Harmonic Force Field Research Articles

Implementing reactivity in molecular dynamics simulations with harmonic force fields

The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility, reliability, and cost. We introduce a method for reactive molecular dynamics simulations using a clean replacement of non-reactive classical harmonic bond potentials with reactive, energy-conserving Morse potentials, called the Reactive INTERFACE Force Field (IFF-R). IFF-R is compatible with force fields for organic and inorganic compounds such as IFF, CHARMM, PCFF, OPLS-AA, and AMBER. Bond dissociation is enabled by three interpretable Morse parameters per bond type and zero energy upon disconnect. Use cases for bond breaking in molecules, failure of polymers, carbon nanostructures, proteins, composite materials, and metals are shown. The simulation of bond forming reactions is included via template-based methods. IFF-R maintains the accuracy of the corresponding non-reactive force fields and is about 30 times faster than prior reactive simulation methods.

Harmonic Force Fields and Force Constants of Prebiotic Aminomalononitrile and Diaminomalononitrile by Using DFT and SQMFF Calculations

Harmonic Force Fields and Force Constants of Prebiotic Aminomalononitrile and Diaminomalononitrile by Using DFT and SQMFF Calculations

Structural and Vibrational Study of Species Derived from Non-Steroidal Anti-inflammatory Agent Piroxicam Using DFT and Harmonic Force Fields Calculations

Structural and Vibrational Study of Species Derived from Non-Steroidal Anti-inflammatory Agent Piroxicam Using DFT and Harmonic Force Fields Calculations

Vibrational characterization of active drug to the treatment of chagas disease, benznidazole by using force fields and internal coordinates

Two experimental structures of benznidazole active drug used to the treatment of Chagas disease have been structurally characterized and its vibrational spectra completely assigned combining B3LYP/6-311++G** calculations with the experimental FT-IR and FT-Raman spectra and the SQMFF methodology. The most stable conformer of benznidazole found in the study of the potential energy surface is in agreement with that experimentally observed by X-ray diffraction at room temperature while the other one was observed with the heating up to 195 ºC. Both differs in the positions of CH2 groups of acetamide fragment. Their structural properties in gas phase and ethanol solution were computed by using natural bond orbital (NBO), atoms in molecules (AIM), Merz-Kollman (MK) charges, molecular electrostatic potentials (MEP) and frontier orbitals calculations by using the hybrid B3LYP method and the 6-31G* and 6-311++G** basis sets. Additional WB97XD/6-311++G** calculations show that the energy values optimized for the most stable species in both media present lower values than the obtained with the B3LYP/6-31G* method. The vibrational assignments for those two conformers in both media were obtained from their corresponding harmonic force fields together with the scaled force constants.

Impact of Different Groups on Properties of All Members of the Series of 1-X-Benzotriazole Derivatives (X= H, OH, NH2, Cl and CH3)

Here, the impact of different groups on the geometrical parameters, dipole moments, atomic charges, stabilization and solvation energies, molecular electrostatic potentials, densities rings, positions IR and UV bands and NMR chemical shifts of all members of the series of 1X-benzotriazole derivatives (X= H, CH3, Cl, NH2 and OH) have been investigated by using hybrid B3LYP/6-311++G** calculations because, so far, correlations among their properties neither the vibrational analyses are reported yet. The polarity of N-X bonds, electronegativity, donor/acceptor characteristics of the different X groups were analysed for all members. The polarity of N1-X4 bonds have influence on dipole moments, volumes and on bond lengths of both rings while the chlorinated derivative has a higher reactivity due to its higher global electrophilicity index. NBO and AIM studies reveal the strong influence of Cl on densities of both rings of CBT and, on this derivative. Harmonic force fields evidence very good correlations between stretching force constants and assignments.

Structural, harmonic force field and vibrational studies of cholinesterase inhibitor tacrine used for treatment of Alzheimer's disease

Different structures of free base (FB), two cationic forms (CA) and three hydrochloride forms (HCl) of cholinesterase inhibitor tacrine used for treatment of Alzheimer ’s disease was evaluated using hybrid B3LYP calculations in order to perform their complete vibrational assignments using the scaled harmonic force fields. Structures of anhydrous form of tacrine have been optimized in gas phase and in aqueous solution. The structure of form III HCl is in agreement with the experimental determined by X-ray diffraction while the predicted IR, Raman, 1H– 13C NMR and UV spectra show good correlations with the corresponding experimental ones. Energy values show that the three forms of HCl can exist in both media because these energetic values decrease from 35.15 kJ/mol in gas phase to 5.51 kJ/mol in solution. For the most stable species of tacrine, the following stability order using natural bond orbital (NBO) studies was found: form I HCl > form III HCl > form I CA > FB. CA presents the higher solvation energy value, as reported for hydrochloride species of alkaloids and antihypertensive agents. The structural parameters of form III of HCl present better concordance and corresponds to that experimental observed in the solid phase. Higher topological properties of form III together with the strong N2–H26⋯Cl31 interaction could justify the presence of this form in the solid phase and in solution and the higher stabilities in both media. The gap values support the higher reactivity of form III while FB is the less reactive species in both media. Complete vibrational assignments for FB, CA and HCl species together with the corresponding scaled force constants are reported.

Insights into structural and vibrational characteristics of 1-methoxy-4-[2-(phenylsulfonyl)vinyl]benzene: An application of experimental vibrational spectroscopy and density functional theory

Fourier transform infrared and Raman spectra, in the spectral range 4000- 400 and 4000–50 cm−1, respectively, were measured for 1‑methoxy-4-[2-(phenylsulfonyl)vinyl]benzene (MPB). Initial values of torsion angles around five flexible bonds C1-S, S-C15, C17-C19, C22-O and OC30 (see Fig. 1 for numbering), essential for starting geometry optimization, were determined using "bond-pairing method" proposed earlier by us. Optimized structure parameters, harmonic general valence force field, vibrational fundamentals, potential energy distribution and infrared and Raman band intensities were determined using density functional theory, employing B3LYP/ 6–311++G(d,p) formalism. Good agreement was found, between measured and computed quantities investigated here. The r.m.s error between experimental and theoretical vibrational wavenumbers was 8.6 cm−1, for MPB. With the help of PED and eigenvectors, all vibrational fundamentals of the molecule were assigned unambiguously for the first time.

Anharmonic Correction to Free Energy Barriers from DFT-Based Molecular Dynamics Using Constrained Thermodynamic Integration.

For the calculation of anharmonic contributions to free energy barriers, constrained thermodynamic λ-path integration (λ-TI) from a harmonic reference force field to density functional theory is presented as an alternative to the established Blue Moon ensemble method (ξ-TI), in which free energy gradients along the reaction coordinate ξ are integrated. With good agreement in all cases, the λ-TI method is benchmarked against the ξ-TI method for several reactions, including the internal CH3 group rotation in ethane, a nucleophilic substitution of CH3Cl, a retro-Diels-Alder reaction, and a proton transfer in zeolite H-SSZ-13. An advantage of λ-TI is that one can use virtually any reference state to compute anharmonic contributions to reaction free energies or free energy barriers. This is particularly relevant for catalysis, where it is now possible to compute anharmonic corrections to the free energy of a transition state relative to any reference, for example, the most stable state of the active site and the reactants in the gas phase. This is in contrast to ξ-TI, where free energy barriers can only be computed relative to an initial state with all reactants coadsorbed. Finally, the Bennett acceptance ratio method combined with λ-TI is demonstrated to reduce the number of required integration grid points with tolerable accuracy, favoring thus λ-TI over ξ-TI in terms of computational efficiency.

Toward an efficient implementation of internally contracted coupled-cluster methods.

A new implementation of the internally contracted multireference coupled-cluster with singles and doubles (icMRCCSD) method is presented. The new code employs an efficient tensor contraction kernel and can also avoid full four-external integral transformations, which significantly extends the scope of the applicability of icMRCCSD. The new implementation is currently restricted to the simple case of two active electrons in two orbitals and also supports the computation of spin-adapted doublet and triplet coupled-cluster wavefunctions. This contribution describes the basic approach for the automated derivation of working equations and benchmarks the current code against efficient implementations of standard methods, such as single-reference coupled-cluster singles and doubles (CCSD) and internally contracted multireference configuration interaction (icMRCI). Run times for linearized variants of icMRCCSD are only twice as long as comparable CCSD runs and similar to those of the icMRCI implementation, while non-linear terms of more complete variants of icMRCCSD lead to an order of magnitude longer computation times. Nevertheless, the new code allows for computations at larger scales than it was possible previously, with less demands on memory and disk-space resources. This is exemplified by numerical structure optimizations and harmonic force field determinations of NC2H5 isomers and the singlet and triplet states of m-benzyne. In addition, the exchange coupling of a dinuclear copper complex is determined. This work also defines a new commutator approximation for icMRCCSD, which includes all terms that are also present in the single-reference CCSD method, thus yielding a consistent pair of single-reference and multireference coupled-cluster methods.

A quinoline-benzotriazole derivative: Synthesis, crystal structure and characterization by using spectroscopic, DFT and molecular docking methods

In this research, FT-IR, NMR (1H &13C), mass spectrometry and single-crystal X-ray diffraction has been used to characterize the synthesized 5-((1H-benzo[d][1,2,3]triazol-1-yl)methyl)quinolin-8-ol (DD2) derivative. B3LYP calculations with the 6-31G* and 6–311++G** basis sets have shown that the most stable C2 structure in gas phase and aqueous solution is in agreement with the experimental determined by X-ray diffraction. Higher dipole moments for C2 in aqueous solution, predicted with both methods, are probably related to its higher stability resulting higher volume contraction (ΔV −1.0 Å3) in solution with the B3LYP/6-31G* method. Similar behaviours in the Mulliken and NPA charges but different from MK charges are observed. Bond orders studies reveal that the O15-H16···N17 bonds are present in both media, as was experimentally observed in the solid state. MEP surfaces have evidenced nucleophilic sites on N of triazol ring while weak electrophilic ones on aromatic H of three rings being the H atom of OH the most labile. Gap values support a lower reactivity of C2 in solution, in agreement with the higher stability evidenced by AIM analyses. The higher electronic density on triazol ring could justify that C2 is unstable in solution, as revealed by NBO analyses. Complete assignments of 93 expected vibration normal modes of C2 and a set of scaled force constants were obtained in both media by using harmonic force fields. Comparisons between experimental and theoretical infrared and 1H- and 13C NMR spectra show reasonable concordances. Intermolecular interactions in the crystal packing of DD2 were studied by using Hirshfeld surface analysis. Furthermore, DD2 was investigated against two targets of SARS-CoV-2 (PDB ID: 6WCF and PDB ID: 6Y84) by using molecular docking studies. Finally, drug likeness and ADME properties of DD2 were researched and compared with hydroxychloroquine, remdesivir, oseltamivir, lopinavir, ritonavir molecules associated as SARS-CoV-2 inhibitors.

Effect of external fields on pattern formation of charged grains in plasma

AbstractTwo‐dimensional cluster and pattern formation by charged grains in plasma under external harmonic force and transverse magnetic field is investigated using molecular dynamics simulation. It is found that, as a result of the Yukawa‐like grain‐grain interaction and the external fields, the asymptotic quasistationary state of an initially homogeneous and Maxwellian velocity distributed grain system can be a disk cluster with the grain trajectories having flowery zonal patterns.

A combined study on structures and vibrational spectra of the antiviral rimantadine using SQMFF and DFT calculations

In this research, a combined study on structures and vibrational spectra of antiviral rimantadine have been performed using hybrid B3LYP/6–311++G∗∗ calculations and the scaled quantum force field (SQMFF) procedure. Harmonic force fields and scaled force constants of Free Base (FB), Cationic (CA) and Hydrochloride (HCl) species derived from the antiviral rimantadine have been calculated in gas phase and in aqueous solution using normal internal coordinates and scaling factors. Good correlations were acquired comparing the theoretical IR, Raman, 1H– 13C-NMR and UV spectra of three species with the analogous experimental ones, suggesting probably, the presence of all them in both phases. The main force constants of three species have evidenced lower values than the corresponding to antiviral amantadine. The ionic character of N1–H33⋯Cl36 bond of HCl species in aqueous solution evidence positive Mulliken charge on N1 atom indicating that this species is as CA one. Rimantadine presents higher solvation energies in water than other antiviral species, such as chloroquin, niclosamide, cidofovir and brincidofovir. The FB and HCl species of rimantadine are slightly less reactive than the corresponding to amantadine while the opposite is observed for the CA species. The predicted ECD spectra for the FB and CA species show positive Cotton effect different from the negative observed for the HCl one. These different behaviours of three species of rimantadine could probably explain the differences observed in the intensities of bands predicted in the electronic spectra of these species.

Brownian motion with time-dependent friction and single-particle dynamics in liquids.

A microscopic theory of molecular motion in classical monatomic liquids, proposed by Glass and Rice [Phys. Rev. 176, 239 (1968)10.1103/PhysRev.176.239], is revisited and extended to incorporate the dynamic friction in the Brownian description of the atomic diffusion in a mean-time-dependent harmonic force field. A modified, non-Markovian Langevin equation is utilized to derive an equation of motion for the velocity autocorrelation function with time-dependent friction coefficient. Numerical solution of the equation gives an excellent account of the velocity autocorrelation function in Lennard-Jones liquids, liquid alkali, and transition metals over a broad range of density and temperature. Derivation of the equation of motion leads to a self-consistent expression for the time dependence of friction coefficient. Our results demonstrate that the nature of time dependence of the friction coefficient changes dramatically with the liquid density. At low and moderate densities, the dynamic friction decays exponentially whereas it increases exponentially at high liquid densities. Our findings provide an opportunity for a different outlook of the Brownian description of atomic dynamics in liquids.

Behaviours of antiviral Oseltamivir in different media: DFT and SQMFF calculations.

The synthetic cyclohexenecarboxylate ester antiviral Oseltamivir (O) have been theoretically studied by B3LYP/6–311 + + G** calculations to estimate its reactivity and behaviour in gas and aqueous media. The most stable structure obtained in above media is consistent with that reported experimental for Oseltamivir phosphate. The solvation energy value of (O) in aqueous media is between the predicted for antiviral Idoxuridine and Ribavirin. Besides, (O) containing a NH2 group and NH group reveals lower solvation energy compared with other antiviral agents with an NH2 group, such as Ribavirin, Cidofovir, and Brincidofovir. Atomic charges on N and O atoms in acceptors and donor groups reveal different behaviours in both media, while the natural bond orbital (NBO) studies show a raised stability of (O) in aqueous solution. This latter resulted is in concordance with the lower reactivity evidenced in water. Frontier orbital studies have revealed that (O) in gas phase has a very similar gap value to antiviral Cidofovir used against the ebola disease, while Chloroquine in the two media are more reactive than (O). This study will allow to identify (O) by using vibrational spectroscopy because the 144 vibration modes expected have been assigned using the harmonic force fields calculated from the scaled mechanical force field methodology (SQMFF). Scaled force constants for (O) in the mentioned media are also reported for first time. Due to hydration of the C = O and NH2 groups by solvent molecules, the calculations in solution produce variations not only in the IR wavenumbers bands, but also in their intensities.Graphical abstract Supplementary InformationThe online version contains supplementary material available at 10.1007/s00894-021-04962-3.

Time-squeezing and time-expanding transformations in harmonic force fields.

A variety of real life phenomena exhibit complex time-inhomogeneous nonlinear diffusive motion in the presence of an external harmonic force. In capturing the characteristics of such dynamics, the class of Ornstein-Uhlenbeck processes, with its physical time appropriately modulated, has long been regarded as the most relevant model on the basis of its mean reversion property. In this paper, we contrast two similar, yet definitely different, time-changing mechanisms in harmonic force fields by systematically deriving and presenting a variety of key properties all at once, that is, whether or not and how those time-changing mechanisms affect the characteristics of mean-reverting diffusion through sample path properties, the marginal probability density function, the asymptotic degeneracy of increments, the stationary law, the second-order structure, and the ensemble- and time-averaged mean square displacements. Some of those properties turn out rather counter-intuitive due to, or irrespective of, possible degeneracy of time-changing mechanisms in the long run. In light of those illustrative comparisons, we examine whether such time-changing operations are worth the additional operational cost, relative to physically relevant characteristics induced, and deduce practical implications and precautions from modeling and inference perspectives, for instance, on the experimental setup involving those anomalous diffusion processes, such as the observation start time and stepsize when measuring mean square displacements, so as to preclude potentially misleading results and paradoxical interpretations.

Reply to a Comment on “The Nature of Chalcogen‐Bonding‐Type Tellurium–Nitrogen Interactions”

AbstractWe reply to the comment by J.‐M. Mewes, A. Hansen and S. Grimme (MHG), who challenged the accuracy of our re value for the N⋅⋅⋅Te distance in (C6F5)Te(CH2)3NMe2 determined by gas electron diffraction (GED). We conclusively demonstrate that MHG′s quoted reference calculations are less accurate than they claim for solid state and gas phase. We show by higher level calculations, that we did not miss substantial contributions from open‐chain conformers. Refinements on simulated scattering data show that such contributions would have had only an almost negligible effect on re(N⋅⋅⋅Te). MHG suggested the use of a H0‐tuned GFN method for calculating vibrational corrections ra−re, but this did not change these values substantially. Alternative amplitude calculations using higher level analytic harmonic and numeric cubic force fields (PBE0‐D3BJ/def2‐TZVP) yield a GED value for re(N⋅⋅⋅Te)=2.852(25) Å that is well within the experimental error of our original value 2.918(31) Å but far from the 2.67(8) Å predicted by MHG. A now improved error estimation accounts for inaccuracies in the calculated auxiliary values. The gas/solid difference of the weak N⋅⋅⋅Te interaction is in a realistic range compared to other systems involving weak chemical interactions.

Cryogenic Messenger-IR Ion Spectroscopy Study of Phenol & Aniline Molecular Ions and of the common Fragment Ion [C5H6][rad]+ formed by EI-MS

Molecular ions of phenol and aniline as well as the fragment ion at m/z 66 formed by electron ionization are examined with cryogenic messenger-IR ion spectroscopy and theory. According to the recorded IR spectra aromatic ground state molecular ions of phenol and aniline are clearly identified. Similar to earlier reports our new set of spectroscopic and computational results supports the assumption that tautomeric molecular ions of phenol and aniline are only short-lived intermediates in the reaction path to the ultimate CO loss reaction product of phenol as well as the HNC loss product of aniline. Even the present cryogenic messenger-IR ion spectroscopy approach failed to collect spectroscopic evidence of the intermediate presence of these elusive tautomers of phenol and aniline molecular ions. However, our study clearly shows that the electron ionization mass spectrometry dissociation product ion of phenol and aniline at m/z 66 is the cyclopentadiene radical cation [C5H6]+ for the presence of which convincing spectroscopic evidence could be collected proving the structure assignment and identification. All messenger-IR ion spectroscopy experiments were conducted on a cryogenic 22-pole ion trap with the use of neon atoms for tagging. The MS instrument was coupled to a free electron laser delivering wavelength tunable IR radiation for spectroscopy. Harmonic and anharmonic force field calculations complement the experiments and support band assignments of the recorded IR spectra and general data interpretation.

Experimental and quantum-chemical characterization of heavy carbon subchalcogenides: Infrared detection of SeC3Se

High-resolution infrared studies of laser ablation products from carbon-selenium targets have revealed a new vibrational band at 2057 cm−1 that is identified as the ν3 vibrational fundamental of the SeC3Se cluster. Because of the rich isotopic composition of selenium and the heavy nuclear masses involved, the vibrational band shows a relatively compact and complex structure despite the simple linear geometric arrangement. Overall, rotational-vibrational lines of six isotopologues could be assigned and fitted permitting the derivation of an accurate selenium-carbon bond length.Spectroscopic analysis has been greatly supported by high-level quantum-chemical calculations of the molecular structure and the harmonic and anharmonic force fields performed at the CCSD(T) level of theory. Scalar-relativistic effects on the molecular structure were also considered but found of little importance.

Synthesis, molecular structure, and properties of DABCO bromide based ionic liquid combining spectroscopic studies with DFT calculations

Through N-alkylation of 1,4-diazabicyclo [2.2.2] octane with 1-bromooctane a new ionic liquid, namely 1‐octyl‐1,4‐diazabicyclo [2.2.2] octan‐1‐ium Bromide [C8DABCO+][Br−] has been synthesized and characterized by FT-IR, FT-Raman and by 1H and 13C-NMR spectroscopies. Three ionic C-H•••Br bonds were predicted by natural bond orbital (NBO), atoms in molecules (AIM) calculations and bond orders but a monodentate coordination between cation and anion is suggested because only one of them has higher energy and lower distance. The effect of Br on properties of IL is clearly observed by the change in orientation and direction of dipole moment vector in the IL, as compared with the cation. NBO studies reveal that the Br anion strongly stabilizes to cation to form the IL. The complete vibrational assignments of 129 and 132 vibration modes expected for the cation and its IL were performed by using two harmonic force fields with the SQMFF methodology and transferable scaling factors. The scaled harmonic force constants were also reported for both species. The Br confers a higher reactivity to [C8DABCO+][Br−], as suggested by analyses of frontier orbitals. Reasonable correlations were found between the experimental IR, Raman and NMR spectra and the corresponding theoretical ones.

Synthesis, thermal properties, vibrational spectra and computational studies of Trioctylmethylammonium bis(trifluoromethylsulfonyl)imide ionic liquid

In this work, Aliquat 336 ([Aliquat+]) based ionic liquids containing the fluorinated anion bis(trifluoromethylsulfonyl)imide [NTf2−] was successfully prepared by the anionic exchange replacement of the chloride anion. The reaction of lithium bis(trifluoromethylsulfonyl)imide with N-Methyl-N,N,N-trioctylammonium chloride ([N1,8,8,8][Cl] in water lead to the corresponding IL, namely ([Aliquat+][NTf2−]). The obtained ionic liquid was characterized by using infrared and Raman spectra and its structure was confirmed by 1H NMR, 13C NMR, and 19F-NMR. The thermal properties were investigated by two complementary thermal analysis techniques: TGA and DTA. A hexadentate coordination mode between cation-anion was predicted by atoms in molecules (AIM) studies for the [Aliquat+][NTf2−] IL by using B3LYP/6–31G* calculations where three O atoms of the anion in Cis conformation are linked to six H atoms of cation by S-O•••H interactions. Changes in the bond orders of S and O atoms of the cation supported such observations. The predicted cation-anion distances were in the range 2.30–2.60 Å. The harmonic force fields of cation and anion were calculated and the complete assignments were performed for both species while the most important bands observed in the infrared and Raman spectra of the IL were assigned. In addition, the scaled force constants of cation and anion of the IL were also reported.