Molecular mechanics study of conformational trends in simple alcohols and ethers. II. Intramolecular hydrogen bonding

In this article we present an extension of our modified MM2(80) force field MM2MOD in which a potential function for hydrogen bonding in alcohols and ethers is included. The results of applying MM2(85), MM2(87), and MM2MOD on ethylene glycol, 2-methoxyethanol and 1,3-propanediol are reported and compared with available experimental data and ab initio results. It is concluded that hydrogen bonding plays an important role in determining the molecular conformations of these systems. © 1992 by John Wiley & Sons, Inc.     

Force field parameters for carbohydrates

A new set of force field parameters for carbohydrates is reported. The parameter set is based on the CHARMM22 force field of Karplus and co-workers. The parameterization is based on newly performed high-level ab initio calculations [MP2/6-311 + G (2d, 2p)/ /6-31G**] of fragment molecules. A good agreement of the modified force field and ab initio data is achieved, which is demonstrated with a variety of molecules. © 1996 by John Wiley & Sons, Inc.     

A molecular mechanics study of the Si?O bond and alkyl-silanes

The standard MM2 force field and program have been modified to include Si? O groups, the force constants being derived from ab initio wavefunctions, and using partial atomic charges calculated from the empirical algorithm CHARGE2. Molecular mechanics calculations have been carried out on disiloxane, dimethoxy-dimethylsilane, methyl silyl ether, and cyclotrisiloxane, and reasonable agreement has been obtained between the observed and calculated geometries. In addition, the energies obtained using the modified force field have been tested against experimental data on alkyl silanes where energetic and structural information is available. Again good agreement is obtained. The application of the force field to extended Si? O systems will also be discussed.     

Improved treatment of cyclic β‐amino acids and successful prediction of β‐peptide secondary structure using a modified force field: AMBER*C

We added parameters to the AMBER* force field to model cyclic β‐amino acid derivatives more accurately within the commonly used MacroModel program. In an effort to generate an improved treatment of cyclohexane and cyclopentane conformational preferences, carbon–carbon torsional parameters were modified and incorporated into a force field we call AMBER*C. Simulation of trans‐2‐aminocyclohexanecarboxylic acid (trans‐ACHC) and trans‐2‐aminocyclopentanecarboxylic acid (trans‐ACPC) derivatives using AMBER*C produces more realistic energy differences between (pseudo)diaxial and (pseudo)diequatorial conformations than does simulation using AMBER*. AMBER*C molecular dynamics simulations more accurately reproduce the experimental hydrogen‐bonding tendencies of simple diamide derivatives of trans‐ACHC and trans‐ACPC than do simulations using the AMBER* force field. More importantly, this modified force field allows accurate qualitative prediction of the helical secondary structures adopted by β‐amino acid homo‐oligomers. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 763–773, 2000     

Peptide free‐energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

The C96 and AMBER95 force fields were compared with small model peptides Ac‐(Ala)_n‐NMe (Ac = CH₃CO, NMe = NHCH₃, n=2 and 3) in vacuo and in TIP3P water by computing the free‐energy profiles using multicanonical molecular dynamics method. The C96 force field is a modified version of the AMBER95 force field, which was adjusted to reproduce the energy difference between extended β‐ and constrained α‐helical energies for the alanine tetrapeptide, obtained by the high level ab initio MO method. The slight modification resulted in a large difference in the free energy profiles. The C96 force field prefers relatively extended conformers, whereas the AMBER95 force field favors turn conformations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 748–762, 2000     

Force field parameters for the simulation of modified histone tails

We describe the development of force field parameters for methylated lysines and arginines, and acetylated lysine for the CHARMM all‐atom force field. We also describe a CHARMM united‐atom force field for modified sidechains suitable for use with fragment‐based docking methods. The development of these parameters is based on results of ab initio quantum mechanics calculations of model compounds with subsequent refinement and validation by molecular mechanics and molecular dynamics simulations. The united‐atom parameters are tested by fragment docking to target proteins using the MCSS procedure. The all‐atom force field is validated by molecular dynamics simulations of multiple experimental structures. In both sets of calculations, the computational predictions using the force field were compared to the corresponding experimental structures. We show that the parameters yield an accurate reproduction of experimental structures. Together with the existing CHARMM force field, these parameters will enable the general modeling of post‐translational modifications of histone tails. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

On the use of conformationally dependent geometry trends from ab initio dipeptide studies to refine potentials for the empirical force field CHARMM

Previous 4-21G ab initio geometry optimizations of various conformations of the model dipeptides (N-acetyl N'methyl amides) of glycine (GLY) and the alanine (ALA) have been used to help refine the empirical force constants and equilibrium geometry in the CHARMM force field for peptides. Conformationally dependent geometry trends from ab initio calculations and positions of energy minima on the ab initio energy surfaces have been used as guides in the parameter refinement, leading to modifications in the bond stretch, angle bending, and some torsional parameters. Preliminary results obtained with these refined empirical parameters are presented for the protein Crambin. Results for the cyclic (Ala-Pro-DPhe)₂ are compared with those from other calculations. It seems that the dihedral angle fit achieved by the new parameters is significantly improved compared with results from force fields whose derivation does not include ab initio geometry trends.     

Molecular mechanics calculations of conjugated amides and an ab initio investigation of acrylamide and its β-amino derivative: Conformational analysis and rotational barriers

Conformations and rotational barriers in a series of conjugated primary and tertiary amides have been analyzed by a modified MM2(91) force field, which treats the amide nitrogen as part of the conjugated system by redefining the atom type for the nitrogen. Ab initio molecular orbital calculations at the MP2/6-31G* level have been performed on the stable conformers and transition structures of acrylamide and β-trans-aminoacrylamide. The results have been used, with published experimental and computational data, to generate parameters for the MM2 force field. The force field has been applied to various conjugated amides, such as reduced nicotinamide adenine dinucleotide (NADH) and NAD⁺ analogues, nicotinamide, urea, vinylogous urea derivatives, and nucleic acid bases. The fundamental difference between primary and tertiary conjugated amides with respect to both conformation and barrier is highlighted. © 1996 by John Wiley & Sons, Inc.     

The conformation of alkyl sulfoxides

Parameters for sulfoxides used in force field MM1 were modified to be incorporated into force field MM2. The conformations of ten alkyl sulfoxides were then calculated using MM2 with these new parameters. The alkyl groups used were methyl, ethyl, isopropyl, and t-butyl. It was found that of the many possible conformations for these compounds, only one or two stable conformers exist, and that the number of these conformers agrees with the number of reported S? O stretching frequencies in almost every case. No apparent correlation between the vibration frequency and the molecular structure was found.     

Modified MM2 scheme for computation of O?C?N-containing systems

A modification of Allinger's MM2 force field for the anomeric effect in O? C? N systems is presented. For optimal consistency, it was parameterized by alternate use of ab initio (3-21G level) and X-ray results to account for the energetic and structural manifestations of the effect in the gas or condensed phase, respectively. The results obtained with the modified force field are in good agreement with those from both theoretical and experimental methods. The parameterization scheme explicitly treats all structural parameters of the C? O? C? N? C moiety as well as C? N bond lengths in tertiary amines contained within an anomeric unit. In addition, it includes directional H-bond type interactions. A limited number of parameters is put forward, in accord with the general MM2 force-field approach. © 1993 John Wiley & Sons, Inc.     

Reparameterizations of the χ Torsion and Lennard‐Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines

The currently available force field parameters for modified RNA residues in AMBER show significant deviations in conformational properties from experimental observations. The examination of the transferability of the recently revised torsion parameters revealed that there was an overall improvement in the conformational properties for some of the modifications but the improvements were still insufficient in describing the sugar pucker preferences (J. Chem. Inf. Model. 2014, 54, 1129–1142). Here, we report an approach for the development and fine tuning of the AMBER force field parameters for 2‐thiouridine, 4‐thiouridine, and pseudouridine with diverse conformational preferences. The χ torsion parameters were reparameterized at the individual nucleoside level. The effect of combining the revised γ torsion parameter and modifying the Lennard‐Jones σ parameters were also tested by directly comparing the conformational preferences obtained from our extensive molecular dynamics simulations with those from experimental observations. © 2016 Wiley Periodicals, Inc.     

Nano P(VDF-TrFE) doped polyimide alignment layers for twisted nematic liquid crystal devices

ABSTRACT

The rapid development of consumer electronics and portable devices imposes a great demand for energy efficient information display systems. Among the information display devices, liquid crystal display (LCD) devices stands in the front. The fabrication of energy-efficient LCD systems demands new material and techniques. In this work, the conventional polyimide alignment layer of twisted nematic liquid crystal device (TNLCD) was replaced with ferroelectric polymer nanoparticle doped alignment layer. Morphology of the alignment layer was analysed using field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM). The ferroelectric nature of the polymer alignment layer was studied using dynamic contact electrostatic force microscopy (DC-EFM). TNLCD cells are fabricated with this modified alignment layer and the switching characteristics are compared with the conventional TNLCD devices. The TNLCD with modified alignment layer has shown a reduction of 50% in threshold (V_thr) and 47% reduction in saturation voltage (V_sat).     

Potentialfeld- und Kraftkonstanten voncis- undtrans-Difluordiazin

Zusammenfassung Ancis-Difluordiazin planarer Konfiguration mit C_2v-Symmetrie und antrans-Difluordiazin planarer Konfiguration mit zentrosymmetrischer Struktur mit C_2h-Symmetrie wurde eine Schwingungs- und Strukturanalyse unter Verwendung eines modifizierten Valenzkraftfeldes mit sechs Kraftkonstanten ausgeführt. Die Berechnung der Kraftkonstanten erfolgte nach gruppentheoretischen Methoden auf der Grundlage der Ergebnisse neuerer Struktur- und verfeinerter Schwingungsanalysen. Die Ergebnisse werden mit den an Molekülen mit ähnlichen chemischen Bindungen und angenähert identischen Kernabständen erhobenen verglichen.

---

Potential field and force constants of cis- and trans-difluorodiazines

Vibrational and structural analysis ofcis-difluorodiazine possessing a planar configuration with C_2v symmetry and oftrans-difluorodiazine possessing a planar configuration of centrosymmetrical structure with C_2h symmetry has briefly been made. A modified six-force constant valence force field has been employed and the force constants have been evaluated from the recent structural and refined vibrational data for bothcis- andtrans-difluorodiazines by the group theoretical method. A brief discussion of the results has been made in relation to other molecules having similar chemical bonds with nearly identical internuclear distances.

---

---

Mit 2 Abbildungen     

All-trans- and t,T,t,C,t,T,t-deca-1,3,5,7,9-Pentaenes: Ab Initio Structures,Vibrational Analyses,and Some Regularities in the Series of Related Molecules

Total geometry optimization and calculation of the force constants for all-transand t,T,t,C,t,T,tdeca-1,3,5,7,9-pentaene were carried out at the ab initio, HF/6-31G level. The HF/6-31G//HF/ 6-31G force fields were modified using empirical scale factors transferred from trans-buta-1,3-diene augmented by an additional scale factor for the central formal carbon-carbon double bond coordinates (determined previously for all-trans-hexa-1,3,5-triene). The total number of scale factors was seven. The vibrational problems for both decapentaenes were solved using the respective scaled HF/6-31G//HF/6-31G force field. Infrared intensities and Raman activities were calculated from the unscaled HF/6-31G//HF/6-31G force fields. Complete assignment of all the fundamental vibrational frequencies is given. Geometrical parameters, vibrational frequencies and force constants are compared with the corresponding values of buta-1,3-diene, hexa-1,3,5-triene and octa-1,3,5,7-tetraene. Regularities in the properties of this molecular series are discussed. Special attention is given to the possibility of using the vibrational spectra for detection of distortions from the regular trans structure of these oligoenes.     

非对称流场流分离技术的现状及发展趋势

场流分离是生物分析领域一项成熟的技术,将流体与外场联合作用于待分离物质,利用分析物某些理化参数上的差异进行分离。非对称流场流是其重要的分支之一,所施加的外力场为垂直方向的液流,分离过程于开放型的通道中在某种组成的载液迁移推动下进行,主要根据分析物与垂直施加的第二维液流之间的相互作用完成分离。非对称流场流在蛋白质、蛋白质复合物、衍生纳米级/微米级粒子、亚细胞单元和聚合物等分离中的应用日益广泛,主要归功于其直接应用于生物样品时可进行无损分离,因此生物分析物如蛋白质可以在生物友好型的环境中完成分离而不改变其构型,也无需使用降解载液。分离设备便于保持无菌状态,分析物可在生物友好的环境中维持其自然状态。该文简要描述了场流分离原理并罗列出其在生物分析领域一些卓越的发展和应用。     

Heat capacity and vibrational dynamics of polyvinylidene fluoride (β-form)

Polyvinylidene fluoride (PVDF) is a polymer of industrial importance, mainly due to its piezoelectric and pyroelectric properties. A comprehensive study of the normal modes and their dispersion in PVDF (β-form) has been reported in the reduced zone scheme using Wilson’s GF matrix method as modified by Higgs. A Urey-Bradley force field has been used. The evaluation of normal modes and their dispersion has been taken to logical conclusion by calculating the heat capacity as a function of temperature. The extent of agreement with the experimental data supports the potential field. Characteristic features of the dispersion curves such as repulsion and exchange of character have also been discussed.     

Huggins constant k′ for flexible chain polymers

The Huggins constant k′ in the expression for the viscosity of dilute nonelectrolytic polymer solutions, η = η(1 + [η] c + k′[η]²c² + …), is calculated. For polymers in the theta condition, k′ is estimated to be 0.5 < k_θ′ ≤ 0.7. For good solvent systems, the Peterson-Fixman theory of k′ has been modified; the equilibrium radial distribution function in the original theory is replaced with a parametric distribution for interpenetrating macromolecules in the shear force field. Comparison of the modified theory with experimental k′ for polystyrenes and poly(methyl methacrylates) of different molecular weights in various solvents shows good agreement. An empirical equation which correlates the Huggins constant k′ and the viscosity expansion factor α_η for polymers has been found to coincide well with the modified theory.     

Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation

Molecular dynamics (MD) simulations are extensively used in the study of the structures and functions of proteins. Ab initio protein structure prediction is one of the most important subjects in computational biology, and many trials have been performed using MD simulation so far. Since the results of MD simulations largely depend on the force field, reliable force field parameters are indispensable for the success of MD simulation. In this work, we have modified atom charges in a standard force field on the basis of water-phase quantum chemical calculations. The modified force field turned out appropriate for ab initio protein structure prediction by the MD simulation with the generalized Born method. Detailed analysis was performed in terms of the conformational stability of amino acid residues, the stability of secondary structure of proteins, and the accuracy for prediction of protein tertiary structure, comparing the modified force field with a standard one. The energy balance between alpha-helix and beta-sheet structures was significantly improved by the modification of charge parameters.     

Transition structure modeling by intersecting potential energy surfaces

A previously proposed method of modeling force field transition structures as the lowest energy structure on the seam of two intersecting potential energy surfaces is improved with respect to the force field expression and the efficiency of the optimization algorithm. Comparison with ab initio and experimental results show that the force field method may have the potential of achieving almost quantitative results. It appears that the results from transition state modeling are currently limited by the accuracy of the underlying force field. © 1994 by John Wiley & Sons, Inc.