Hydrogen bond lifetime for water in classic and quantum molecular dynamics

The lifetime of hydrogen bonds in water at T = 298 K and p = 0.1 MPa is computed by means of classic molecular dynamics with eight different potentials of pair lifetime interaction and Car-Parinello molecular dynamics. The results obtained using various computational techniques for hydrogen bond life-times are compared. It is shown that they can differ from one another by several times. The dependence for the hydrogen bond lifetime computed in our numerical experiment upon the method of its determination is found.     

Fast centroid molecular dynamics: a force-matching approach for the predetermination of the effective centroid forces

A fast centroid molecular dynamics (CMD) methodology is proposed in which the effective centroid forces are predetermined through a force-matching algorithm applied to a standard path integral molecular dynamics simulation. The resulting method greatly reduces the computational cost of generating centroid trajectories, thus extending the applicability of CMD. The method is applied to the study of liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point. The static and dynamical results are compared to those obtained from full adiabatic CMD simulations and found to be in excellent agreement for all three systems; the transport properties are also compared to experiment and found to have a similar level of agreement.     

Photodissociation dynamics of acetaldehyde at 267 nm: A computational study of the CO-forming channels

A recent experiment on the 267 nm photolysis of gaseous acetaldehyde reveals that the molecular products (CO + CH₄) present product state distributions with computation –experiment discrepancy. This work aims to provide solution to such issue. The direct dynamics simulation of classical trajectories and the generalized multi-center impulsive model (GMCIM) are both utilized to predict the product state distributions of CO and CH₄ from 267 nm photolysis of acetaldehyde. Comparison with the experimental observation provides an assessment of the conventional approach of minimum energy path within the framework of three-center transition state (TS) and CH₃-roaming pathways. The result shows that the high-speed products observed in experiment are likely formed via the three-center TS pathway. The reasons that lead to the discrepancy between computation and experiments in previous studies are also investigated. A better agreement between computational and state-resolved experimental results can be achieved by selecting specific internal states of CO product from the computational data.     

New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations

A dicationic ferrocene derivative has previously been shown to bind cucurbit[7]uril (CB[7]) in water with ultrahigh affinity (ΔG(o) = -21 kcal/mol). Here, we describe new compounds that bind aqueous CB[7] equally well, validating our prior suggestion that they, too, would be ultrahigh affinity CB[7] guests. The present guests, which are based upon either a bicyclo[2.2.2]octane or adamantane core, have no metal atoms, so these results also confirm that the remarkably high affinities of the ferrocene-based guest need not be attributed to metal-specific interactions. Because we used the M2 method to compute the affinities of several of the new host-guest systems prior to synthesizing them, the present results also provide for the first blinded evaluation of this computational method. The blinded calculations agree reasonably well with experiment and successfully reproduce the observation that the new adamantane-based guests achieve extremely high affinities, despite the fact that they position a cationic substituent at only one electronegative portal of the CB[7] host. However, there are also significant deviations from experiment, and these lead to the correction of a procedural error and an instructive evaluation of the sensitivity of the calculations to physically reasonable variations in molecular energy parameters. The new experimental and computational results presented here bear on the physical mechanisms of molecular recognition, the accuracy of the M2 method, and the usefulness of host-guest systems as test-beds for computational methods.     

Special Collection: Computational Chemistry

Chemists know well the value of an experimental or a theoretical result, but what is the value of a computational result? Simulation is neither theory nor experience, nor a mere calculation tool, but a genuine way of approaching reality that is transforming the scientific method. In some cases, it offers explanations to observations or experiments that seem incomprehensible because they are too complex. In this case, the computation serves as a relief. An experiment that converges with a certain computation has more scientific value than an experiment that does not converge with anything at all. In other cases, contribution of computational chemistry is essential because there is no experimental manner to determine what happens during a chemical process; for instance, in the path from reactants to products in (fast) reactions. Now, computational chemistry provides additional information that is not possible to obtain from experiments, so it is a valuable complement to them. Indeed, fruitful synergy between computation and experiment has led to the approach of theory-driven experimentation. Finally, computational chemistry helps to legitimize models or theories that have little opportunity to be contrasted with reality. In this situation, computational chemistry is not experience, but it does substitute it in relation to theory. In the present special collection, we have examples of the different ways computational chemistry helps chemists to interpret the electronic and molecular structure of molecules and their reactivity.     

Modeling electrochemical interfaces from ab initio molecular dynamics: water adsorption on metal surfaces at potential of zero charge

The origin of the potential difference between the potential of zero charge of a metal/water interface and the work function of the metal is a recurring issue because it is related to how water interacts with metal surface in the absence of surface charge. Recently ab initio molecular dynamics method has been used to model electrochemical interfaces to study interfacial potential and the structure of interface water. Here, we will first introduce the computational standard hydrogen electrode method, which allows for ab initio determination of electrode potentials that can be directly compared with experiment. Then, we will review the recent progress from ab initio molecular dynamics simulation in understanding the interaction between water and metal and its impact on interfacial potential. Finally, we will give our perspective for future development of ab initio computational electrochemistry.     

An Update on Molecularly Imprinted Polymer Design through a Computational Approach to Produce Molecular Recognition Material with Enhanced Analytical Performance

Molecularly imprinted polymer (MIP) computational design is expected to become a routine technique prior to synthesis to produce polymers with high affinity and selectivity towards target molecules. Furthermore, using these simulations reduces the cost of optimizing polymerization composition. There are several computational methods used in MIP fabrication and each requires a comprehensive study in order to select a process with results that are most similar to properties exhibited by polymers synthesized through laboratory experiments. Until now, no review has linked computational strategies with experimental results, which are needed to determine the method that is most appropriate for use in designing MIP with high molecular recognition. This review will present an update of the computational approaches started from 2016 until now on quantum mechanics, molecular mechanics and molecular dynamics that have been widely used. It will also discuss the linear correlation between computational results and the polymer performance tests through laboratory experiments to examine to what extent these methods can be relied upon to obtain polymers with high molecular recognition. Based on the literature search, density functional theory (DFT) with various hybrid functions and basis sets is most often used as a theoretical method to provide a shorter MIP manufacturing process as well as good analytical performance as recognition material.     

Relativistically corrected geometries obtained with analytical gradients: normalized elimination of the small component using an effective potential

For the quasi-relativistic normalized elimination of small component using an effective potential (NESC-EP) method, analytical energy gradients were developed, programmed, and implemented in a standard quantum chemical program package. NESC-EP with analytical gradients was applied to determine geometry, vibrational frequencies, and dissociation enthalpies of ferrocene, tungsten hexafluoride, and tungsten hexacarbonyle. Contrary to non-relativistic calculations and calculations carried out with RECPs for the same compounds, NESC-EP provided reliable molecular properties in good agreement with experiment. The computational power of NESC-EP results from the fact that reliable relativistic corrections are obtained at a cost level only slightly larger than that of a non-relativistic calculation.     

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm

This study applies a novel computational method to study molecular recognition for three sets of synthetic hosts: molecular clips, molecular tweezers, and a synthetic barbiturate receptor. The computed standard free energies of binding for the 12 binding reactions agree closely with experiment and provide insight into the roles of configurational entropy, preorganization, and induced fit in the systems studied. The computed changes in configurational entropy are comparable in magnitude to the changes in mean potential plus solvation energy, and they result primarily from changes in the average width of the energy wells upon binding. A strong correlation is observed between the changes in configurational energy and configurational entropy upon binding, resulting in near-linear compensation analogous to classical entropy-enthalpy compensation.     

On use of the Amber potential with the Langevin dipole method

Inclusion of solvent effects in biomolecular simulations is most ideally done using explicit methods, as they are able to capture the heterogeneous environment typical of biomolecules and systems involving them (e.g., proteins at solid interfaces). Common explicit methods based on molecular solvent models (e.g., TIP and SPC models) and molecular dynamic or Monte Carlo simulation are computationally expensive and are, therefore, not well-suited to situations where many simulations are required (e.g., in the ab initio structure prediction or design contexts). In such cases, more coarse-grained explicit approaches such as the Langevin dipole (LD) method of Warshel and co-workers are more appropriate. The recent incarnations of the LD method appear to produce good solvation free energy estimates. These incarnations use charges and solute structures obtained from high-level quantum mechanics simulations. As such an approach is clearly not possible for larger solutes or when many structures are to be considered, an alternative must be sought. One possibility is to use structures and charges derived from an existing analytical potential model-we report on such a coupling here with the Amber potential model. The accuracy and computational performance of this hybrid approach, which we term LD-Amber to distinguish it from previous incarnations of the LD method, was assessed by comparing results obtained from the approach with those from experiment and other theoretical methods for the solvation of 18 amino acid analogues and the alanine dipeptide. This comparison shows that the LD-Amber approach can yield results in line with experiment both qualitatively and quantitatively and is as accurate as other explicit methods while being computationally much cheaper.     

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.     

二酰胺吡啶修饰杯[4]芳烃与脂肪二羧酸主客体相互作用的理论研究

本文用分子力学和分子动力学方法对二酰胺吡啶修饰杯[4]芳烃与脂肪二羧酸的主客体相互作用进行了研究.     

Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy

The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide‐and‐conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction‐type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre‐exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude).     

Implementation of quantum gate operations in molecules with weak laser fields

We numerically propose a way to perform quantum computations by combining an ensemble of molecular states and weak laser pulses. A logical input state is expressed as a superposition state (a wave packet) of molecular states, which is initially prepared by a designed femtosecond laser pulse. The free propagation of the wave packet for a specified time interval leads to the specified change in the relative phases among the molecular basis states, which corresponds to a computational result. The computational results are retrieved by means of quantum interferometry. Numerical tests are implemented in the vibrational states of the B state of I2 employing controlled-NOT gate, and 2 and 3 qubits Fourier transforms. All the steps involved in the computational scheme, i.e., the initial preparation, gate operation, and detection steps, are achieved with extremely high precision.     

The binding domain of the HMGB1 inhibitor carbenoxolone: Theory and experiment

We present a combined computational and experimental study of the interaction of the Box A of the HMGB1 protein and carbenoxolone, an inhibitor of its pro-inflammatory activity. The computational approach consists of classical molecular dynamics (MD) simulations based on the GROMOS force field with quantum-refined (QRFF) atomic charges for the ligand. Experimental data consist of fluorescence intensities, chemical shift displacements, saturation transfer differences and intermolecular Nuclear Overhauser Enhancement signals. Good agreement is found between observations and the conformation of the ligand–protein complex resulting from QRFF–MD. In contrast, simple docking procedures and MD based on the unrefined force field provide models inconsistent with experiment. The ligand–protein binding is dominated by non-directional interactions.     

Calculation of molecular quadrupole moments and a demonstration of the importance of overlap densities in the theory of polyatomic molecules

A computational method for calculating quadrupole moments from molecular wave functions in a Slater orbital basis set is described. Using both IEHT and CNDO wave functions quadrupole moments for a series of polyatomic molecules are calculated. They are compared with experimental results and the IEHT wave functions are found to give agreement with experiment while CNDO wave functions do not. The importance of bicentric densities (overlap densities) in the calculation of multipole moments is shown. This is followed by a discussion of the usefulness of these wave functions for a quantitative characterization of the electronic structure of large molecules.     

Molecular Flexibility and Bend in Semi-Rigid Liquid Crystals: Implications for the Heliconical Nematic Ground State

The N_TB phase phases possess a local helical structure with a pitch length of a few nanometers and is typically exhibited by materials consisting of two rigid mesogenic units linked by a flexible oligomethylene spacer of odd parity, giving a bent shape. We report the synthesis and characterisation of two novel dimeric liquid crystals, and perform a computational study on 10 cyanobiphenyl dimers with varying linking groups, generating a large library of conformers for each compound; this allows us to present molecular bend angles as probability weighted averages of many conformers, rather than use a single conformer. We validate conformer libraries by comparison of interproton distances with those obtained from solution-based 1D ¹H NOESY NMR, finding good agreement between experiment and computational work. Conversely, we find that using any single conformer fails to reproduce experimental interproton distances. We find the use of a single conformer significantly overestimates the molecular bend angle while also ignoring flexibility; in addition, we show that the average bend angle and flexibility are both linked to the relative stability of the N_TB phase.     

One-center expansion method with model potentials. I. Formulation and test calculations

The one-center expansion (OCE ) method is extended to evaluate molecular wave functions for molecules with heavy off-center nuclei. This extension is achieved through the use of model potentials (MP ) to approximate the highly bound core orbitals. The remaining diffuse valence charge distribution is then rather easy to simulate using OCE . The formulation of the method is described. New molecular integrals are solved to a high degree of accuracy. Successful results are reported for H₂O, H₂S, and N₂. The valence electron distributions and orbital energies are in good agreement with those obtained from more complete calculations. The method combines the computational economy of both OCE and MP procedures, resulting in a potentially useful package for further chemical applications.     

Self consistent tight binding model for dissociable water

We report results of development of a self consistent tight binding model for water. The model explicitly describes the electrons of the liquid self consistently, allows dissociation of the water and permits fast direct dynamics molecular dynamics calculations of the fluid properties. It is parameterized by fitting to first principles calculations on water monomers, dimers, and trimers. We report calculated radial distribution functions of the bulk liquid, a phase diagram and structure of solvated protons within the model as well as ac conductivity of a system of 96 water molecules of which one is dissociated. Structural properties and the phase diagram are in good agreement with experiment and first principles calculations. The estimated DC conductivity of a computational sample containing a dissociated water molecule was an order of magnitude larger than that reported from experiment though the calculated ratio of proton to hydroxyl contributions to the conductivity is very close to the experimental value. The conductivity results suggest a Grotthuss-like mechanism for the proton component of the conductivity.