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2. Implementation of the locally renormalized CCSD(T) approaches for arbitrary reference function.
- Author
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Kowalski, Karol
- Subjects
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CHEMICAL reagents , *INDICATORS & test-papers , *ABDERHALDEN reaction , *ACTIVE metals , *ALKYLATING agents , *BIOLOGICAL reagents - Abstract
Several new variants of the locally-renormalized coupled-cluster (CC) approaches that account for the effect of triples (LR-CCSD(T)) have been formulated and implemented for arbitrary reference states using the TENSOR CONTRACTION ENGINE functionality, enabling the automatic generation of an efficient parallel code. Deeply rooted in the recently derived numerator–denominator-connected (NDC) expansion for the ground-state energy [K. Kowalski and P. Piecuch, J. Chem. Phys. 122, 074107 (2005)], LR-CCSD(T) approximations use, in analogy to the completely renormalized CCSD(T) (CR-CCSD(T)) approach, the three-body moments in constructing the noniterative corrections to the energies obtained in CC calculations with singles and doubles (CCSD). In contrast to the CR-CCSD(T) method, the LR-CCSD(T) approaches discussed in this paper employ local denominators, which assure the additive separability of the energies in the noninteracting system limit when the localized occupied spin-orbitals are employed in the CCSD and LR-CCSD(T) calculations. As clearly demonstrated on several challenging examples, including breaking the bonds of the F2, N2, and CN molecules, the LR-CCSD(T) approaches are capable of providing a highly accurate description of the entire potential-energy surface (PES), while maintaining the characteristic N7scaling of the ubiquitous CCSD(T) approach. Moreover, as illustrated numerically for the ozone molecule, the LR-CCSD(T) approaches yield highly competitive values for a number of equilibrium properties including bond lengths, angles, and harmonic frequencies. [ABSTRACT FROM AUTHOR]
- Published
- 2005
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3. Comments on a paper by Straub, Borkovec, and Berne.
- Author
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Zwanzig, Robert
- Subjects
- *
COMPUTER simulation , *MARKOV processes , *PERTURBATION theory - Abstract
The paper referred to in the title, in J. Chem. Phys. 84, 1788 (1986), presented results of computer simulations of non-Markovian barrier crossing dynamics, and compared these results with various theoretical predictions. One comment made here is that the observed limited applicability of the Grote–Hynes theory can be explained by singular perturbation theory. The other comment concerns the importance of a second constant of the motion when the non-Markovian friction has a very long relaxation time. [ABSTRACT FROM AUTHOR]
- Published
- 1987
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4. Phase separation and aggregation in multiblock chains.
- Author
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Panagiotopoulos, Athanassios Z.
- Subjects
PHASE separation ,MONTE Carlo method ,PHASE transitions ,GAS condensate reservoirs ,BLOCKCHAINS - Abstract
This paper focuses on phase and aggregation behavior for linear chains composed of blocks of hydrophilic and hydrophobic segments. Phase and conformational transitions of patterned chains are relevant for understanding liquid–liquid separation of biomolecular condensates, which play a prominent role in cellular biophysics and for surfactant and polymer applications. Previous studies of simple models for multiblock chains have shown that, depending on the sequence pattern and chain length, such systems can fall into one of two categories: displaying either phase separation or aggregation into finite-size clusters. The key new result of this paper is that both formation of finite-size aggregates and phase separation can be observed for certain chain architectures at appropriate conditions of temperature and concentration. For such systems, a bulk dense liquid condenses from a dilute phase that already contains multi-chain finite-size aggregates. The computational approach used in this study involves several distinct steps using histogram-reweighting grand canonical Monte Carlo simulations, which are described in some level of detail. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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5. Reactivity indicators for degenerate states in the density-functional theoretic chemical reactivity theory.
- Author
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Cárdenas, Carlos, Ayers, Paul W., and Cedillo, Andrés
- Subjects
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REACTIVITY (Chemistry) , *INDICATORS & test-papers , *DENSITY functionals , *QUANTUM perturbations , *MOLECULAR orbitals , *POTENTIAL energy surfaces , *THEORY of distributions (Functional analysis) - Abstract
Density-functional-theory-based chemical reactivity indicators are formulated for degenerate and near-degenerate ground states. For degenerate states, the functional derivatives of the energy with respect to the external potential do not exist, and must be replaced by the weaker concept of functional variation. The resultant reactivity indicators depend on the specific perturbation. Because it is sometimes impractical to compute reactivity indicators for a specific perturbation, we consider two special cases: point-charge perturbations and Dirac delta function perturbations. The Dirac delta function perturbations provide upper bounds on the chemical reactivity. Reactivity indicators using the common used 'average of degenerate states approximation' for degenerate states provide a lower bound on the chemical reactivity. Unfortunately, this lower bound is often extremely weak. Approximate formulas for the reactivity indicators within the frontier-molecular-orbital approximation and special cases (two or three degenerate spatial orbitals) are presented in the supplementary material. One remarkable feature that arises in the frontier molecular orbital approximation, and presumably also in the exact theory, is that removing electrons sometimes causes the electron density to increase at the location of a negative (attractive) Dirac delta function perturbation. That is, the energetic response to a reduction in the external potential can increase even when the number of electrons decreases. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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6. Theory of vibrational energy relaxation in liquids: Vibrational–vibrational energy transfer.
- Author
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Adelman, S. A., Muralidhar, R., and Stote, R. H.
- Subjects
ENERGY transfer ,VIBRATIONAL spectra ,MOLECULAR spectra - Abstract
A theoretical treatment of the vibrational–vibrational (VV) contribution to the vibrational energy relaxation time T1 of a solute normal mode in a molecular solvent, which extends a previous treatment [S. A. Adelman, R. H. Stote, and R. Muralidhar, J. Chem. Phys. 99, 1320 (1993), henceforth called Paper I] of the vibrational–translational–rotational (VTR) contribution to T1, is outlined and expressions for this VV contribution, valid for the infinitely dilute diatomic solution, are presented. The treatment is based on the formula T1=β-1(ωl), where β(ω) is the friction kernel of the relaxing solute mode and where ωl is its liquid phase frequency. β(ω) is evaluated as the cosine transform of the autocorrelation function 〈F(t)Fĩ〉0v of the fluctuating generalized force exerted by the vibrating solvent on the solute normal mode coordinate conditional that this coordinate is fixed at its equilibrium value. 〈F(t)F〉0v is expressed as a superposition of the rigid solvent autocorrelation function 〈F(t)F〉0 and a correction which accounts for solvent vibrational motion. For diatomic solvents one has 〈F(t)F〉0v= 〈F(t)F〉0+NSMD(t) cos ωDt F(ΩD), where NS=number of solvent molecules, MD(t) is the vibrational force gradient autocorrelation function, ωD and ΩD are solvent molecule liquid phase frequencies, and F(Ω)=1/2hΩ-1 coth[hΩ/2kBT].The Gaussian model is assumed for 〈F(t)F〉0 and MD(t) yielding β(ω) as a superposition of a Gaussian centered at ω=0 which mediates VTR processes and a Gaussian centered at ω=ωD which mediates VV processes. Vector integral expressions for MD(t), ωD, and ΩD are presented which are similar to the expressions for ωl and 〈F(t)F〉0 given in Paper I. These expressions permit the evaluation of the VV contribution to T1 from the atomic masses, bondlengths, vibrational frequencies, and site–site interaction... [ABSTRACT FROM AUTHOR]
- Published
- 1993
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7. Nonlinear measurements of kinetics and generalized dynamical modes. II. Application to a simulation of solvation dynamics in an ionic liquid.
- Author
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Hodge, Stuart R., Corcelli, Steven A., and Berg, Mark A.
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IONIC liquids ,SOLVATION ,SUPERCOOLED liquids - Abstract
Solvation dynamics in ionic liquids show features that are often associated with supercooled liquids, including "stretched" nonexponential relaxation. To better understand the mechanism behind the stretching, the nonlinear mode-correlation methods proposed in Paper I [S. R. Hodge and M. A. Berg, J. Chem. Phys. 155, 024122 (2021)] are applied to a simulation of a prototypical ionic liquid. A full Green's function is recovered. In addition, specific tests for non-Gaussian dynamics are made. No deviations from Gaussian dynamics are found. This finding is incompatible with rate heterogeneity as a cause of the nonexponential relaxation and appears to be in conflict with an earlier multidimensional analysis of the same data. Although this conflict is not resolved here, this work does demonstrate the practicality of mode-correlation analysis in the face of finite datasets and calculations. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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8. Limitations and generalizations of the first order kinetics reaction expression for modeling diffusion-driven exchange: Implications on NMR exchange measurements.
- Author
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Ordinola, Alfredo, Özarslan, Evren, Bai, Ruiliang, and Herberthson, Magnus
- Subjects
CHEMICAL kinetics ,RATE coefficients (Chemistry) ,MAGNETIC relaxation ,MAGNETIC resonance ,GENERALIZATION - Abstract
The study and modeling of water exchange in complex media using different applications of diffusion and relaxation magnetic resonance (MR) have been of interest in recent years. Most models attempt to describe this process using a first order kinetics expression, which is appropriate to describe chemical exchange; however, it may not be suitable to describe diffusion-driven exchange since it has no direct relationship to diffusion dynamics of water molecules. In this paper, these limitations are addressed through a more general exchange expression that does consider such important properties. This exchange fraction expression features a multi-exponential recovery at short times and a mono-exponential decay at long times, both of which are not captured by the first order kinetics expression. Furthermore, simplified exchange expressions containing partial information of the analyzed system's diffusion and relaxation processes and geometry are proposed, which can potentially be employed in already established estimation protocols. Finally, exchange fractions estimated from simulated MR data and derived here were compared, showing qualitative similarities but quantitative differences, suggesting that the features of the derived exchange fraction in this paper can be partially recovered by employing an existing estimation framework. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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9. Fractional Extended Diffusion Theory to capture anomalous relaxation from biased/accelerated molecular simulations.
- Author
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Rapallo, Arnaldo
- Subjects
BROWNIAN motion ,MOLECULAR rotation ,ROTATIONAL motion ,STATISTICAL correlation ,PEPTIDES ,MOLECULAR dynamics ,GENERALIZATION - Abstract
Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A. Rapallo et al., J. Comput. Chem. 42, 586–599 (2021)], it has been shown how the coupling of BAMS (which destroys the dynamics but allows to calculate average properties) with Extended Diffusion Theory (EDT) (which requires input appropriate equilibrium averages calculated over the BAMS trajectories) allows to effectively use the Smoluchowski equation to calculate the orientational time correlation function of the head–tail unit vector defined over a peptide in water solution. Orientational relaxation of this vector is the result of the coupling of internal molecular motions with overall molecular rotation, and it was very well described by correlation functions expressed in terms of weighted sums of suitable time-exponentially decaying functions, in agreement with a Brownian diffusive regime. However, situations occur where exponentially decaying functions are no longer appropriate to capture the actual dynamical behavior, which exhibits persistent long time correlations, compatible with the so called subdiffusive regimes. In this paper, a generalization of EDT will be given, exploiting a fractional Smoluchowski equation (FEDT) to capture the non-exponential character observed in the relaxation of intramolecular distances and molecular radius of gyration, whose dynamics depend on internal molecular motions only. The calculation methods, proper to EDT, are adapted to implement the generalization of the theory, and the resulting algorithm confirms FEDT as a tool of practical value in recovering dynamics from BAMS, to be used in general situations, involving both regular and anomalous diffusion regimes. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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10. NMR spectroscopy of a 18O-labeled rhodium paddlewheel complex: Isotope shifts, 103Rh–103Rh spin–spin coupling, and 103Rh singlet NMR.
- Author
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Harbor-Collins, Harry, Sabba, Mohamed, Bengs, Christian, Moustafa, Gamal, Leutzsch, Markus, and Levitt, Malcolm H.
- Subjects
ISOTOPE shift ,SPIN-spin coupling constants ,RHODIUM ,GYROMAGNETIC ratio ,NUCLEAR magnetic resonance ,CHEMICAL shift (Nuclear magnetic resonance) ,NUCLEAR magnetic resonance spectroscopy - Abstract
Despite the importance of rhodium complexes in catalysis, and the favorable 100% natural abundance of the spin-1/2
103 Rh nucleus, there are few reports of103 Rh nuclear magnetic resonance (NMR) parameters in the literature. In part, this is the consequence of the very low gyromagnetic ratio of103 Rh and its dismal NMR sensitivity. In a previous paper [Harbor-Collins et al., J. Chem. Phys. 159, 104 307 (2023)], we demonstrated an NMR methodology for1 H-enhanced103 Rh NMR and demonstrated an application to the103 Rh NMR of the dirhodium formate paddlewheel complex. In this paper, we employ selective18 O labeling to break the magnetic equivalence of the103 Rh spin pair of dirhodium formate. This allows the estimation of the103 Rh–103 Rh spin–spin coupling and provides access to the103 Rh singlet state. We present the first measurement of a18 O-induced103 Rh secondary isotope shift as well as the first instance of singlet order generated in a103 Rh spin pair. The field-dependence of103 Rh singlet relaxation is measured by field-cycling NMR experiments. [ABSTRACT FROM AUTHOR]- Published
- 2024
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11. Electronic spectroscopy of gemcitabine and derivatives for possible dual-action photodynamic therapy applications.
- Author
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Abdelgawwad, Abdelazim M. A., Roca-Sanjuán, Daniel, and Francés-Monerris, Antonio
- Subjects
PHOTODYNAMIC therapy ,GEMCITABINE ,SPIN-orbit coupling ,LIGHT absorption ,SPECTROMETRY ,REDSHIFT ,ATOMS - Abstract
In this paper, we explore the molecular basis of combining photodynamic therapy (PDT), a light-triggered targeted anticancer therapy, with the traditional chemotherapeutic properties of the well-known cytotoxic agent gemcitabine. A photosensitizer prerequisite is significant absorption of biocompatible light in the visible/near IR range, ideally between 600 and 1000 nm. We use highly accurate multiconfigurational CASSCF/MS-CASPT2/MM and TD-DFT methodologies to determine the absorption properties of a series of gemcitabine derivatives with the goal of red-shifting the UV absorption band toward the visible region and facilitating triplet state population. The choice of the substitutions and, thus, the rational design is based on important biochemical criteria and on derivatives whose synthesis is reported in the literature. The modifications tackled in this paper consist of: (i) substitution of the oxygen atom at O
2 position with heavier atoms (O → S and O → Se) to red shift the absorption band and increase the spin–orbit coupling, (ii) addition of a lipophilic chain at the N7 position to enhance transport into cancer cells and slow down gemcitabine metabolism, and (iii) attachment of aromatic systems at C5 position to enhance red shift further. Results indicate that the combination of these three chemical modifications markedly shifts the absorption spectrum toward the 500 nm region and beyond and drastically increases spin–orbit coupling values, two key PDT requirements. The obtained theoretical predictions encourage biological studies to further develop this anticancer approach. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
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12. Electronic spectroscopy of carbon chains (C2n+1, n = 7–10) of astrophysical importance. II. Quantum dynamics.
- Author
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Ghosh, Arpita, Reddy, S. Rajagopala, and Mahapatra, Susanta
- Subjects
QUANTUM theory ,LORENTZIAN function ,SPECTRUM analysis ,AB-initio calculations - Abstract
In continuation with Paper I [S. R. Reddy et al., J. Chem. Phys. 151, 054303 (2019)], the vibronic structure and dynamics of the 1 Σ u + electronic state of C
15 , C17 , C19 , and C21 chains in the coupled manifold of 1 Σ u + –1 Πg –1 Πu – 1 Σ g + electronic states have been investigated in this paper. The model vibronic Hamiltonian developed through extensive ab initio quantum chemistry calculations in Paper I is employed, and first principles nuclear dynamics calculations are carried out to obtain the photoabsorption band of the 1 Σ u + electronic state. Both time-independent and time-dependent quantum mechanical calculations are carried out to precisely locate the vibrational levels, assign them with the progression of vibrational modes, and elucidate the impact of both Renner-Teller and pseudo-Renner-Teller couplings on them. The nonradiative decay of the 1 Σ u + electronic state is studied, and it is found that the decay rate is comparable with the prediction made for them to be qualified as a carrier of diffuse interstellar bands in the literature. The theoretical results are found to be in good accord with the available experimental results. [ABSTRACT FROM AUTHOR]- Published
- 2019
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13. State of charge estimation for lithium-ion battery based on whale optimization algorithm and multi-kernel relevance vector machine.
- Author
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Chen, Kui, Zhou, Shuyuan, Liu, Kai, Gao, Guoqiang, and Wu, Guangning
- Subjects
MATHEMATICAL optimization ,ELECTRIC vehicle batteries ,LITHIUM-ion batteries ,ENERGY storage ,KERNEL functions ,SERVICE life - Abstract
Lithium–ion batteries are key elements of electric vehicles and energy storage systems, and their accurate State of Charge (SOC) estimation is momentous for battery energy management, safe operation, and extended service life. In this paper, the Multi-Kernel Relevance Vector Machine (MKRVM) and Whale Optimization Algorithm (WOA) are used to estimate the SOC of lithium–ion batteries under different operating conditions. In order to better learn and estimate the battery SOC, MKRVM is used to establish a model to estimate lithium–ion battery SOC. WOA is used to automatically adjust and optimize weights and kernel parameters of MKRVM to improve estimation accuracy. The proposed model is validated with three lithium–ion batteries under different operating conditions. In contrast to other optimization algorithms, WOA has a better optimization effect and can estimate the SOC more accurately. In contrast to the single kernel function, the proposed multi-kernel function greatly improves the precision of the SOC estimation model. In contrast to the traditional method, the WOA-MKRVM has a higher precision of SOC estimation. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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14. Infrared and Raman spectroscopy of carbohydrates. Paper V. Normal coordinate analysis of cellulose I.
- Author
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Cael, J. J., Gardner, K. H., Koenig, J. L., and Blackwell, J.
- Published
- 1975
- Full Text
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15. Computational optimal transport for molecular spectra: The semi-discrete case.
- Author
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Seifert, Nathan A., Prozument, Kirill, and Davis, Michael J.
- Subjects
MOLECULAR spectra ,ELECTRONIC spectra ,ABSORPTION spectra - Abstract
Comparing a discrete molecular spectrum to a continuous molecular spectrum in a quantitative manner is a challenging problem, for example, when attempting to fit a theoretical stick spectrum to a continuous spectrum. In this paper, the use of computational optimal transport is investigated for such a problem. In the optimal transport literature, the comparison of a discrete and a continuous spectrum is referred to as semi-discrete optimal transport and is a situation where a metric such as least-squares may be difficult to define except under special conditions. The merits of an optimal transport approach for this problem are investigated using the transport distance defined for the semi-discrete case. A tutorial on semi-discrete optimal transport for molecular spectra is included in this paper, and several well-chosen synthetic spectra are investigated to demonstrate the utility of computational optimal transport for the semi-discrete case. Among several types of investigations, we include calculations showing how the frequency resolution of the continuous spectrum affects the transport distance between a discrete and a continuous spectrum. We also use the transport distance to measure the distance between a continuous experimental electronic absorption spectrum of SO
2 and a theoretical stick spectrum for the same system. The comparison of the theoretical and experimental SO2 spectra also allows us to suggest a theoretical value for the band origin that is closer to the observed band origin than previous theoretical values. [ABSTRACT FROM AUTHOR]- Published
- 2022
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16. Time correlation function approach to liquid phase vibrational energy relaxation: H[sub 2] and D[sub 2] solutes in Ar solvent.
- Author
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Miller, David W. and Adelman, Steven A.
- Subjects
HALOGEN compounds ,VIBRATIONAL spectra ,SOLUTION (Chemistry) - Abstract
The theoretical treatment in Paper I [D. W. Miller and S. A. Adelman, J. Chem. Phys. 117, 2672, (2002), preceding paper] of the vibrational energy relaxation (VER) of low-frequency, large mass dihalogen solutes is extended to the VER of the high-frequency, small mass molecular hydrogen solutes H[sub 2] and D[sub 2] in a Lennard-Jones argon-like solvent. As in Paper I, values of the relaxation times T[sub 1] predicted by the theory are tested against molecular dynamics (MD) results and are found to be of semiquantitative accuracy. To start, it is noted that standard Lennard-Jones site-site potentials derived from macroscopic data can be very inaccurate in the steep repulsive slope region crucial for T[sub 1]. Thus, the H-Ar Lennard-Jones diameter σ[sub uv] is not taken from literature values but rather is chosen as σ[sub UV] = 1.39 Å, the value needed to make the theory reproduce the experimental H[sub 2]/Ar gas phase VER rate constant. Next, by MD simulation it is shown that the vibrational coordinate fluctuating force autocorrelation function 〈&Ftilde;(t)&Ftilde;〉[sub 0] of Paper I decays roughly an order of magnitude more rapidly for the molecular hydrogen solutions than for the dihalogen solutions. This result implies a relatively slow decay for the molecular hydrogen friction kernels β(ω) = (k[sub B]T)[sup -1] ∫[sup ∞, sub 0] 〈&Ftilde;(t)&Ftilde;〉[sub 0] cos ω tdt, yielding for the H[sub 2]/Ar and D[sub 2]/Ar systems at T= 150 K physical millisecond values for T[sub 1] =beta;[sup -1](ω) despite the high liquid phase vibrational frequencies ω[sub 1] of H[sub 2] and D[sub 2]. The rapid decay of 〈&Ftilde;(t)&Ftilde;&ran;[sub 0] is due to both the steepness of the repulsive slope of the H-Ar potential and the small masses of H and D. Thus, the small value chosen for σ[sub UV] is needed to avoid unphysically long T[sub 1]'s. Next, an analytical treatment of the H[sub 2]/D[sub... [ABSTRACT FROM AUTHOR]
- Published
- 2002
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17. 2020 JCP Emerging Investigator Special Collection.
- Author
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Ceriotti, Michele, Jensen, Lasse, Manolopoulos, David E., Martinez, Todd J., Michaelides, Angelos, Ogilvie, Jennifer P., Reichman, David R., Shi, Qiang, Straub, John E., Vega, Carlos, Wang, Lai-Sheng, Weiss, Emily, Zhu, Xiaoyang, Stein, Jennifer L., and Lian, Tianquan
- Subjects
ENERGY budget (Geophysics) ,PHYSICAL & theoretical chemistry ,STIMULATED Raman scattering ,MOLECULAR vibration ,THERMOCHEMISTRY ,NONEQUILIBRIUM statistical mechanics ,MEAN field theory - Abstract
Jiang and co-workers use high resolution STM to investigate the reaction and self-assembly of (3,6-dibromo-9,10-phenanthrenequinone, or DBPQ) molecules on Ag (100) and Ag (110) surfaces in order to understand the mechanism of bottom-up assembly on surfaces.[31] They show that, through the inclusion of multiple functional groups within a precursor molecule, it becomes possible to fabricate new low-dimensional materials with unique chemical, physical, and electronic properties. Herbst and Fransson consider the core-valence separation approximation that is often used in the calculation of core-level spectra.[5] They show how to quantify the errors in this approximation, thereby opening the door to error-quantified predictions relevant to x-ray spectroscopy. 153(16), 164108 (2020).10.1063/5.0019557 5 M. F. Herbst and T. Fransson, "Quantifying the error of the core-valence separation approximation", J. Chem. Phys. Zhu and co-workers tackle this problem for a model system containing a 2D semiconductor heterojunction and show convincingly the efficient hot electron transfer from photoexcited MoTe SB 2 sb to WS SB 2 sb .[30] This finding provides important insight into the competition between hot electron cooling and transfer at 2D semiconductor interfaces and suggests an intriguing possibility for the exploration of hot electron devices. [Extracted from the article]
- Published
- 2021
- Full Text
- View/download PDF
18. Computing excited OH stretch states of water dimer in 12D using contracted intermolecular and intramolecular basis functions.
- Author
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Wang, Xiao-Gang and Carrington Jr., Tucker
- Subjects
VIBRATIONAL spectra ,CESIUM isotopes ,MONOMERS ,CONTRACTS - Abstract
Due to the ubiquity and importance of water, water dimer has been intensively studied. Computing the (ro-)vibrational spectrum of water dimer is challenging. The potential has eight wells separated by low barriers, which makes harmonic approximations of limited utility. A variational approach is imperative, but difficult because there are 12 coupled vibrational coordinates. In this paper, we use a product contracted basis whose functions are products of intramolecular and intermolecular functions computed using an iterative eigensolver. An intermediate matrix F facilitates calculating matrix elements. Using F, it is possible to do calculations on a general potential without storing the potential on the full quadrature grid. We find that surprisingly many intermolecular functions are required. This is due to the importance of coupling between inter- and intra-molecular coordinates. The full G
16 symmetry of water dimer is exploited. We calculate, for the first time, monomer excited stretch states and compare P(1) transition frequencies with their experimental counterparts. We also compare with experimental vibrational shifts and tunneling splittings. Surprisingly, we find that the largest tunneling splitting, which does not involve the interchange of the two monomers, is smaller in the asymmetric stretch excited state than in the ground state. Differences between levels we compute and those obtained with a [6+6]D adiabatic approximation [Leforestier et al. J. Chem. Phys. 137 014305 (2012)] are ∼ 0.6 cm−1 for states without monomer excitation, ∼ 4 cm−1 for monomer excited bend states, and as large as ∼ 10 cm−1 for monomer excited stretch states. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
19. Crystal nucleation in a glass during relaxation well below Tg.
- Author
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Abyzov, Alexander S., Fokin, Vladimir M., Yuritsyn, Nikolay S., Nascimento, Marcio L. F., Schmelzer, Jürn W. P., and Zanotto, Edgar D.
- Subjects
CRYSTAL glass ,SUPERCOOLED liquids ,LITHIUM silicates ,RATE of nucleation ,GLASS transition temperature ,METASTABLE states ,CRYSTAL models - Abstract
Until quite recently, in almost all papers on crystal nucleation in glass-forming substances, it was assumed that nucleation proceeds in a completely relaxed supercooled liquid and, hence, at constant values of the critical parameters determining the nucleation rate for any given set of temperature, pressure, and composition. Here, we analyze the validity of this hypothesis for a model system by studying nucleation in a lithium silicate glass treated for very long times (up to 250 days) in deeply supercooled states, reaching 60 K below the laboratory glass transition temperature, T
g . At all temperatures in the considered range, T < Tg , we observed an enormous difference between the experimental number of nucleated crystals, N(t), and its theoretically expected value computed by assuming the metastable state of the relaxing glass has been reached. Analyzing the origin of this discrepancy, we confirmed that the key parameters determining the nucleation rates change with time as a result of the glass relaxation process. Finally, we demonstrate that, for temperatures below 683 K, this particular glass almost fully crystallizes prior to reaching the ultimate steady-state nucleation regime (e.g., at 663 K, it would take 176 years for the glass to reach 99% crystallization, while 2600 years would be needed for complete relaxation). This comprehensive study proves that structural relaxation strongly affects crystal nucleation in deeply supercooled states at temperatures well below Tg ; hence, this phenomenon has to be accounted for in any crystal nucleation model. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
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20. Understanding dynamics in coarse-grained models. II. Coarse-grained diffusion modeled using hard sphere theory.
- Author
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Jin, Jaehyeok, Schweizer, Kenneth S., and Voth, Gregory A.
- Subjects
SUPERCOOLED liquids ,SPHERES ,EQUATIONS of state ,DIFFUSION coefficients ,PERTURBATION theory ,MOLECULAR dynamics - Abstract
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of the scaling relationship was not possible due to the semi-empirical nature. In this second paper, an analytical excess entropy scaling relation is derived for bottom-up CG systems. At the single-site CG resolution, effective hard sphere systems are constructed that yield near-identical dynamical properties as the target CG systems by taking advantage of how hard sphere dynamics and excess entropy can be analytically expressed in terms of the liquid packing fraction. Inspired by classical equilibrium perturbation theories and recent advances in constructing hard sphere models for predicting activated dynamics of supercooled liquids, we propose a new approach for understanding the diffusion of molecular liquids in the normal regime using hard sphere reference fluids. The proposed "fluctuation matching" is designed to have the same amplitude of long wavelength density fluctuations (dimensionless compressibility) as the CG system. Utilizing the Enskog theory to derive an expression for hard sphere diffusion coefficients, a bridge between the CG dynamics and excess entropy is then established. The CG diffusion coefficient can be roughly estimated using various equations of the state, and an accurate prediction of accelerated CG dynamics at different temperatures is also possible in advance of running any CG simulation. By introducing another layer of coarsening, these findings provide a more rigorous method to assess excess entropy scaling and understand the accelerated CG dynamics of molecular fluids. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
21. Derivation and implementation of the optical rotation tensor for chiral crystals.
- Author
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Balduf, Ty and Caricato, Marco
- Subjects
OPTICAL rotation ,MOLECULAR clusters ,DENSITY functional theory ,CRYSTALS ,INTERMOLECULAR interactions - Abstract
This paper reports the derivation and implementation of the electric dipole-magnetic dipole and electric dipole-electric quadrupole polarizability tensors at the density functional theory level with periodic boundary conditions (DFT-PBC). These tensors are combined to evaluate the Buckingham/Dunn tensor that describes the optical rotation (OR) in oriented chiral systems. We describe several aspects of the derivation of the equations and present test calculations that verify the correctness of the tensor formulation and their implementation. The results show that the full OR tensor is completely origin invariant as for molecules and that PBC calculations match molecular cluster calculations on 1D chains. A preliminary investigation on the choice of density functional, basis set, and gauge indicates a similar dependence as for molecules: the functional is the primary factor that determines the OR magnitude, followed by the basis set and to a much smaller extent the choice of gauge. However, diffuse functions may be problematic for PBC calculations even if they are necessary for the molecular case. A comparison with experimental data of OR for the tartaric acid crystal shows reasonable agreement given the level of theory employed. The development presented in this paper offers the opportunity to simulate the OR of chiral crystalline materials with general-purpose DFT-PBC methods, which, in turn, may help to understand the role of intermolecular interactions on this sensitive electronic property. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
22. Synergetic enhancement effect of two-dimensional MoS2 nanosheets and metal organic framework-derived porous ZnO nanorods for photodegradation performance.
- Author
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Yin, Huimin, Zhou, Suyu, Liu, Junhui, and Huang, Mingju
- Subjects
MOLYBDENUM sulfides ,NANORODS ,METAL oxide semiconductors ,NANOSTRUCTURED materials ,ORGANOMETALLIC compounds ,ZINC oxide - Abstract
Two-dimensional transition metal dichalcogenides and semiconductor metal oxides have shown great potential in photocatalysis. However, their stability and efficiency need to be further improved. In this paper, porous ZnO nanorods with high specific surface area were prepared from metal-organic framework ZIF-8 by a simple hydrothermal method. A MoS
2 /ZnO composite was constructed by loading MoS2 onto the surface of porous ZnO nanorods. Compared with ZnO materials prepared by other methods, MoS2 /ZnO prepared in this paper exhibits superior photocatalytic performance. The enhanced photocatalytic activity of the MoS2 /ZnO composite can be attributed to the formation of heterojunctions and strong interaction between them, which greatly facilitate the separation of electrons and holes at the contact interface. In addition, due to the wide absorption region of the visible spectrum, MoS2 can greatly broaden the light absorption range of the material after the formation of the composite material, increase the utilization rate of visible light, and reduce the combination of electrons and holes. This study provides a new way to prepare cheap and efficient photocatalysts. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
23. Multimode vibrational dynamics and orientational effects in fluorescence-encoded infrared spectroscopy. II. Analysis of early-time signals.
- Author
-
Whaley-Mayda, Lukas, Guha, Abhirup, and Tokmakoff, Andrei
- Subjects
INFRARED spectroscopy ,VIBRONIC coupling ,SIGNALS & signaling ,NONLINEAR functions ,SPECTROMETRY - Abstract
Developing fluorescence-encoded infrared (FEIR) vibrational spectroscopy for single-molecule applications requires a detailed understanding of how the molecular response and external experimental parameters manifest in the detected signals. In Paper I [L. Whaley-Mayda, A. Guha, and A. Tokmakoff, J. Chem. Phys. 159, 194201 (2023)] we introduced a nonlinear response function theory to describe vibrational dynamics, vibronic coupling, and transition dipole orientation in FEIR experiments with ultrashort pulses. In this second paper, we apply the theory to investigate the role of intermode vibrational coherence, the orientation of vibrational and electronic transition dipoles, and the effects of finite pulse durations in experimental measurements. We focus on measurements at early encoding delays—where signal sizes are largest and therefore of most value for single-molecule experiments, but where many of these phenomena are most pronounced and can complicate the appearance of data. We compare experiments on coumarin dyes with finite-pulse response function simulations to explain the time-dependent behavior of FEIR spectra. The role of the orientational response is explored by analyzing polarization-dependent experiments and their ability to resolve relative dipole angles in the molecular frame. This work serves to demonstrate the molecular information content of FEIR experiments, and develop insight and guidelines for their interpretation. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
24. Multimode vibrational dynamics and orientational effects in fluorescence-encoded infrared spectroscopy. I. Response function theory.
- Author
-
Whaley-Mayda, Lukas, Guha, Abhirup, and Tokmakoff, Andrei
- Subjects
INFRARED spectroscopy ,OPTIMAL designs (Statistics) ,VIBRONIC coupling ,DIPOLE moments ,SINGLE molecules ,ULTRA-short pulsed lasers - Abstract
Fluorescence-encoded infrared (FEIR) spectroscopy is an emerging technique for performing vibrational spectroscopy in solution with detection sensitivity down to single molecules. FEIR experiments use ultrashort pulses to excite a fluorescent molecule's vibrational and electronic transitions in a sequential, time-resolved manner, and are therefore sensitive to intervening vibrational dynamics on the ground state, vibronic coupling, and the relative orientation of vibrational and electronic transition dipole moments. This series of papers presents a theoretical treatment of FEIR spectroscopy that describes these phenomena and examines their manifestation in experimental data. This first paper develops a nonlinear response function description of Fourier-transform FEIR experiments for a two-level electronic system coupled to multiple vibrations, which is then applied to interpret experimental measurements in the second paper [L. Whaley-Mayda et al., J. Chem. Phys. 159, 194202 (2023)]. Vibrational coherence between pairs of modes produce oscillatory features that interfere with the vibrations' population response in a manner dependent on the relative signs of their respective Franck–Condon wavefunction overlaps, leading to time-dependent distortions in FEIR spectra. The orientational response of population and coherence contributions are analyzed and the ability of polarization-dependent experiments to extract relative transition dipole angles is discussed. Overall, this work presents a framework for understanding the full spectroscopic information content of FEIR measurements to aid data interpretation and inform optimal experimental design. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
25. Polarization-dependent intensity ratios in double resonance spectroscopy.
- Author
-
Lehmann, Kevin K.
- Subjects
RESONANCE ,QUANTUM numbers ,DOPPLER broadening ,SPECTROMETRY - Abstract
Double Resonance is a powerful spectroscopic method that unambiguously assigns the rigorous quantum numbers of one state of a transition. However, there is often ambiguity as to the branch (ΔJ) of that transition. Spectroscopists have resolved this ambiguity by using the dependence of the double resonance intensity on the relative polarization directions of pump and probe radiation. However, published theoretical predictions for this ratio are based upon a weak (i.e., non-saturating) field approximation. This paper presents theoretical predictions for these intensity ratios for cases where the pump field is strongly saturating in the two limits of transitions dominated by homogeneous or of inhomogeneous broadening. Saturation reduces but does not eliminate the magnitude of the polarization effect (driving the intensity ratio closer to unity) even with strong pump saturation. For the case of an inhomogeneously broadened line, such as when Doppler broadened linewidth dominates over the power-broadened homogeneous line width, a large fraction of the low pump power polarization anisotropy remains. This paper reports predicted polarization ratios for both linear and circular pump and probe field polarizations. The present predictions are compared with experimental measurements on CH
4 ground state → ν3 → 3ν3 transitions recently reported by de Oliveira et al.63 and these are in better agreement than with the weak field predictions. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
26. Multicomponent solutions: Combining rules for multisolute osmotic virial coefficients.
- Author
-
Binyaminov, Hikmat and Elliott, Janet A. W.
- Subjects
OSMOTIC coefficients ,VIRIAL coefficients ,THERMODYNAMICS ,GIBBS' free energy ,SOLUTION (Chemistry) ,BINARY mixtures ,CAHN-Hilliard-Cook equation - Abstract
This paper presents an exploration of a specific type of a generalized multicomponent solution model, which appears to be first given by Saulov in the current explicit form. The assumptions of the underlying theory and a brief derivation of the main equation have been provided preliminarily for completeness and notational consistency. The resulting formulae for the Gibbs free energy of mixing and the chemical potentials are multivariate polynomials with physically meaningful coefficients and the mole fractions of the components as variables. With one additional assumption about the relative magnitudes of the solvent–solute and solute–solute interaction exchange energies, combining rules were obtained that express the mixed coefficients of the polynomial in terms of its pure coefficients. This was done by exploiting the mathematical structure of the asymmetric form of the solvent chemical potential equation. The combining rules allow one to calculate the thermodynamic properties of the solvent with multiple solutes from binary mixture data only (i.e., each solute with the solvent), and hence, are of practical importance. Furthermore, a connection was established between the osmotic virial coefficients derived in this work and the original osmotic virial coefficients of Hill found by employing a different procedure, illustrating the equivalency of what appears to be two different theories. A validation of the combining rules derived here has been provided in a separate paper where they were successfully used to predict the freezing points of ternary salt solutions of water. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
27. Understanding dynamics in coarse-grained models. III. Roles of rotational motion and translation-rotation coupling in coarse-grained dynamics.
- Author
-
Jin, Jaehyeok, Lee, Eok Kyun, and Voth, Gregory A.
- Subjects
ROTATIONAL diffusion ,TRANSLATIONAL motion ,DIFFUSION coefficients ,MOLECULAR dynamics ,MOTION capture (Human mechanics) ,ROTATIONAL motion - Abstract
This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in CG systems using a hard sphere mapping, the absence of rotational motions in single-site CG models introduces differences between FG and CG dynamics. In this third paper, our objective is to faithfully recover atomistic diffusion coefficients from CG dynamics by incorporating rotational dynamics. By extracting FG rotational diffusion, we unravel, for the first time reported to our knowledge, a universality in excess entropy scaling between the rotational and translational diffusion. Once the missing rotational dynamics are integrated into the CG translational dynamics, an effective translation-rotation coupling becomes essential. We propose two different approaches for estimating this coupling parameter: the rough hard sphere theory with acentric factor (temperature-independent) or the rough Lennard-Jones model with CG attractions (temperature-dependent). Altogether, we demonstrate that FG diffusion coefficients can be recovered from CG diffusion coefficients by (1) incorporating "entropy-free" rotational diffusion with translation-rotation coupling and (2) recapturing the missing entropy. Our findings shed light on the fundamental relationship between FG and CG dynamics in molecular fluids. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
28. Entropy, pressure, and chemical potential of multiple chain systems from computer simulation. II. Application of the Metropolis and the hypothetical scanning methods.
- Author
-
Meirovitch, Hagai
- Subjects
ENTROPY ,PRESSURE ,CHEMICAL processes ,COMPUTER simulation - Abstract
As in the preceding paper (Paper I) we study here a model of chains with excluded volume enclosed in a ‘‘box’’ on a square lattice. The system is simulated by the Metropolis Monte Carlo method and the entropy is extracted from the samples by using the ‘‘hypothetical scanning method.’’ With this method each system configuration is treated as if it has been generated step by step with the scanning method (studied in Paper I). The transition probabilities are reconstructed and three approximations of the entropy are obtained. Thus the pressure and the chemical potential are calculated directly from the results of the entropy as in Paper I using standard thermodynamic relations. These results are found to be in a very good agreement with those obtained in Paper I, which are considered to be exact within the statistical error. [ABSTRACT FROM AUTHOR]
- Published
- 1992
- Full Text
- View/download PDF
29. Theoretical characterization of temperature and density dependence of liquid water electronic excitation energy: Comparison with recent experimental data.
- Author
-
D'Abramo, Marco, Di Nola, Alfredo, Aschi, Massimiliano, and Amadei, Andrea
- Subjects
ABSORPTION ,SPECTRUM analysis ,MOLECULAR dynamics ,MOLECULAR spectroscopy ,ABSORPTION spectra - Abstract
In a recent paper [Aschi et al., ChemPhysChem 6, 53 (2005)], we characterized, by means of theoretical-computational procedures, the electronic excitation of water along the typical liquid state isochore (55.32 mol/l) for a large range of temperature. In that paper we were able to accurately reproduce the experimental absorption maximum at room temperature and to provide a detailed description of the temperature dependence of the excitation spectrum along the isochore. In a recent experimental work by Marin et al. [J. Chem. Phys. 125, 104314 (2006)], water electronic excitation energy was carefully analyzed in a broad range of density and temperature, finding a remarkable agreement of the temperature behavior of the experimental data with our theoretical results. Here, by means of the same theoretical-computational procedures (molecular dynamics simulations and the perturbed matrix method), we investigate water electronic absorption exactly in the same density-temperature range used in the experimental work, hence, now considering also the absorption density dependence. Our results point out that, (1) for all the densities and temperatures investigated, our calculated absorption spectra are in very good agreement with the experimental ones and (2) the gradual maxima redshift observed increasing the temperature or decreasing the density has to be ascribed to a real shift of the lowest X→A electronic transition, supporting the conclusions of Marin et al. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
30. Response to the paper: ‘‘Conformation kinetics of methyl nitrite. IV’’.
- Author
-
Bauer, S. H.
- Subjects
- *
NITRITES , *METHYL groups , *ISOMERIZATION - Abstract
Our measurements of the relaxation times for the syn–anti isomerization of CH3ONO have been criticized by True et al. However, their recounting of the flaws in our procedure was based on distortions. Furthermore, the basic disagreement concerns the interpretation of the pressure dependence of the relaxation times they reported which differed insignificantly from our initial observations. The clear increase with decreasing pressure of the bimolecular rate constant (at low pressures) is not consistent with any RRKM model which has yet been proposed contrary to the claim by True. It is consistent with the limited phase space model proposed by Bauer and Lazaar. [ABSTRACT FROM AUTHOR]
- Published
- 1987
- Full Text
- View/download PDF
31. Addendum to the paper ‘‘On the dynamics of polyelectrolyte solutions’’.
- Author
-
Benmouna, M., Akcasu, A. Z., and Hammouda, B.
- Subjects
- *
POLYELECTROLYTES , *POLYMERS - Abstract
Hydrodynamic effect on the relaxation modes for a system of charged particles is reexamined. This effect is shown to produce a decrease in the diffusion coefficient due to the cloud of particles surrounding each charge. [ABSTRACT FROM AUTHOR]
- Published
- 1986
- Full Text
- View/download PDF
32. Linearly scaling computation of ddPCM solvation energy and forces using the fast multipole method.
- Author
-
Mikhalev, A., Nottoli, M., and Stamm, B.
- Subjects
FAST multipole method ,FORCE & energy ,ENERGY consumption ,SPHERICAL harmonics ,INTEGRAL equations ,SOLVATION - Abstract
This paper proposes the first linear scaling implementation for the domain decomposition approach of the polarizable continuum model (ddPCM) for the computation of the solvation energy and forces. The ddPCM-equation consists of a (non-local) integral equation on the van der Waals or solvent accessible surface of the solute's cavity resulting in a dense solution matrix, and, in turn, one matrix–vector multiplication has a quadratic arithmetic complexity with respect to the number of atoms of the solute molecule. The use of spherical harmonics as basis functions makes it natural to employ the fast multipole method (FMM) in order to provide an asymptotically linear scaling method. In this paper, we employ the FMM in a non-uniform manner with a clusterization based on a recursive inertial bisection. We present some numerical tests illustrating the accuracy and scaling of our implementation. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
33. Approximations of density matrices in N-electron valence state second-order perturbation theory (NEVPT2). II. The full rank NEVPT2 (FR-NEVPT2) formulation.
- Author
-
Guo, Yang, Sivalingam, Kantharuban, Kollmar, Christian, and Neese, Frank
- Subjects
DENSITY matrices ,PERTURBATION theory ,WAVE functions - Abstract
In Paper I, the performances of pre-screening (PS), extended PS (EPS), and cumulant (CU) approximations to the fourth-order density matrix were examined in the context of second-order N-electron valence state perturbation theory (NEVPT2). It has been found that the CU, PS, and even EPS approximations with loose thresholds may introduce intruder states. In the present work, the origin of these "false intruder" states introduced by approximated density matrices is discussed. Canonical NEVPT2 implementations employ a rank reduction trick. By analyzing its residual error, we find that the omission of the rank reduction leads to a more stable multireference perturbation theory for incomplete active space reference wave functions. Such a full rank (FR)-NEVPT2 formulation is equivalent to the conventional NEVPT2 method for the complete active space self-consistent field/complete active space configuration interaction reference wave function. A major drawback of the FR-NEVPT2 formulation is the necessity of the fifth-order density matrix. To avoid the construction of the high-order density matrices, the combination of the FR-NEVPT2 with the CU approximation is studied. However, we find that the CU approximation remains problematic as it still introduces intruder states. The question of how to robustly and efficiently perform internally contracted multireference perturbation theories with approximate densities remains a challenging field of investigation. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
34. Effect of the geometry of confining media on the stability and folding rate of <italic>α</italic>-helix proteins.
- Author
-
Wang, Congyue, Piroozan, Nariman, Javidpour, Leili, and Sahimi, Muhammad
- Subjects
MOLECULAR dynamics method of protein folding ,PROTEIN stability ,PORE size distribution ,NANOPORES ,MOLECULAR dynamics - Abstract
Protein folding in confined media has attracted wide attention over the past 15 years due to its importance to both
in vivo andin vitro applications. It is generally believed that protein stability increases by decreasing the size of the confining medium,if the medium’s walls are repulsive, and that the maximum folding temperature in confinement is in a pore whose sizeD 0 is only slightly larger than the smallest dimension of a protein’s folded state. Until recently, the stability of proteins in pores with a size very close to that of the folded state has not received the attention it deserves. In a previous paper [L. Javidpour and M. Sahimi, J. Chem. Phys.135 , 125101 (2011)], we showed that, contrary to the current theoretical predictions, the maximum folding temperature occurs inlarger pores forsmaller α -helices. Moreover, in very tight pores, the free energy surface becomes rough, giving rise to a new barrier for protein folding close to the unfolded state. In contrast to unbounded domains, in small nanopores proteins with anα -helical native state that contain theβ structures are entropically stabilized implying that folding rates decrease notably and that the free energy surface becomes rougher. In view of the potential significance of such results to interpretation of many sets of experimental data that could not be explained by the current theories, particularly the reported anomalously low rates of folding and the importance of entropic effects on proteins’ misfolded states in highly confined environments, we address the following question in the present paper: To what extent the geometry of a confined medium affects the stability and folding rates of proteins? Using millisecond-long molecular dynamics simulations, we study the problem in three types of confining media, namely, cylindrical and slit pores and spherical cavities. Most importantly, we find that the prediction of the previous theories that the dependence of the maximum folding temperatureT on the sizef D of a confined medium occurs in larger media for larger proteins is correctonly in spherical geometry, whereas the opposite is true in the two other geometries that we study. Also studied is the effect of the strength of the interaction between the confined media’s walls and the proteins. If the walls are only weakly or moderately attractive, a complex behavior emerges that depends on the size of the confining medium. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
35. Multimode two-dimensional vibronic spectroscopy. II. Simulating and extracting vibronic coupling parameters from polarization-selective spectra.
- Author
-
Weakly, Robert B., Gaynor, James D., and Khalil, Munira
- Subjects
VIBRONIC coupling ,EXCITED states ,SPATIAL orientation ,SPECTROMETRY ,ELECTRONIC spectra - Abstract
Experimental demonstrations of polarization-selection two-dimensional Vibrational-Electronic (2D VE) and 2D Electronic-Vibrational (2D EV) spectroscopies aim to map the magnitudes and spatial orientations of coupled electronic and vibrational coordinates in complex systems. The realization of that goal depends on our ability to connect spectroscopic observables with molecular structural parameters. In this paper, we use a model Hamiltonian consisting of two anharmonically coupled vibrational modes in electronic ground and excited states with linear and bilinear vibronic coupling terms to simulate polarization-selective 2D EV and 2D VE spectra. We discuss the relationships between the linear vibronic coupling and two-dimensional Huang–Rhys parameters and between the bilinear vibronic coupling term and Duschinsky mixing. We develop a description of the vibronic transition dipoles and explore how the Hamiltonian parameters and non-Condon effects impact their amplitudes and orientations. Using simulated polarization-selective 2D EV and 2D VE spectra, we show how 2D peak positions, amplitudes, and anisotropy can be used to measure parameters of the vibronic Hamiltonian and non-Condon effects. This paper, along with the first in the series, provides the reader with a detailed description of reading, simulating, and analyzing multimode, polarization-selective 2D EV and 2D VE spectra with an emphasis on extracting vibronic coupling parameters from complex spectra. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
36. Multimode two-dimensional vibronic spectroscopy. I. Orientational response and polarization-selectivity.
- Author
-
Gaynor, James D., Weakly, Robert B., and Khalil, Munira
- Subjects
ANHARMONIC oscillator ,VIBRONIC coupling ,SPECTROMETRY ,DIPOLE moments ,ELECTRIC fields - Abstract
Two-dimensional Electronic–Vibrational (2D EV) spectroscopy and two-dimensional Vibrational–Electronic (2D VE) spectroscopy are among the newest additions to the coherent multidimensional spectroscopy toolbox, and they are directly sensitive to vibronic couplings. In this first of two papers, the complete orientational response functions are developed for a model system consisting of two coupled anharmonic oscillators and two electronic states in order to simulate polarization-selective 2D EV and 2D VE spectra with arbitrary combinations of linearly polarized electric fields. Here, we propose analytical methods to isolate desired signals within complicated spectra and to extract the relative orientation between vibrational and vibronic dipole moments of the model system using combinations of polarization-selective 2D EV and 2D VE spectral features. Time-dependent peak amplitudes of coherence peaks are also discussed as means for isolating desired signals within the time-domain. This paper serves as a field guide for using polarization-selective 2D EV and 2D VE spectroscopies to map coupled vibronic coordinates on the molecular frame. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
37. Quantum signatures for screening metavalent solids.
- Author
-
Giri, Deepesh, Williams, Logan, Mukherjee, Arpan, and Rajan, Krishna
- Subjects
SOLIDS ,METALLIC bonds ,SURFACE analysis ,COVALENT bonds ,DATA integrity - Abstract
The objective of this paper is to describe a new data-driven framework for computational screening and discovery of a class of materials termed "metavalent" solids. "Metavalent" solids possess characteristics that are nominally associated with metallic and covalent bonding (in terms of conductivity and coordination numbers) but are distinctly different from both because they show anomalously large response properties and a unique bond-breaking mechanism that is not observed in either covalent or metallic solids. The paper introduces the use of Hirshfeld surface analysis to provide quantum level descriptors that can be used for rapid screening of crystallographic data to identify potentially new "metavalent" solids with novel and emergent properties. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
38. Formation of hot ice caused by carbon nanobrushes. II. Dependency on the radius of nanotubes.
- Author
-
Matsumoto, Masakazu, Yagasaki, Takuma, and Tanaka, Hideki
- Subjects
ICE crystals ,ICE ,CARBON nanotubes ,CRYSTAL structure ,MOLECULAR dynamics ,CARBON - Abstract
Stable crystalline structures of confined water can be different from bulk ice. In Paper I [T. Yagasaki et al., J. Chem. Phys. 151, 064702 (2019)] of this study, it was shown, using molecular dynamics (MD) simulations, that a zeolite-like ice structure forms in nanobrushes consisting of (6,6) carbon nanotubes (CNTs) when the CNTs are located in a triangle arrangement. The melting temperature of the zeolite-like ice structure is much higher than the melting temperature of ice I
h when the distance between the surfaces of CNTs is ∼0.94 nm, which is the best spacing for the bilayer structure of water. In this paper, we perform MD simulations of nanobrushes of CNTs that are different from (6,6) CNTs in radius. Several new porous ice structures form spontaneously in the MD simulations. A stable porous ice forms when the radius of its cavities matches the radius of the CNTs well. All cylindrical porous ice structures found in this study can be decomposed into a small number of structural blocks. We provide a new protocol to classify cylindrical porous ice crystals on the basis of this decomposition. [ABSTRACT FROM AUTHOR]- Published
- 2021
- Full Text
- View/download PDF
39. A multiscale approach to coupled nuclear and electronic dynamics. II. Exact and approximated evaluation of nonradiative transition rates.
- Author
-
Cortivo, R., Campeggio, J., and Zerbetto, M.
- Subjects
POTENTIAL energy surfaces ,MOLECULAR dynamics ,DIHEDRAL angles ,QUANTUM states ,BOND angles - Abstract
This work follows a companion article, which will be referred to as Paper I [Campeggio et al., J. Chem. Phys. 158, 244104 (2023)] in which a quantum-stochastic Liouville equation for the description of the quantum–classical dynamics of a molecule in a dissipative bath has been formulated in curvilinear internal coordinates. In such an approach, the coordinates of the system are separated into three subsets: the quantum coordinates, the classical relevant nuclear degrees of freedom, and the classical irrelevant (bath) coordinates. The equation has been derived in natural internal coordinates, which are bond lengths, bond angles, and dihedral angles. The resulting equation needs to be parameterized. In particular, one needs to compute the potential energy surfaces, the friction tensor, and the rate constants for the nonradiative jumps among the quantum states. While standard methods exist for the calculation of energy and dissipative properties, an efficient evaluation of the transition rates needs to be developed. In this paper, an approximated treatment is introduced, which leads to a simple explicit formula with a single adjustable parameter. Such an approximated expression is compared with the exact calculation of transition rates obtained via molecular dynamics simulations. To make such a comparison possible, a simple sandbox system has been used, with two quantum states and a single internal coordinate (together with its conjugate momentum). Results show that the adjustable parameter, which is an effective decoherence time, can be parameterized from the effective relaxation times of the autocorrelation functions of the conjugated momenta of the relevant nuclear coordinates. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
40. ℏ2 expansion of the transmission probability through a barrier.
- Author
-
Pollak, Eli and Cao, Jianshu
- Subjects
MOLECULAR dynamics - Abstract
Ninety years ago, Wigner derived the leading order expansion term in ℏ
2 for the tunneling rate through a symmetric barrier. His derivation included two contributions: one came from the parabolic barrier, but a second term involved the fourth-order derivative of the potential at the barrier top. He left us with a challenge, which is answered in this paper, to derive the same but for an asymmetric barrier. A crucial element of the derivation is obtaining the ℏ2 expansion term for the projection operator, which appears in the flux-side expression for the rate. It is also reassuring that an analytical calculation of semiclassical transition state theory (TST) reproduces the anharmonic corrections to the leading order of ℏ2 . The efficacy of the resulting expression is demonstrated for an Eckart barrier, leading to the conclusion that especially when considering heavy atom tunneling, one should use the expansion derived in this paper, rather than the parabolic barrier approximation. The rate expression derived here reveals how the classical TST limit is approached as a function of ℏ and, thus, provides critical insights to understand the validity of popular approximate theories, such as the classical Wigner, centroid molecular dynamics, and ring polymer molecular dynamics methods. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
41. A density scaling conjecture for aging glasses.
- Author
-
Niss, Kristine
- Subjects
LOGICAL prediction ,DENSITY - Abstract
The aging rate of glasses has traditionally been modeled as a function of temperature, T, and fictive temperature, while density, ρ, is not explicitly included as a parameter. However, this description does not naturally connect to the modern understanding of what governs the relaxation rate in equilibrium. In equilibrium, it is well known that the relaxation rate, γ
eq , depends on temperature and density. In addition, a large class of systems obeys density scaling, which means the rate specifically depends on the scaling parameter, Γ = e(ρ)/T, where e(ρ) is a system specific function. This paper presents a generalization of the fictive temperature concept in terms of a fictive scaling parameter, Γfic , and a density scaling conjecture for aging glasses in which the aging rate depends on Γ and Γfic . [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
42. A general structural order parameter for the amorphous solidification of a supercooled liquid.
- Author
-
Sun, Gang and Harrowell, Peter
- Subjects
GLASS transitions ,AMORPHOUS substances ,SOLIDIFICATION ,SUPERCOOLED liquids ,ATOMS - Abstract
The persistent problem posed by the glass transition is to develop a general atomic level description of amorphous solidification. The answer proposed in this paper is to measure a configuration's capacity to restrain the motion of the constituent atoms. Here, we show that the instantaneous normal modes can be used to define a measure of atomic restraint that accounts for the difference between fragile and strong liquids and the collective length scale of the supercooled liquid. These results represent a significant simplification of the description of amorphous solidification and provide a powerful systematic treatment of the influence of microscopic factors on the formation of an amorphous solid. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
43. Modified genetic algorithm to model crystal structures. II. Determination of a polymorphic structure of benzene using enthalpy minimization.
- Author
-
Bazterra, Victor E., Ferraro, Marta B., and Facelli, Julio C.
- Subjects
BENZENE ,CRYSTALS ,ENTHALPY ,GENETIC algorithms ,CHEMICAL structure - Abstract
The Modified Genetic Algorithm scheme, presented in Paper I to model crystal structures in organic compounds (MGAC), is applied here to test its performance in the determination of a polymorphic crystalline structure of benzene that has been observed at 25 Kbar. This polymorph, named here benzene II, is not a global minimum of the energy or even close to any of the local minimum determined using the energy evolution of benzene structures described in the previous paper. The benzene II structure corresponds to an enthalpy minimum. This paper shows that it is possible to use the MGAC procedure, modified to use the minimization of the enthalpy instead of the energy in the GA (Genetic Algorithm) selection process, to find this high pressure structure of benzene. [ABSTRACT FROM AUTHOR]
- Published
- 2002
- Full Text
- View/download PDF
44. Ultrafast dichroism spectroscopy of anthracene in solution. III. Nonpolar solvation dynamics in benzyl alcohol.
- Author
-
Zhang, Yunhan and Berg, Mark A.
- Subjects
SOLVATION ,DICHROISM - Abstract
Results on single-wavelength transient hole burning (SW-THB) developed in paper II [J. Chem. Phys. 115, 4223 (2001)] are applied to the dichroism experiments on anthracene in benzyl alcohol reported in paper I [J. Chem. Phys. 115, 4212 (2001)]. The intermediate component of the dichroism decay is assigned to a SW-THB effect caused by nonpolar electronic solvation. The presence of a solvation component in dichroism experiments has not been demonstrated previously. The sparseness of anthracene’s electronic spectrum eliminates vibrational dynamics from the solvation measurement. Because data collection is focused on a single dimension, the viscosity dependence of the nonpolar solvation is determined with greater accuracy than in our previous two-dimensional transient hole-burning studies. The solvation time is obtained as a function of viscosity/temperature from 14.4 to 2.7 cP (1–56 °C). The times show good agreement with a viscoelastic theory of the diffusive component of nonpolar solvation. Combining the results of this paper with those of paper I allows for comparison of solvation and rotation dynamics within a single system. A correlation between the ratio of diffusive solvation and rotation times and the magnitude of the inertial rotation is suggested. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]
- Published
- 2001
- Full Text
- View/download PDF
45. Differential steric effects in Cl reactions with aligned CHD3(v1 = 1) by the R(0) and Q(1) transitions. II. Abstracting the unexcited D-atoms.
- Author
-
Fengyan Wang and Kopin Liu
- Subjects
DIFFERENTIAL cross sections ,EXCITATION energy (In situ microanalysis) ,STERIC hindrance ,HYDROGEN atom ,PHASE transitions - Abstract
A complete set of four polarization-dependent differential cross sections in the reactions of Cl + aligned-CHD
3 (v1 = 1, |jK) → DCl(v = 0) + CHD2 (v1 = 1) is reported here for two different, rotationally polarized states with j = 1: specifically the |jK = |10 state prepared via the R(0) excitation and the |1 ± 1 state via Q(1). In stark contrast to the complicated situation of the HCl(v) + CD3(v = 0) channel reported in Paper-I, the stereo-requirement of this isotopic channel for both polarized reactants appears quite straightforward and consistent with a direct rebound mechanism. The extent of steric effects is moderate and relatively smaller than the alternative H-atom abstraction channel. All major findings reported here can qualitatively be understood by first noting that the present reaction invokes abstracting a D-atom, which is the spectator in the IR-excitation process. Next, it is recognized that the directional properties of two polarized states of CHD3 (v1 = 1, |jK) should manifest primarily in the IR-excited C-H bond, leaving secondary imprints in the unexcited CD3 -moiety. The stereo-specificity of the DCl + CHD2 product channel is further reduced by the fact that the abstraction can occur with any one of the three spatially distinct D-atoms. [ABSTRACT FROM AUTHOR]- Published
- 2016
- Full Text
- View/download PDF
46. Dissipative tunneling rates through the incorporation of first-principles electronic friction in instanton rate theory. II. Benchmarks and applications.
- Author
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Litman, Y., Pós, E. S., Box, C. L., Martinazzo, R., Maurer, R. J., and Rossi, M.
- Subjects
QUANTUM tunneling ,QUANTUM theory ,FRICTION - Abstract
In Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], we presented the ring-polymer instanton with explicit friction (RPI-EF) method and showed how it can be connected to the ab initio electronic friction formalism. This framework allows for the calculation of tunneling reaction rates that incorporate the quantum nature of the nuclei and certain types of non-adiabatic effects (NAEs) present in metals. In this paper, we analyze the performance of RPI-EF on model potentials and apply it to realistic systems. For a 1D double-well model, we benchmark the method against numerically exact results obtained from multi-layer multi-configuration time-dependent Hartree calculations. We demonstrate that RPI-EF is accurate for medium and high friction strengths and less accurate for extremely low friction values. We also show quantitatively how the inclusion of NAEs lowers the crossover temperature into the deep tunneling regime, reduces the tunneling rates, and, in certain regimes, steers the quantum dynamics by modifying the tunneling pathways. As a showcase of the efficiency of this method, we present a study of hydrogen and deuterium hopping between neighboring interstitial sites in selected bulk metals. The results show that multidimensional vibrational coupling and nuclear quantum effects have a larger impact than NAEs on the tunneling rates of diffusion in metals. Together with Paper I [Litman et al., J. Chem. Phys. (in press) (2022)], these results advance the calculations of dissipative tunneling rates from first principles. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
47. Brownian bridges for stochastic chemical processes—An approximation method based on the asymptotic behavior of the backward Fokker–Planck equation.
- Author
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Wang, Shiyan, Venkatesh, Anirudh, Ramkrishna, Doraiswami, and Narsimhan, Vivek
- Subjects
BROWNIAN bridges (Mathematics) ,STOCHASTIC processes ,FOKKER-Planck equation ,CHEMICAL processes ,MASS transfer ,PHASE space ,RANDOM walks - Abstract
A Brownian bridge is a continuous random walk conditioned to end in a given region by adding an effective drift to guide paths toward the desired region of phase space. This idea has many applications in chemical science where one wants to control the endpoint of a stochastic process—e.g., polymer physics, chemical reaction pathways, heat/mass transfer, and Brownian dynamics simulations. Despite its broad applicability, the biggest limitation of the Brownian bridge technique is that it is often difficult to determine the effective drift as it comes from a solution of a Backward Fokker–Planck (BFP) equation that is infeasible to compute for complex or high-dimensional systems. This paper introduces a fast approximation method to generate a Brownian bridge process without solving the BFP equation explicitly. Specifically, this paper uses the asymptotic properties of the BFP equation to generate an approximate drift and determine ways to correct (i.e., re-weight) any errors incurred from this approximation. Because such a procedure avoids the solution of the BFP equation, we show that it drastically accelerates the generation of conditioned random walks. We also show that this approach offers reasonable improvement compared to other sampling approaches using simple bias potentials. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
48. Nucleic acid folding simulations using a physics-based atomistic free energy model.
- Author
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Mak, Chi H.
- Subjects
DNA folding ,MONTE Carlo method ,BASE pairs ,NUCLEIC acids ,COMPUTER simulation - Abstract
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces—base stacking, counterion-induced backbone self-interactions, and base pairing—via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
49. The He–H3+ complex. II. Infrared predissociation spectrum and energy term diagram.
- Author
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Salomon, Thomas, Brackertz, Stefan, Asvany, Oskar, Savić, Igor, Gerlich, Dieter, Harding, Michael E., Lipparini, Filippo, Gauss, Jürgen, van der Avoird, Ad, and Schlemmer, Stephan
- Subjects
PARITY (Physics) ,INFRARED spectra ,POTENTIAL energy surfaces ,OPTICAL parametric oscillators ,K-spaces ,QUANTUM numbers ,ION traps - Abstract
The rotationally resolved infrared (IR) spectrum of the He– H 3 + complex has been measured in a cryogenic ion trap experiment at a nominal temperature of 4 K. Predissociation of the stored complex has been invoked by excitation of the degenerate ν
2 mode of the H 3 + sub-unit using a pulsed optical parametric oscillator system. An assignment of the experimental spectrum became possible through one-to-one correlations with bands of the spectrum theoretically predicted in Paper I [Harding et al., J. Chem. Phys. 156, 144307 (2022)]. 19 bands have been assigned and analyzed, and the energy term diagram of the lower states of this floppy molecular complex has been derived from combination differences (CDs) in the experimental spectrum. Ground state combination differences (GSCDs) reveal a large part of the energy term diagram for the He– H 3 + complex in its vibrational ground state, v = 0. Experimental and theoretical term energies agree within experimental accuracy for the rotational fine structure associated with the total angular momentum quantum number J and the parity e/f as well as for the coarse spacing of the lowest K states of the complex. This favorable comparison shows that the potential energy surface (PES) calculated in Paper I is accurate. The barriers between the three equivalent global minima in this PES are relatively low and the He– H 3 + complex is extremely floppy, with nearly unhindered internal rotation of the H 3 + sub-unit. The resulting Coriolis interactions couple the internal and end-over-end rotation of the complex and contribute significantly to the energy terms. They are observed both in experiment and theory and are, e.g., the origin of different rotational constants for states of e and f parity. Also in this respect, experiment and theory agree very well. Despite the assignment and analysis of many bands of the extremely rich IR spectrum of He– H 3 + , higher levels of excitation, including the complex stretching mode, need further attention. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
50. Origin of thiocyanate spectral shifts in water and organic solvents.
- Author
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Zhao, Ruoqi, Shirley, Joseph C., Lee, Euihyun, Grofe, Adam, Li, Hui, Baiz, Carlos R., and Gao, Jiali
- Subjects
QUANTUM perturbations ,MOLECULAR dynamics ,VIBRATIONAL spectra ,INTERMOLECULAR interactions ,BIOLOGICAL models - Abstract
Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute–solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
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