Dynamic Properties Of Molecules Research Articles

Potential energy surfaces and dynamic properties via ab initio composite and density functional approaches.

Vibrational spectroscopy enables critical insight into the structural and dynamic properties of molecules. Presently, the majority of theoretical approaches to spectroscopy employ wavefunction-based ab initio or density functional methods that rely on the harmonic approximation. This approximation breaks down for large molecules with strongly anharmonic bonds or for molecules with large internuclear separations. An alternative to these methods involves generating molecular anharmonic potential energy surfaces (potentials) and using them to extrapolate the vibrational frequencies. This study examines the efficacy of density functional theory (DFT) and the correlation consistent Composite Approach (ccCA) in generating anharmonic frequencies from potentials of small main group molecules. Vibrational self-consistent field Theory (VSCF) and post-VSCF methods were used to calculate the fundamental frequencies of these molecules from their potentials. Functional choice, basis set selection, and mode-coupling are also examined as factors in influencing accuracy. The absolute deviations for the calculated frequencies using potentials at the ccCA level of theory were lower than the potentials at the DFT level. With DFT resulting in bending modes that are better described than those of ccCA, a multilevel DFT:ccCA approach where DFT potentials are used for single vibrational mode potentials and ccCA is used for vibrational mode-mode couplings can be utilized for larger polyatomic systems. The frequencies obtained with this multilevel approach using VCIPSI-PT2 were closer to experimental frequencies than the scaled harmonic frequencies, indicating the success of utilizing post-VSCF methods to generate more accurate representations of computed infrared spectra.

NMR spectrum prediction for dynamic molecules by machine learning: A case study of trefoil knot molecule.

Nuclear magnetic resonance (NMR) spectroscopy is one of the indispensable techniques in chemistry because it enables us to obtain accurate information on the chemical, electronic, and dynamic properties of molecules. Computational simulation of the NMR spectra requires time-consuming density functional theory (DFT) calculations for an ensemble of molecular conformations. For large flexible molecules, it is considered too high-cost since it requires time-averaging of the instantaneous chemical shifts of each nuclear spin across the conformational space of molecules for NMR timescales. Here, we present a Gaussian process/deep kernel learning-based machine learning (ML) method for enabling us to predict, average in time, and analyze the instantaneous chemical shifts of conformations in the molecular dynamics trajectory. We demonstrate the use of the method by computing the averaged 1H and 13C chemical shifts of each nuclear spin of a trefoil knot molecule consisting of 24 para-connected benzene rings (240 atoms). By training ML model with the chemical shift data obtained from DFT calculations, we predicted chemical shifts for each conformation during dynamics. We were able to observe the merging of the time-averaged chemical shifts of each nuclear spin in a singlet 1H NMR peak and two 13C NMR peaks for the knot molecule, in agreement with experimental measurements. The unique feature of the presented method is the use of the learned low-dimensional deep kernel representation of local spin environments for comparing and analyzing the local chemical environment histories of spins during dynamics. It allowed us to identify two groups of protons in the knot molecule, which implies that the observed singlet 1H NMR peak could be composed of the contributions from protons with two distinct local chemical environments.

Topological aspects of cavity‐induced degeneracies in polyatomic molecules

AbstractConical intersections are degeneracies between multidimensional potential energy surfaces of molecular systems. It is well known that, besides these phenomena significantly modify the spectroscopic and dynamical properties of molecules, their presence in a molecular system has noticeable topological implications, as well. Such a consequence is the appearance of the topological or geometric phase. Conical intersections not only occur in nature but they can also be created by light. This can either be classical laser light or quantum light in an optical cavity. As a showcase example, by placing the formaldehyde (H2CO) molecule into a cavity, the topological properties (e.g., geometric or Berry phase) of the emerging light‐induced conical intersection have been investigated for different cavity parameters and geometrical arrangements.

Perturbed path integrals in imaginary time: Efficiently modeling nuclear quantum effects in molecules and materials.

Nuclear quantum effects (NQE), which include both zero-point motion and tunneling, exhibit quite an impressive range of influence over the equilibrium and dynamical properties of molecules and materials. In this work, we extend our recently proposed perturbed path-integral (PPI) approach for modeling NQE in molecular systems [I. Poltavsky and A. Tkatchenko, Chem. Sci. 7, 1368 (2016)], which successfully combines the advantages of thermodynamic perturbation theory with path-integral molecular dynamics (PIMD), in a number of important directions. First, we demonstrate the accuracy, performance, and general applicability of the PPI approach to both molecules and extended (condensed-phase) materials. Second, we derive a series of estimators within the PPI approach to enable calculations of structural properties such as radial distribution functions (RDFs) that exhibit rapid convergence with respect to the number of beads in the PIMD simulation. Finally, we introduce an effective nuclear temperature formalism within the framework of the PPI approach and demonstrate that such effective temperatures can be an extremely useful tool in quantitatively estimating the "quantumness" associated with different degrees of freedom in the system as well as providing a reliable quantitative assessment of the convergence of PIMD simulations. Since the PPI approach only requires the use of standard second-order imaginary-time PIMD simulations, these developments enable one to include a treatment of NQE in equilibrium thermodynamic properties (such as energies, heat capacities, and RDFs) with the accuracy of higher-order methods but at a fraction of the computational cost, thereby enabling first-principles modeling that simultaneously accounts for the quantum mechanical nature of both electrons and nuclei in large-scale molecules and materials.

Multi-color single-molecule tracking and subtrajectory analysis for quantification of spatiotemporal dynamics and kinetics upon T cell activation

The dynamic properties of molecules in living cells are attracting increasing interest. We propose a new method, moving subtrajectory analysis using single-molecule tracking, and demonstrate its utility in the spatiotemporal quantification of not only dynamics but also the kinetics of interactions using single-color images. Combining this technique with three-color simultaneous single-molecule imaging, we quantified the dynamics and kinetics of molecules in spatial relation to T cell receptor (TCR) microclusters, which trigger TCR signaling. CD3ε, a component of the TCR/CD3 complex, and CD45, a phosphatase positively and negatively regulating signaling, were each found in two mobility states: faster (associated) and slower (dissociated) states. Dynamics analysis suggests that the microclusters are loosely composed of heterogeneous nanoregions, possibly surrounded by a weak barrier. Kinetics analysis quantified the association and dissociation rates of interactions with the microclusters. The associations of both CD3ε and CD45 were single-step processes. In contrast, their dissociations were each composed of two components, indicating transient and stable associated states. Inside the microclusters, the association was accelerated, and the stable association was increased. Only CD45 showed acceleration of association at the microcluster boundary, suggesting specific affinity on the boundary. Thus, this method is an innovative and versatile tool for spatiotemporal quantification.

Impact of theoretical chemistry on chemical and biological sciences

The Nobel Prize in Chemistry, 2013 has been awarded to Martin Karplus, Michael Levitt and Arieh Warshel for their studies on development of multi-scale models for complex chemical systems. This article introduces the readers to the theoreticalmethods developed for the study of complex chemical and biological systems and connects the works of the awardees to this vast area of research. The development of quantum chemistry (QC or QM) to study molecules at electronic level is briefly mentioned. The growth of methods based on classical physics to study large systems at the molecular level (MM) is discussed. The origin of hybridQM/MM techniques to perform multi-scale modelling is then presented. Further, the parallel development of molecular simulations, which connects the macroscopic and the microscopic world elucidating the dynamical properties of molecules, is introduced. Finally, the impact of theoretical chemistry on the advancement of our understanding of complex chemical and biological systems is highlighted.

Trust-Region Algorithm for the Inversion of Molecular Diffusion NMR Data

Diffusion NMR experiments are very useful in studying structural and dynamical properties of molecules and in sorting out components from mixtures. A number of numerical approaches have been developed for the processing of diffusion NMR data. In this paper, numerical problems of the direct regularization methods such as CONTIN, MaxEnt, and the newly proposed ITAMeD approach are illustrated by analyzing simulated and experimental data. It allows us to further develop a new method to calculate the distribution of diffusion coefficients. Therefore, we present here an iterative regularization method based on the Trust-Region Algorithm for the Inversion (TRAIn) of molecular diffusion NMR data. It is demonstrated in this paper that our approach overcomes major numerical difficulties of the direct regularization methods mentioned above. Besides, this method reconstructs more reliable diffusion coefficient distributions, especially for real world samples of which the diffusion coefficients are nonsymmetrically distributed.

Computational tools for the interpretation of electron spin resonance spectra in solution

Spectroscopic observables can be used for monitoring relaxation processes of molecules. In particular, electron spin resonance of stable multi-radicals is sensitive to the details of the rotational and internal dynamics in rigid and flexible molecules. Integration with advanced theoretical/computational methods proves to be particularly effective to acquire direct information on long-range relaxation processes, based on molecular dynamics, multi-scale approaches and coarse-graining treatments. Together, experimental data and computational interpretation provide a way to understand the effect of chemical changes on specific systems. In this paper we review computational tools aimed at the characterisation of dynamical properties of molecules gathered from electron spin resonance measurements. Stochastic models are employed, based on a number of structural parameters that are calculated at atomistic and/or mesoscopic level depending on their nature. Open source software tools built as user-friendly ‘virtual spectroscopes’ targeted for use by experimentalists are provided as a kind of extension of the laboratory equipment. An overview of their range of applicability is provided.

Unidirectional Rolling Motion of Nanocars Induced by Electric Field

Understanding microscopic mechanisms of motion of artificial molecular machines is fundamentally important for scientific and technological progress. It is known that electric field might strongly influence structures and dynamic properties of molecules at the nanoscale level. Specifically, it is possible to induce conformational changes and the directional motion in many surface-bound molecules by electric field in scanning tunneling microscopy (STM) experiments. Utilizing a recently developed theoretical method to describe charge transfer phenomena for fullerenes near metal surfaces, in this work we theoretically investigated dynamics of fullerene-based nanocars in the presence of external electric field. Our approach is based on classical rigid-body molecular dynamics simulations that allow us to fully analyze dynamics of nanocars on gold surfaces. Theoretical calculations predict that it is possible to drive nonpolar nanocars unidirectionally with the help of external electric field. It is shown also that charge transfer effects play a critical role in driving nanocars and for understanding mechanisms of the directionality of the observed motion. Our theoretical predictions explain experimental observations on moving nanocars along metal surfaces.

Information Content in Fluorescence Correlation Spectroscopy: Binary Mixtures and Detection Volume Distortion

When properly implemented, fluorescence correlation spectroscopy (FCS) reveals numerous static and dynamic properties of molecules in solution. However, complications arise whenever the measurement scenario is complex. Specific limitations occur when the detection region does not match the ideal Gaussian geometry ubiquitously assumed by FCS theory, or when properties of multiple fluorescent species are assessed simultaneously. A simple binary solution of diffusers, where both mole fraction and diffusion constants are sought, can face interpretive difficulty. In order to better understand the limits of FCS, this study systematically explores the relationship between detection-volume distortion, diffusion constants, species mole fraction, and fitting methodology in analyses that utilize a two-component autocorrelation model. FCS measurements from solution mixtures of dye-labeled protein and free dye are compared to simulations, which predict the performance of FCS under a variety of experimental circumstances. The results reveal a range of conditions necessary for performing accurate measurements and describe experimental scenarios that should be avoided. The findings also provide guidelines for obtaining meaningful measurements when grossly distorted detection volumes are utilized and generally assess the latent information contained in FCS datasets.

Dielectric and X-ray Studies of Substances with the Smectic B phase

Several substances of different chemical structures exhibiting the smectic B polymorphism in a wide temperature range [accompanied by the nematic (N) phase in few cases] were studied with the aid of the dielectric relaxation and X-ray methods. The dielectric relaxation time τ∥ connected with the end-over-end rotations of molecules was determined. It elongates considerably at the N–B transition whereas the activation barrier hindering the flip--flop motion decreases. The parameters of the hexagonal unit cell were determined as functions of temperature. The packing parameter, p = ZV mol /V u.c. , was calculated which exceeds value of c. 0.6, thus is typical for the plastic crystals. The dynamical properties of molecules are discussed in relation to their packing in the smectic layers. The applicability of the Arrhenius equation to calculation of the activation barrier from the temperature dependence of τ∥ in the B phase seems to be doubtful in view of the experimental data collected. It was concluded that all examined substances have rather the hexatic than the crystalline B phase.

Generation of Clebsch–Gordan coefficients for the point and double groups

The theory of the point and double groups has been widely used in quantum physics to understand the structure and dynamical properties of molecules and solids. In order to construct wave functions for such systems, one often needs the Clebsch–Gordan coefficients for the symmetry groups. Here, we present an extension of the Bethe program to support the calculation of the Clebsch–Gordan coefficients as applied, for instance, in crystal field theory. Apart from the generation of the Clebsch–Gordan coefficients, the program also provides a simple access to the group theoretical data for all frequently applied point and double groups. Program summary Title of program: Bethe Catalogue number:ADUH_v3_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADUH_v3_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Reference in CPC to previous versions: Comput. Phys. Comm. 162 (2004) 124–142; Comput. Phys. Comm. 171 (2005) 119–132 Catalog identifiers of previous versions: ADUH, ADVU Does the new version supersede the old version?: Yes Licensing provisions: None Computers for which the program is designed: All computers with a license of the computer algebra package Maple [Maple is a registered trademark of Waterloo Maple Inc.] Installations: University of Kassel (Germany) Operating systems under which the program has been tested: Linux 8.1+ and Windows 2000 Programming language used: Maple 7 and 8 Memory required to execute with typical data: 10–30 MB No. of lines in distributed program, including test data, etc.: 11 024 No. of bytes in distributed program, including test data, etc.: 210 244 Distribution format:tar.gz Nature of the physical problem: The energy levels of atoms, placed into a crystal environment, can be classified by using group theory. In order to represent, for instance, the wave functions, which are associated with these atomic levels, one often requires the Clebsch–Gordan coefficients of the underlying symmetry group of the overall system. These coefficients arise in the coupling of the electronic wave functions (subsystems) and therefore help investigate the interaction between the many-electron atom and the external field of the crystal. Method of solution: In the framework of the Bethe program [K. Rykhlinskaya, S. Fritzsche, Comput. Phys Comm. 162 (2004) 124–142; K. Rykhlinskaya, S. Fritzsche, Comput. Phys Comm. (2005), in press], we previously defined data structures to deal with a large number of group parameters of the point and double groups. Among other parameters, here we also implemented the irreducible (matrix) representations of these groups which are utilized in the present extension of the program in order to generate the Clebsch–Gordan coefficients for the point and double groups. In practice, of course, these coefficients are obtained by means of a proper summation over the matrix elements of the irreducible representations of the group. Reasons for the new version: Extension of the program. Summary of revision: A number additional procedure have been created to generate the Clebsch–Gordan coefficients for the symmetry groups (Bethe_CG_matrix(), Bethe_CG_coefficient(), Bethe_group_direct_product(), etc.) Restrictions onto the complexity of the problem: The generation of the Clebsch–Gordan coefficients is supported for the cyclic and related groups C i , C s , C n , C n h , C n v , the dihedral groups D n , D n h , D n d , the improper cyclic groups S 2 n ( n ⩽ 10 ) , the cubic groups O, T, O h , T h , T d as well as the icosahedral groups I and I h . Both the point and the double groups are supported. Unusual features of the program: All commands of the Bethe program are available for interactive work. Apart from the generation of the Clebsch–Gordan coefficients, the program also provides a simple access to the group theoretical data for all the groups specified above. The notation of the symmetry operations and of the irreducible representations follows the compilation by Altmann and Herzig [S. Altmann, P. Herzig, Point-Group Theory Tables, Clarendon Press, Oxford, 1994]. For a quick reference to the program, a description of all user-relevant commands is given in the (user) manual Bethe-commands.pdf which is distributed together with the code. Typical running time: Although the program replies ‘promptly’ on most requests, the running time depends strongly on the particular task.

A molecular dynamics study on liquid–vapor interface adsorbed by impurities

In this paper, we focus on the microscopic structure of the liquid–vapor interface and the effect of impurities such as surfactants or electrolytes in the aqueous solution on interfacial properties. We perform molecular dynamics (MD) simulations of a simple planar interface system and a bubble system in which a nanometer-size void region is maintained. In these MD systems, some static and dynamic properties of molecules near the interface are investigated and we elucidate some microscopic features of the interface. Especially, we show the difference of the dynamics of water molecules between the surfactant and electrolyte solutions. We also consider the definition of the interface at the molecular level which can treat the local and instantaneous structure, and discuss the physical properties which we calculate including the effect of molecular fluctuations of the interface.

The use of the cohen–turnbull model for calculation of the self-diffusion coefficients of liquid dichloroalkanes

The paper presents the self-diffusion coefficients calculated for liquid dichloroalkanes C6H12Cl2, C8H16Cl2, C10H22Cl2 and C12H24Cl2, with the use of the Cohen and Turnbull model. Determination of self-diffusion coefficients permits a separate analysis of intra- and intermolecular motions and provides information on geometrical and dynamical properties of molecules. The self-diffusion coefficients of selected dichloroalkanes have been determined by X-ray diffraction and compared with the corresponding NMR results. The suitability of the Cohen–Turnbull model of the translating motion for prediction of self-diffusion coefficients for molecules whose shape significantly differs from the spherical symmetry is analysed. Angular distributions of X-ray scattered intensity were measured, and differential radial distribution functions of electron density (DRDFs) were calculated. The mean coordination numbers were obtained from the area delimited by the minima of the DRDFs, and their dependence on the length of the methylene chain is also presented subsequently. On the basis of the DRDFs the average free volume of the molecules and total free volume of the liquids were calculated. The activation volume of the diffusion was found to make about 0.6 of the van der Waals volume of the molecule. As expected the diffusion coefficients decrease with increasing molecular weight. The equation relating the self-diffusion coefficient with the volume of the coordination spheres in the liquid has been derived.

Dynamics of the Hck-SH3 domain: comparison of experiment with multiple molecular dynamics simulations.

Molecular dynamics calculations provide a method by which the dynamic properties of molecules can be explored over timescales and at a level of detail that cannot be obtained experimentally from NMR or X-ray analyses. Recent work (Philippopoulos M, Mandel AM, Palmer AG III, Lim C, 1997, Proteins 28:481-493) has indicated that the accuracy of these simulations is high, as measured by the correspondence of parameters extracted from these calculations to those determined through experimental means. Here, we investigate the dynamic behavior of the Src homology 3 (SH3) domain of hematopoietic cell kinase (Hck) via 5N backbone relaxation NMR studies and a set of four independent 4 ns solvated molecular dynamics calculations. We also find that molecular dynamics simulations accurately reproduce fast motion dynamics as estimated from generalized order parameter (S2) analysis for regions of the protein that have experimentally well-defined coordinates (i.e., stable secondary structural elements). However, for regions where the coordinates are not well defined, as indicated by high local root-mean-square deviations among NMR-determined structural family members or high B-factors/low electron density in X-ray crystallography determined structures, the parameters calculated from a short to moderate length (less than 5-10 ns) molecular dynamics trajectory are dependent on the particular coordinates chosen as a starting point for the simulation.

Local structure and dynamic properties of molecules in anisotropic liquids extracted from molecular dynamic simulations. The case of acetonitrile in polyacrylamide hydrogels

The diversity of the local mobility of probe molecules in hydrogels, caused by local structural inhomogeneity has been investigated by molecular simulation. Molecular dynamics (MD) is used, to examine both qualitative concepts to get insight into molecular processes in local structures and quantitative concepts to clarify and calculate the local MD in anisotropic liquids. We extend the global correlation concept, to calculate the reorientational correlation on pieces of trajectories of individual probe molecules in equivalent local environments. It shows that, as experimental results indicate, local water structures exist around acetonitrile molecules in a water–acetonitrile system and are conserved in water-rich domains of a polyacrylamide (PAA)-hydrogel–acetonitrile system. Over and above that, local structures exist in water-poor regions of the PAA-hydrogel, where the dynamics of acetonitrile probe molecules slow down. An understanding at the atomic level of the variation in dynamics of acetonitrile in PAA-hydrogel is given. The averaged reorientational time over all time origins and all acetonitrile molecules in the simulation system reveals very good agreement with Raman spectroscopical data.

A Monte Carlo study of properties of protein-like heteropolymers

The structure of a polypeptide model by means of the Monte Carlo method has been studied. The model chains consisting of two kinds of residues (hydrophobic and hydrophilic) were confined on the (3 1 0) hybrid lattice. The residues interacted with the long-range contact potential. The short-range potential was also used by introducing the preferences of conformations corresponding to the helical structure. Simulations of the coil-to-globule collapse have been done by an annealing process starting from high-temperature structures and then gradual cooling of the system. It has been found that in a case of a helical pattern –HHPPHPP– the collapsed chains consisted of longer helical fragments. The results show the influence of the potentials used in a model on final static and dynamic properties of molecules.

Spectroscopic Studies of the Triplet-state 4 He 2 * Molecules in Superfluid Helium Up to the Solidification Pressure

We report detailed investigations of the absorption spectra of the triplet excimer helium molecules in superfluid helium in a wide pressure range. The width of the (0–0) a → c absorption band shows peculiar dependence on helium pressure with maximum near 24 bar. Studies of dynamic properties of molecules in the controlled geometry allow for the first time to perform independent measurements of their mutual decay coefficient, light absorption cross section and probability of molecules formation in the ions recombination process.

A Molecular Dynamics Simulation of Pressure Induced Liquid-Plastic Phase Transition of Pure Cyclohexane and Cyclohexane in Silica Cavities

Abstract Molecular dynamics simulations at temperature 313 K and pressures up to 4 kbar for six-centre Lennard-Jones model of C6H12 are reported. The calculations are performed for pure cyclohexane and cyclohexane in pores. A cavity is obtained by placing silica clusters at the corners of a cubic box. Two cavities of diameter of about 30 A and 50 A are considered. Thermodynamic, structural and dynamic properties of molecule confined to the pores are compared with the results for pure cyclohexane. Changes of molecular behaviour with diminishing pore size are observed and the liquid-plastic transition point shifts to higher pressures.

Dynamical properties of molecules physisorbed on a metal particle

The response potential of a small metallic sphere to a fluctuating dipole moment is determined from spherical-tensor theory. The non-local character of the electron response is included by using the random-phase approximation and by introducing a jellium model. The response field obtained from this calculation allows us to define a new expression of the effective linear polarisability of a molecule physisorbed on a metal particle. Two limiting cases are then considered: the dielectric approximation and the non-local homogeneous one.