, geometric and polar parameters, which describe the course of the tautomerization along the intrinsic reaction coordinate (IRC), we showed for the first time that the biologically important A∙A base pair (Cs symmetry) formed by the amino and imino tautomers of adenine (A) tautomerizes via asynchronous concerted double proton transfer (DPT) through a transition state (TS), which is the A(+)∙A(-) zwitterion with the separated charge, with Cs symmetry. The nine key points, which can be considered as electron-topological "fingerprints" of the asynchronous concerted A∙A ↔A ∙A tautomerization process via the DPT, were detected and completely investigated along the IRC of the A∙A*↔A*∙A tautomerization. Based on the sweeps of the H-bond energies, it was found that intermolecular antiparallel N6Н⋯N6 (7.01 kcal mol(-1)) and N1H⋯N1 (6.88 kcal mol(-1)) H-bonds are significantly cooperative and mutually reinforce each other. It was shown for the first time that the A∙A ↔A ∙A tautomerization is assisted by the third C2H⋯HC2 dihydrogen bond (DHB), which, in contrast to the two others N6H⋯N6 and N1H⋯N1 H-bonds, exists within the IRC range from -2.92 to 2.92 Å. The DHB cooperatively strengthens, reaching its maximum energy 0.42 kcal mol(-1) at IRC = -0.52 Å and minimum energy 0.25 kcal mol(-1) at IRC = -2.92 Å, and is accompanied by strengthening of the two other aforementioned classical H-bonds. We established that the C2H⋯HC2 DHB completely satisfies the electron-topological criteria for H-bonding, in particular Bader's and all eight "two-molecule" Koch and Popelier's criteria. The positive value of the Grunenberg's compliance constant (5.203 Å/mdyn) at the TSA∙A ↔A ∙A proves that the C2H⋯HC2 DHB is a stabilizing interaction. NBO analysis predicts transfer of charge from σ(C2-H) bonding orbital to σ (H-C2) anti-bonding orbital; at this point, the stabilization energy E((2)) is equal to 0.19 kcal mol(-1) at the TSA∙A ↔A ∙A.

Natural gas storage on silicon, carbon, and silicon carbide nanotubes: a combined quantum mechanics and grand canonical Monte Carlo simulation study

Grand canonical Monte Carlo (GCMC) simulation combined with ab initio quantum mechanics calculations were employed to study methane storage in homogeneous armchair open-ended single-walled silicon nanotubes (SWSiNTs), single-walled carbon nanotubes (SWCNTs), and single-walled silicon carbide nanotubes (SWSiCNTs) in triangular arrays. Two different groups of nanotubes were studied: the first were (12,12) SiNTs, (19,19) CNTs, and (15,15) SiCNTs and the second were (7,7) SiNTs, (11,11) CNTs, and (9,9) SiCNTs with the diameters of 26 and 15 A for the first and second groups, respectively. The simulations were carried out at different thermodynamic states. The potential energy functions were calculated using ab initio quantum mechanics and then fitted with (12,6) Lennard–Jones potential model as a bridge between first-principles calculations and GCMC simulations. The absolute, excess, and delivery adsorption isotherms of methane were calculated for two groups of nanotubes. The specific surface area and the isosteric heat of adsorption were computed. The radial distribution functions for the adsorbed molecules on different nanotubes were also calculated. Different isotherm models were fitted with the simulation adsorption data. According to the results, the excess uptake value of methane adsorption in (11,11) CNT array exceeded the US Department of Energy target (180 V/V at 298 K and 35 bar). The results also indicate that SiNTs and SiCNTs are not desirable materials compared with corresponding CNTs for natural gas storage.